16. Changelog¶
The following includes a list of changes in the OWL package relevant to the usage of the MCAM.
To obtain the version of the MCAM software you currently have installed, open the graphical interface and navigate use the Help Menu on the top bar to access the About page. The version number should be listed in the resulting dialog.
Migration guide¶
We suggest that users attempt to stay updated with the latest release of the owl package. Warnings are emitted when a change of behavior is planned and allow users to adapt their code as required.
To update to the latest version of owl, paste the command (Ctrl+Shift+V)
mamba install "owl-base>=0.19.128"
If you have any trouble migrating to a new version, please contact help@ramonaoptics.com.
Software release notes¶
Below is the list of reported changes on a per version basis of the owl
package.
owl 0.19.128 (2024/09/13)¶
No significant changes.
owl 0.19.127 (2024/09/13)¶
Bug fixes¶
Fix bug that prevented video acquisitions in screening for systems without xy stages. (#6098)
owl 0.19.126 (2024/09/10)¶
Bug fixes¶
Fix a bug that caused the inability to change between lens sets in Kestrel (i.e. between Behavior and Screening mode) systems. This error occurred in version 0.19.113. (#6100)
owl 0.19.125 (2024/09/09)¶
Bug fixes¶
Ensure the stitching panel opens with the correct sizing. (#6094)
owl 0.19.124 (2024/09/09)¶
Bug fixes¶
Fix stitching images acquired from Z stacks in the image exporter. (#6082)
owl 0.19.123 (2024/09/09)¶
Fix bug causing resegmentation in the Brain Organoid Segmentation panel to keep the frame dimension in resegmented datasets.
owl 0.19.122 (2024/09/09)¶
Fix bug causing resegmentation in the Brain Organoid Segmentation panel to fail.
owl 0.19.121 (2024/09/08)¶
No significant changes.
owl 0.19.120 (2024/09/05)¶
Improvements¶
Include the plate map with the protocol file when saving the protocol file. If a users wishes to have a protocol file without the plate map attached they should save the protocol file before creating the plate map. (#6075)
owl 0.19.119 (2024/09/04)¶
Improvements¶
Reorganize plate map window. - Prevent empty label from being removed from plate map labels. - Remove all instances of a label from the plate map once it is removed. - Add Apply Label button to the plate map window to apply the currently selected label to the selected well cells (#6067)
Added option to export plate map in assay panel. Plate maps will no longer be saved automatically alongside the acquired data. (#6069)
owl 0.19.118 (2024/09/03)¶
Fix bug with opening Acquire Video panel with no stages connected.
owl 0.19.117 (2024/08/30)¶
No significant changes.
owl 0.19.116 (2024/08/30)¶
No significant changes.
owl 0.19.115 (2024/08/28)¶
No significant changes.
owl 0.19.114 (2024/08/28)¶
No significant changes.
owl 0.19.113 (2024/08/28)¶
Deprecations¶
Python API – Removal of the internal dataset variables from the MCAM object. (#5978)
owl 0.19.112 (2024/08/27)¶
No significant changes.
owl 0.19.111 (2024/08/26)¶
No significant changes.
owl 0.19.110 (2024/08/23)¶
Bug fixes¶
Fix acquiring Z stacks from the MCAM GUI, this has been broken since 0.19.101. (#5995)
owl 0.19.109 (2024/08/20)¶
Improvements¶
Bounding boxes are now stored in datasets in yxyx ragged array format with the sensor’s frame of reference. (#5976)
Bug fixes¶
Fix bug where XYZ stacks acquired to netcdf were being saved with 3x the data. This bug has existed since 0.19.102. (#5989)
owl 0.19.108 (2024/08/15)¶
Fix the ability to run batched activity metric assays.
owl 0.19.107 (2024/08/14)¶
Improvements to experimental workflows.
owl 0.19.106 (2024/08/12)¶
Ensure error messages are adequately communicated to end users when an acquisition assay fails in the case that they didn’t opt in to the analytics.
owl 0.19.105 (2024/08/08)¶
Addressed a bug in volumetric scans where in certain cases specific exposures would throw an error upon acquisitions.
owl 0.19.104 (2024/08/06)¶
No significant changes.
owl 0.19.103 (2024/08/01)¶
Bug fixes¶
Fix bug where the UI could become warped if a protocol file with a long name was loaded. (#5902)
owl 0.19.102 (2024/07/30)¶
No significant changes.
owl 0.19.101 (2024/07/25)¶
Bug fixes¶
Fix one more edge case with progress bars that occurred since 0.19.95. (#5880)
owl 0.19.100 (2024/07/25)¶
Bug fixes¶
Address progress bar updates for very fast iterations (such as zebrafish tracking or video export). This issue was affecting users since version 0.19.95. (#5875)
owl 0.19.99 (2024/07/23)¶
New features¶
Add button to remove outside edge with Acquisition Mode Calibration
Word wrap selection label in Acquisition Mode Calibration for long selections. (#5860)
Bug fixes¶
Address erroneously reported progress time estimate in progress dialogs. This bug appeared in 0.19.95. (#5865)
owl 0.19.98 (2024/07/22)¶
No significant changes.
owl 0.19.97 (2024/07/19)¶
Bug fixes¶
Fix bug where the file dialog could be lost behind the main GUI window when loading or saving an assay protocol. (#5848)
owl 0.19.96 (2024/07/19)¶
Improvements¶
Location with missing data in XYZC stack will be skipped at acquisition time leading to potential speedsups. (#5841)
Bug fixes¶
Fix a bug where Z stacks (using acquire Z stack) were not saved in the correct location. (#5844)
owl 0.19.95 (2024/07/17)¶
Improvements¶
GUI: Provide an easy button to take screenshots and an option to customize the filename. (#5819)
Address strageness in progress bar in EPMR assay that can occur when the assay is operated in Acquire to RAM mode. - Ensure that the numbers entered for the experiment start delay in the zebrafish tail coil assay are interpreted in minutes. Previously they were treated as seconds. - The EPMR start experiment delay is now requested in minutes instead of seconds. (#5826)
Bug fixes¶
Fix bug preventing the use of bayer patterned images in the Brain Organoid Segmentation analysis panel. (#5717)
Fixed bug created in 0.19.94 that cause updated “Additional Notes” in the assay panel to not be added to metadata. (#5822)
Ensure that the fast computation is used when running the EPMR assay. (#5826)
Deprecations¶
rgb2gray now uses the coefficients from the ITU-R BT.601 standard for converting RGB to grayscale. The coefficients are [0.2989, 0.5870, 0.1140]. This is a change from the BT.709-1 coefficients that were used in previous releases. The BT.709-1 coefficients are [0.2126, 0.7152, 0.0722]. This should not affect many applications since applications that utilized rgb2gray were mostly taken under white light. Should you have any concerns about this please contact Ramona Optics. (#5807)
owl 0.19.94 (2024/07/12)¶
No significant changes.
owl 0.19.93 (2024/07/10)¶
No significant changes.
owl 0.19.92 (2024/07/10)¶
Fix bug preventing access to the webAPI /docs page. Broken since 0.19.89. (#5783)
owl 0.19.91 (2024/07/10)¶
Improvements¶
Tracking models are now only displayed if they match the well plate type of the loaded dataset. (#5720)
Improve GUI responsiveness when vieweing many images at the same time. (#5779)
Bug fixes¶
GUI: Address a crash in the GUI when the number of blobs detected in a zebrafish is exactly zero. (#5769)
owl 0.19.90 (2024/07/09)¶
No significant changes.
owl 0.19.89 (2024/07/08)¶
Improvements¶
Improve display and anchoring of textual information on top of the well images. (#5749)
GUI: Streamline the advanced settings dialog by removing options to adjust minimum and maximum gain and exposure values. They were often unused. If you require these for your workflow, please do not hesitate to contact Ramona Optics. (#5757)
owl 0.19.88 (2024/07/03)¶
Bug fixes¶
Fixed bug that caused the gui to slow down and eventually crash after multiple cycles of closing and reopening the MCAM. (#5739)
owl 0.19.87 (2024/07/01)¶
Fix broken 0.19.86 release.
owl 0.19.86 (2024/07/01)¶
Improve anchoring of textual labels to images of wells.
Allow users to export stitched stacks of images in a single file containing multiple channels.
owl 0.19.85 (2024/06/26)¶
No significant changes.
owl 0.19.84 (2024/06/25)¶
No significant changes.
owl 0.19.82 (2024/06/25)¶
Improvements¶
Improved system diagnostic capabilities. (#5696)
owl 0.19.81 (2024/06/25)¶
Improvements¶
GUI: Improve the look of images acquired of circle wells in the GUI with the Kestrel. (#5678)
In an attempt to better taylor your MCAM experience, we are asking early users of the MCAM to contact Ramona Optics to record their serial number and to provide feedback on their experience with the MCAM to date. Users without a serial number will be asked to contact Ramona Optics. (#5686)
Bug fixes¶
Fix bug where area labels in the organoid segmentation GUI may become detached from the area they are labeling. (#5691)
GUI: Try to address non-responsive GUI when streaming at high resolution with 3072x3072 pixels chosen as the sensor region of interest. (#5693)
owl 0.19.80 (2024/06/23)¶
No significant changes.
owl 0.19.79 (2024/06/20)¶
New features¶
GUI: Provide options to show and hide the scale bar. (#5662)
Improvements¶
Adapted zebrafish segmentation workflow to use YOLO autofocusing. (#5991)
owl 0.19.78 (2024/06/18)¶
Improvements¶
GUI: Allow the images to be displayed behind the textual information. (#5630)
GUI: Improve font rendering when exporting stitched images or videos from the GUI. (#5642)
Bug fixes¶
Address a bug that prevented colormaps from being displayed in certain early acquired datasets. (#5607)
owl 0.19.77 (2024/06/13)¶
No significant changes.
owl 0.19.76 (2024/06/13)¶
New features¶
GUI: Add a few colormaps that have go from white to a color that may be more suitable for creating figures for printed media. (#5625)
Bug fixes¶
GUI: Fix stitching images and making videos through the GUI. This broke in 0.19.74 and 0.19.75. (#5631)
owl 0.19.75 (2024/06/11)¶
No significant changes.
owl 0.19.74 (2024/06/10)¶
New features¶
GUI: The Brain Organoid Segmentation panel now allows users to click and drag the segmentation points to generate a new mask. (#5450)
Bug fixes¶
Address a bug that prevented colormaps from being displayed in certain early acquired datasets. (#5607)
owl 0.19.73 (2024/06/05)¶
Bug fixes¶
Fix loading settings that switch between screening and behavior mode for Kestrel product line. (#5580)
Fix a bug where the GUI would seemingly freeze upon usage. (#5581)
Enable the best focus panel again. Images picked out with the best focus panel will now retain their individual metadata. (#5582)
owl 0.19.72 (2024/06/03)¶
Improvements¶
Increase the speed of exporting images for visualization. (#5533)
owl 0.19.71 (2024/06/03)¶
Improvements¶
Allow users to customize the size of the overview more freely. (#5547)
Provide users with accessible buttons to zoom in and out on the user interface. (#5550)
Reduce the image size of the stitched images generated for visualization purposes. This was done by avoiding saving the alpha channel. (#5562)
owl 0.19.70 (2024/05/31)¶
Ellipse tool!
owl 0.19.69 (2024/05/31)¶
No significant changes.
owl 0.19.68 (2024/05/28)¶
No significant changes.
owl 0.19.67 (2024/05/23)¶
No significant changes.
owl 0.19.66 (2024/05/21)¶
Bug fixes¶
Fix screenshots for 4k screens using 200% scaling. Only 100% and 200% screen scaling are supported. (#5485)
owl 0.19.65 (2024/05/21)¶
Bug fixes¶
Address an issue that prevented users from testing the moving bars stimuli with custom color ratios. (#5472)
Fix bug in stack acquisitions (Z, XYZ, XYZC) where the frame rate was not being set correctly for 1 step acquisitions. (#5482)
owl 0.19.64 (2024/05/17)¶
Fixup broken XYZ panel in GUI
owl 0.19.63 (2024/05/17)¶
Bug fixes¶
Remove deprecated function acquire_z_stack_single_file and deprecated variable usages from acquire_z_stack_video with in our code. (#5427)
Enable users to adjust per color digital gain settings from the GUI. This bug was introduced in 0.19.59. (#5455)
owl 0.19.62 (2024/05/14)¶
Address inconsistencies between switching from 96 well plate acquisition and 384 well plate acquisition in the XYZ stack code.
owl 0.19.61 (2024/05/14)¶
Improvements¶
Improve GUI cropping when missing data is present in the datasets. (#5412)
Bug fixes¶
No longer accept flip_x or flip_y parameters into the xyz or xyzc assays. Previously they were accepted but ignored by these assay. Flipping should be done on the xy positions before passing them to the assay. If users require them they should contact Ramona Optics for assistance at help@ramonaoptics.com. (#5420)
owl 0.19.60 (2024/05/13)¶
Handle the case with corner images are invalid at load time.
owl 0.19.59 (2024/05/13)¶
New features¶
Enable colormaps for all MCAMs and datasets when data is displayed in grayscale. (#5405)
Improvements¶
Streamline interactions with the image adjustment widget. (#5390)
Allow chosen theme (light or dark) to persist when re-opening the MCAM. (#5403)
Allow users to change the resolution of the images in the acquisition GUI without closing and re-opening the MCAM. (#5404)
owl 0.19.58 (2024/05/08)¶
Improvements¶
Help guild users in building better EPMR and tail coil protocols by fixing the acquisition frame to 16 fps. Users that require acquisition at other frame rates are encouraged to contact Ramona Optics by email. (#5382)
Bug fixes¶
Fixed z stacks of “1” z step. Broke in 0.19.56. (#5383)
owl 0.19.57 (2024/05/08)¶
Improvements¶
- Limit the allowable frame rates in the Video acquisition and Zebrafish Assay
Panels to predefined values. Users will be warned if their assay files are loaded with settings different than the values described below: 1, 2, 5,
- 10,
15, 20, 30, 45, 60, 90, 100, 120, 150, 160, 180, 360. (#5374)
owl 0.19.56 (2024/05/08)¶
Deprecations¶
Stop supporting z-stacks with non constant distance between steps. If you need this for your workflow, you should discuss your usecase with Ramona Optics. (#5319)
owl 0.19.55 (2024/05/08)¶
Minor bug fixes.
owl 0.19.54 (2024/05/07)¶
No significant changes.
owl 0.19.53 (2024/05/02)¶
Bug fixes¶
Fix image viewer regression introduced in 0.19.52 when viewing sparse dataset of TIFF images. (#5358)
owl 0.19.52 (2024/05/02)¶
Improvements¶
Zebrafish tracking composite video generation is now off by default.
Options for labeling additional zebrafish metrics were added to the composite video generation. (#5334)
owl 0.19.51 (2024/04/28)¶
System bringup.
owl 0.19.50 (2024/04/26)¶
Bug fixes¶
Fix the ability to open very small images (less than 128 x 128 pixels in size) (#5297)
owl 0.19.49 (2024/04/23)¶
No significant changes.
owl 0.19.48 (2024/04/23)¶
Improvements¶
Provide the ability to show or hide the overview image in the MCAM software. (#5279)
owl 0.19.47 (2024/04/22)¶
No significant changes.
owl 0.19.46 (2024/04/22)¶
Bug fixes¶
Fix display of unstitched images upon opening them in the MCAM Viewer. (#5266)
Fix the use of
mcam_data.save_videowhen used with sliced datasets.
owl 0.19.45 (2024/04/20)¶
System bringup.
owl 0.19.44 (2024/04/19)¶
No significant changes.
owl 0.19.43 (2024/04/18)¶
Bug fixes¶
Address bugs in setting the colomap of the brightfield images back to gray. (#5242)
owl 0.19.42 (2024/04/18)¶
Add false colors to the MCAM-B system acquisition.
owl 0.19.41 (2024/04/17)¶
Bug fixes¶
Address display errors in image blending parameters not being recomputed when the imaging parameters change in the MCAM GUI. (#5205)
owl 0.19.40 (2024/04/15)¶
Improve utility of distance measuring tool in the MCAM Viewer for uncalibrated datasets.
owl 0.19.39 (2024/04/12)¶
No significant changes.
owl 0.19.38 (2024/04/11)¶
Improvements¶
Improve system performance when opening large NC dataset files for analysis. (#5175)
owl 0.19.37 (2024/04/10)¶
No significant changes.
owl 0.19.36 (2024/04/10)¶
Improvements¶
Add ability to perform photometric calibration for monochrome sensors. (#5134)
Improve selecting an quick image from the Preview window. (#5159)
owl 0.19.35 (2024/04/05)¶
No significant changes.
owl 0.19.34 (2024/04/05)¶
No significant changes.
owl 0.19.33 (2024/04/04)¶
Improvements¶
Add ability to perform photometric calibration for monochrome sensors. (#5134)
owl 0.19.32 (2024/04/04)¶
No significant changes.
owl 0.19.31 (2024/04/02)¶
Address inconsistenticies in the dimensions of the
software_timestampproperties introduced in video datasets acquired in version 0.19.29 and 0.19.30. As of 0.19.31, when acquiring video datasets,software_timestampis now a 1D array as it was in version prior to version 0.19.29. (#5115) Version 0.19.29 and 0.19.30 have been removed. Users that have trouble opening datasets with these versions may encounter compatibility issues and are encouraged to contact Ramona Optics for assistance.
owl 0.19.30 (2024/04/01)¶
Improvements¶
Allow for rapid GUI navigation through the preview window. (#5090)
Bug fixes¶
Address errors occurring with the vibration stimuli with the MCAM that occurred for users that updated their system in March 2024. The incompatibility was one with zaber-motion library version 5.0.0 and above. The latest version of the MCAM software is compatible with both motion library version 4 and 5. (#5104)
owl 0.19.29 (2024/03/28)¶
No significant changes.
owl 0.19.28 (2024/03/27)¶
No significant changes.
owl 0.19.27 (2024/03/27)¶
No significant changes.
owl 0.19.26 (2024/03/26)¶
Bug fixes¶
Fix loading configuration files using
image_export_formatthat were created before0.18.325. This has been broken since0.19.23. (#5070)
owl 0.19.25 (2024/03/26)¶
New features¶
Display well names in when used in the zebrafish acquisition panel, video acquisition panel, and well alignment tool. (#5044)
Bug fixes¶
Address errors loading well plate keypoints in the MCAM Viewer when subsets of cameras are used. (#5044)
owl 0.19.24 (2024/03/25)¶
Bug fixes¶
Address bug in home button interaction for MCAM-B systems.
owl 0.19.23 (2024/03/21)¶
Improvements¶
Add a method to find the yx stage positions require to acquire a full well plate (get_well_yx_scan_positions) and another method divide the acquisitions into individual wells and fields based on well plate dimensions (add_well_field_labels_to_dataset). (#4963)
Allow users to customize the color of the flash for the Zebrafish assay. (#4985)
Deprecations¶
Breakage of Well Alignment files (formerly known as keypoint files) generated before owl version 0.18.124. Affected users should contact Ramona Optics is those files need to be recovered.
The use of
Noneornullto not save data in the acquire_and_save assay has been removed. Users who require this feature should contact Ramona Optics. (#5023)
owl 0.19.22 (2024/03/15)¶
No significant changes.
owl 0.19.21 (2024/03/15)¶
New features¶
Zebrafish segmentation backend added. (#4943)
Bug fixes¶
Well Alignment data is now correctly applied when loaded through protocol files for zebrafish EPMR and tail coil assays. (#4987)
Deprecations¶
Drop support for GUI settings from version older than 0.16.0 (released on Aug 8 2021) (#4884)
owl 0.19.20 (2024/03/12)¶
Bug fixes¶
GUI: Fix the appearance of well plate alignments for images where large overlap exists between adjacent images. (#4979)
GUI: Fix the opening of the XYZ Timelapse panel.
GUI: Fix the erroneous warning that appeared about the Nvidia driver.
owl 0.19.19 (2024/03/11)¶
No significant changes.
owl 0.19.18 (2024/03/07)¶
No significant changes.
owl 0.19.17 (2024/03/05)¶
Bug fixes¶
Fix playback of NC file stacks when streaming subsets. This was broken since 0.19.0. (#4961)
owl 0.19.16 (2024/03/04)¶
New features¶
Add cooling fan speed control to the fluorescence driver. (#4929)
owl 0.19.15 (2024/03/03)¶
Improvements¶
Improve responsiveness of the GUI at high image resolutions. (#4949)
owl 0.19.14 (2024/03/01)¶
No significant changes.
owl 0.19.13 (2024/02/28)¶
New features¶
Calibrated MCAM-B systems will now display the well label of each image in the acquisition GUI. (#4926)
Bug fixes¶
Address a bug in the moving bars stimuli where the stimuli appeared to flash on very strobe. This bug first appeared in 0.18.366. (#4889)
owl 0.19.12 (2024/02/21)¶
No significant changes.
owl 0.19.11 (2024/02/21)¶
No significant changes.
owl 0.19.10 (2024/02/21)¶
Fixed EMPR assays and zebrafish analysis which were broken near 0.19.8.
owl 0.19.9 (2024/02/20)¶
System bringup.
owl 0.19.8 (2024/02/20)¶
Fixup GUI bugs resulting from the display engine update.
owl 0.19.7 (2024/02/19)¶
Improvements¶
Overhaul display engine for improve performance. (#4852)
owl 0.19.6 (2024/02/19)¶
No significant changes.
owl 0.19.5 (2024/02/16)¶
Bug fixes¶
Fix bug preventing XYZ, XYCZ, XYC, and XYZ timelapse assay panels from opening. This was introduced in 0.19.4. (#4847)
owl 0.19.4 (2024/02/16)¶
No significant changes.
owl (2024/02/14)¶
No significant changes.
owl 0.19.2 (2024/02/14)¶
New features¶
Implement cooling fan control on fluorescence hardware versions that support it. (#4823)
Bug fixes¶
Fix the best focus selection panel which broke in version 0.19.0. (#4814)
Enable opening data acquired with XYZC stacks that was exported as TIFF. (#4818)
Address bug introduced in 0.19.0 that stopped saving of NC files from subset of other NC files or tif images. (#4821)
owl 0.19.1 (2024/02/13)¶
Deprecations¶
Removal of the methods
saveandexportfrom the MCAM instrument class. (#4800)
owl 0.19.0 (2024/02/12)¶
Exported datasets now use the
metadata.ncfilename instead of themetadata.jsonfilename.Newly exported TIFF images should be faster to navigate inside the MCAM Viewer.
owl 0.18.391 (2024/02/11)¶
Bug fixes¶
Increase video recording stability for MP4 format. (#4761)
owl 0.18.390 (2024/02/06)¶
Bug fixes¶
Fix bug that causes fluorescence LEDs to flash when calling set_brightness() with the same illumination channel. (#4755)
owl 0.18.389 (2024/02/05)¶
No significant changes.
owl 0.18.388 (2024/02/05)¶
Various bug fixes and improvements.
owl 0.18.387 (2024/02/05)¶
Improvements¶
Automatically turn off fluorescence LEDs when switching between channels. (#4737)
owl 0.18.386 (2024/02/04)¶
Bug fixes¶
Fixup XYZ Stack timelapses broken since 0.18.378. (#4742)
owl 0.18.385 (2024/02/03)¶
No significant changes.
owl 0.18.384 (2024/02/02)¶
No significant changes.
owl 0.18.383 (2024/02/02)¶
Improved reliability of z stacks.
System bringup.
owl 0.18.382 (2024/01/31)¶
New features¶
Preview: Integrate four channel illumination capability. (#4572)
owl 0.18.381 (2024/01/31)¶
No significant changes.
owl 0.18.380 (2024/01/30)¶
New features¶
Breaking: Removal of extended exposure acquisitions. Those with the need for this feature should contact Ramona Optics to discuss their usecase. (#4686)
Bug fixes¶
Address memory management errors that would cause the system to crash repeated Z stack acquisitions where color conversion occurred at the output. (#4701)
owl 0.18.379 (2024/01/25)¶
No significant changes.
owl 0.18.378 (2024/01/25)¶
System brightup.
owl 0.18.377 (2024/01/21)¶
Improvements¶
Streamline the options used for selection of sensor pixels. (#4632)
Bug fixes¶
Ensure that per color digital gain values are retained when switching between illumination modes. (#4631)
owl 0.18.376 (2024/01/21)¶
Improvements¶
Improve system stability when streaming from well plates that use disjoint sensors. (#4629)
owl 0.18.375 (2024/01/20)¶
New features¶
Created a new live dead assay (Live/Dead Assay V2) that works with multi channel acquisitions. (#4607)
Provide users to customize the reports for the drosophila analysis workflows. (#4616)
Bug fixes¶
Fixup default visibility for zebrafish analysis assay that were appearing as missing in 0.18.373. (#4619)
owl 0.18.374 (2024/01/16)¶
No significant changes.
owl 0.18.373 (2024/01/15)¶
New features¶
Add the ability to run Two Drosophila workflows from the GUI for those that have the license for it. (#4599)
owl 0.18.372 (2024/01/09)¶
Bug fixes¶
Fix bug where the illumination enable switch could become hidden in the GUI. (#4564)
owl 0.18.371 (2024/01/08)¶
New features¶
Provide a button for users to stop video acquisitions in the zebrafish acquisition assay. (#4317)
Bug fixes¶
Fix acquisition of the timelapse assays, highspeed video and diet assay which were broken since 0.18.367. (#4549)
Fix the broken standard deviation calculation in the Stack Projection panel. This has been incorrect since 0.18.210. (#4554)
Fix bug where the average projections could be calculated incorrectly. This has been broken since 0.18.210. (#4558)
owl 0.18.370 (2024/01/04)¶
Bug fixes¶
Fixed bug where the illumination mode “enabled” switch could become out of sync with the actual illumination mode in the GUI. (#4356)
owl 0.18.369 (2024/01/03)¶
Avoid boot lockup with the transmission boards.
owl 0.18.368 (2024/01/02)¶
No significant changes.
owl 0.18.367 (2024/01/02)¶
Improvements¶
Illumination device selection in the GUI has been simplified. Transmission and Fluorescence illumination devices are now selected through a single menu. Each illumination mode retains its own settings. (exposure, brightness, analog gain, digital gain) (#4440)
owl 0.18.366 (2023/12/21)¶
Improvements¶
Zebrafish tracking data is now denoised/smoothed by default. (#4390)
Zebrafish tracking data can be binned from the GUI. - Zebrafish tracking data is now binned by one second by default. (#4473)
Zebrafish tracking checkboxs have been reorganized within the tracking panel. (#4475)
Confidence / likelihood is no longer exported in tracking data csv’s. This information is still present in the “tracking_metadata.nc” file. (#4478)
Bug fixes¶
Fixed a bug with stimulus data export ensuring this information is exported correctly. (#4488)
owl 0.18.365 (2023/12/18)¶
No significant changes.
owl 0.18.364 (2023/12/15)¶
Bug fixes¶
Fix accessing the Leaf Disk and Diet Assay acquisition panels. This has been broken since 0.18.351. (#4430)
owl 0.18.363 (2023/12/12)¶
Improvements¶
Added function to bin all time series tracking data by a multiple of seconds. (#4246)
Bug fixes¶
Corrected a bug ensuring tracking filtering information is all the same data type. This prevented zebrafish tracking from successfully completing since version 0.18.361. (#4433)
owl 0.18.362 (2023/12/11)¶
Bug fixes¶
Increase the timeout of the MP4 encoder to allow compression of larger dataset. (#4419)
owl 0.18.361 (2023/12/09)¶
Improvements¶
Improve frame rate settings for values near 180 fps. (#4414)
Improve display for total frame count in the GUI. (#4415)
owl 0.18.360 (2023/12/09)¶
No significant changes.
owl 0.18.359 (2023/12/08)¶
Improvements¶
Simplify plate tapper parameter selection process. (#4410)
Bug fixes¶
Adjust edge case where vidoe recording couldn’t happen at 180.0 fps but could at 179.99 fps. (#4409)
owl 0.18.358 (2023/12/06)¶
System bringup.
owl 0.18.357 (2023/12/03)¶
Deprecations¶
This is the last version with support for Python 3.9. Users using python 3.9 will be issued a warning asking them to contact Ramona Optics to upgrade their installed version of Python. (#4386)
owl 0.18.356 (2023/12/03)¶
Bug fixes¶
Fix bug that didn’t backfill the stimulus name in zebrafish acquisition datasets containing a vibration stimulus. (#4375)
Well plate configuration is now correctly detected by the zebrafish tracking panel. (#4376)
owl 0.18.355 (2023/11/28)¶
Bug fixes¶
When tracking animals in datasets with missing videos, the progress bar reports the correct amount of time remaining instead of overestimating it by including the missing wells. (#4367)
owl 0.18.354 (2023/11/28)¶
Bug fixes¶
Ensure that the multi-animal tracking is closed upon widet exit too. (#4361)
owl 0.18.353 (2023/11/27)¶
New features¶
Allow users to load datasets from multi-mp4 formats where some videos are missing. (#4359)
Improvements¶
Allow users to cancel multi-animal tracking workflows. (#4358)
owl 0.18.352 (2023/11/27)¶
No significant changes.
owl 0.18.351 (2023/11/26)¶
New features¶
Provide the ability for end users to customize the name of each stimulus. (#4319)
Improvements¶
Make MP4 the default saving format for video acquisitions. (#4327)
Bug fixes¶
Attempt to resolve a few edge cases where still frames and video frames would arrive corrupt to the computer for analysis. (#4330)
owl 0.18.350 (2023/11/15)¶
No significant changes.
owl 0.18.349 (2023/11/13)¶
New features¶
Enable configuration of moving bars stimuli for zebrafish assays. (#4315)
owl 0.18.348 (2023/11/09)¶
Bug fixes¶
Address a few edge cases in animal tracking with multiple animals. (#4311)
owl 0.18.347 (2023/11/07)¶
No significant changes.
owl 0.18.346 (2023/11/05)¶
Fix loading old z-stack datasets in the MCAM Viewer.
owl 0.18.345 (2023/11/03)¶
Bug fixes¶
Address acquired
multi_mp4being saved with names starting incaminstead of with their well ID when a well plate alignment is provided. (#4291)Fixed bug that incorrectly saved the calibration data after running photometric or stitching calibration data. (#4294)
owl 0.18.344 (2023/11/03)¶
Bug fixes¶
Address vieweing images acquired from color sensors in raw mode and images acquired from monochrome sensors. Broken since 0.18.339. (#4282)
Fix per channel gain compensation for video acquisition as it relates to video acquisition. (#4286)
owl 0.18.343 (2023/11/01)¶
Bug fixes¶
Fix bug that prevented correct color corrections from being applied to IR datasets. (#4280)
owl 0.18.342 (2023/11/01)¶
New features¶
Add “valid_data” key to mark images that are valid. (#4248)
Bug fixes¶
Fix bug introduced in 0.18.341 that prevented stitching calibration from running.
owl 0.18.341 (2023/11/01)¶
No significant changes.
owl 0.18.340 (2023/11/01)¶
Avoid GUI freezing when selecting the workspace in XYZ stacks when streaming is enabled.
owl 0.18.339 (2023/10/31)¶
Improvements¶
Improve display of images acquired with systems equipped with color sensors. (#4263)
owl 0.18.338 (2023/10/31)¶
Improvements¶
Adjust limits on motor drive power limiting the power that can be exerted on external objects. (#4257)
Bug fixes¶
Fix fluorescence bug that causes the lights not to turn on at below ~20% power. (#4264)
owl 0.18.337 (2023/10/25)¶
Improvements¶
Asynchronous assays in the webAPI will now report when saving has begun and when it has completed through the status endpoint. (#4235)
owl 0.18.336 (2023/10/25)¶
No significant changes.
owl 0.18.335 (2023/10/24)¶
New features¶
Hide the PIP window unless the user has moved their cursor in the PIP window area. (#3855)
Improvements¶
Added a function to load tracking metadata along with the MCAM dataset. (#4231)
owl 0.18.334 (2023/10/17)¶
System bringup.
owl 0.18.333 (2023/10/17)¶
Bug fixes¶
Addressed a bug in the Leaf Disk analysis where running the analysis a second time could cause the program to crash. This is fixed with Leaf Disk datasets acquired after version 0.18.333. (#4219)
Fix a bug in the fluorescence driver that causes a crash when no module is connected. (#4223)
owl 0.18.332 (2023/10/11)¶
No significant changes.
owl 0.18.331 (2023/09/29)¶
Improvements¶
Improve compatibility with xarray 2023.9.0 (#4169)
owl 0.18.330 (2023/09/27)¶
New system bringup.
owl 0.18.329 (2023/09/23)¶
New features¶
The Zebrafish assay panel now exposes a plate tapper option for MCAM systems with the hardware option installed. (#4142)
Enable mean and sum projections for Z stack acquisitions and XYZ stack acquisition through the WebAPI and GUI. (#4145)
Bug fixes¶
Ensure that minimum exposure values below 1 ms can be recorded. (#4142)
Address an inssue on particular systems where well plate scans would occur extremely slowly after moving the stages to a given mechanical state. (#4144)
Fix an issue where the digital gain would always get reset to 1 upon opening the MCAM through the GUI. (#4148)
owl 0.18.328 (2023/09/21)¶
WebAPI live documentation page is now organized by function type.
owl 0.18.327 (2023/09/19)¶
Bug fixes¶
Fixed bug that prevented activity metric analysis to be done on stacks with frame number not divisible by 10. (#4129)
owl 0.18.326 (2023/09/13)¶
System bringup.
owl 0.18.325 (2023/09/11)¶
The advanced save options have been added to the Z Stack panel. (#4128)
owl 0.18.324 (2023/09/08)¶
New features¶
Users can now export images in a flat structure (no subfolders) by using the new
save_filename_separatorflag in themcam_data.savefunction. This option is also added as part of our Advanced Save Options in select GUI assay panels. (#4025)
owl 0.18.323 (2023/09/06)¶
No significant changes.
owl 0.18.322 (2023/08/31)¶
New features¶
The export format
'flat_image_stacks'can now be used with datasets with no additional dimensions. This makes it compatible with projections of focal stacks. (#4103)
Improvements¶
Tracking data is now filtered using anomaly detection by default. (#4094)
The tracking model name used for inference is now stored in the dataset. (#4097)
Added an option to the zebrafish tracking panel to allow re-analysis of previously inferred tracking data. (#4098)
The
imagesnow supports image stacks. Image stacks will now automatically be saved on a per micro camera or per well basis. Theimage_export_format'image_stacks'is now deprecated and will be internally converted to'images'issuing a warning. (#4102)
owl 0.18.321 (2023/08/30)¶
New features¶
Added functions to filter anomalies in tracking data. (#3791)
owl 0.18.320 (2023/08/27)¶
Improvements¶
The MCAM Web Server can now be started by right clicking on the Ramona Desktop and selecting the option
WebMCAM Server.
Bug fixes¶
Fix bug in starting up the MCAM introduced in 0.18.319. (#4086)
owl 0.18.319 (2023/08/27)¶
First release where the previously internal library
python-qdmais built into theowlpackage itself.
Bug fixes¶
Ensure MCAM capabilities like the frame rate and datarate usage are updated in the zebrafish assay panel upon assay loading. Previously, if the system resolution changed, then the video acquisition widgets would be out of synchronization with the new MCAM settings. (#4082)
owl 0.18.318 (2023/08/24)¶
No significant changes.
owl 0.18.317 (2023/08/24)¶
Bug fixes¶
Allow access to the live documentation and testing of the WebAPI even when the system is offline. (#4072)
Fixed bug that prevented stacking of image stacks. (#4074)
owl 0.18.316 (2023/08/22)¶
No significant changes.
owl 0.18.315 (2023/08/22)¶
Bug fixes¶
Zebrafish tracking compute skeleton now yields angle measurements with counter-clockwise rotation from zero instead of clockwise. (#4052)
owl 0.18.314 (2023/08/18)¶
No significant changes.
owl 0.18.313 (2023/08/18)¶
Fix bug preventing users from acquiring XYZ stacks. This has existed since 0.18.312
owl 0.18.312 (2023/08/18)¶
Allow users to load exported datasets in the MCAM Viewer. (#4061)
owl 0.18.311 (2023/08/18)¶
No significant changes.
owl 0.18.310 (2023/08/17)¶
No significant changes.
owl 0.18.309 (2023/08/17)¶
New features¶
Calls to assays will fail loudly if they are overwriting previous data (#4045)
Improvements¶
Provide an option to allow users to not overwrite files during the saving process if they exist. This option is only available through the Python API. (#4031)
owl 0.18.308 (2023/08/14)¶
Bug fixes¶
Fix bug preventing video acquisitions in the GUI and WebAPI. This has been broken since 0.18.294. (#4038)
owl 0.18.307 (2023/08/11)¶
Bug fixes¶
Ensure that the background illumination is maintained even after a flash with the transmission illumination board for zebrafish assay. (#4015)
owl 0.18.306 (2023/08/07)¶
Bug fixes¶
Address issue using the property
model_fieldswith pydantic V1. This was broken in versions 0.18.305 and 0.18.304. (#4017)Provide an error message if unsupported kernel versions are detected. (#4022)
owl 0.18.305 (2023/08/04)¶
Bug fixes¶
Fix bug where a user could not do a webAPI acquisition with no parameters specified. This has been a bug since 0.18.304. (#4011)
owl 0.18.304 (2023/08/03)¶
No significant changes.
owl 0.18.303 (2023/08/01)¶
No significant changes.
owl 0.18.302 (2023/07/31)¶
New features¶
Feature preview: Allow users to set a per sensor digital and analog gain. Users are encouraged discuss their usecase with Ramona Optics. (#3978)
Bug fixes¶
Ensure that the chosen EXIF orientation is maintained when the user opens the MCAM in configuration mode. (#3982)
owl 0.18.301 (2023/07/26)¶
Improve compatibility with dependencies.
owl 0.18.300 (2023/07/26)¶
No significant changes.
owl 0.18.299 (2023/07/25)¶
Improvements¶
Slight optimization in video playback parameters enabling faster reading of MP4 based datsaets. (#3941)
Improve video playback speed in MCAM Viewer. (#3952)
Improve MP4 playback speed when attempting to skip frames. (#3955)
Allow the user to control the playback frame rate for datasets backed by MP4 files. (#3957)
Update fluorescence firmware to 0.1.6 to improve firmware responsivity. (#3962)
owl 0.18.298 (2023/07/20)¶
Ensure functionality of the activity metric on mp4 datasets.
owl 0.18.297 (2023/07/20)¶
No significant changes.
owl 0.18.296 (2023/07/20)¶
Improvements¶
- Disable CPU based animal tracking by default providing users with better
insights on why tracking can be slow. (#3878)
Add RGB support to
calculate_activity_metric. (#3920)
Bug fixes¶
Ensure that the schema type of the mcam_state is always returned. (#3918)
owl 0.18.295 (2023/07/14)¶
Bug fixes¶
Fix loading of settle time in the Zebrafish assay. Broken since 0.18.288. (#3906)
owl 0.18.294 (2023/07/14)¶
No significant changes.
owl 0.18.293 (2023/07/14)¶
No significant changes.
owl 0.18.292 (2023/07/13)¶
No significant changes.
owl 0.18.291 (2023/07/13)¶
Bug fixes¶
Address issues loading the background illumination intensity in the zebrafish assay designer. (#3881)
owl 0.18.290 (2023/07/13)¶
Bug fixes¶
Address display and computation errors when opening datasets stored as Multi-MP4 generated prior to version 0.18.167. The computation generated with version prior to 0.18.167 is still valid, however when a dataset acquired with version 0.18.162 was analyzed with version 0.18.268, the computation errors would appear. (#3866)
Address issues where systems without a calibration file would provide erroneous warnings. In these cases the warnings could safely be ignored but they could disrupt the flow of code based applications. (#3871)
owl 0.18.289 (2023/07/12)¶
Improvements¶
Improved “compute_fish_length” computation speed. (#3858)
Bug fixes¶
Fix bug where loading a second configuration file to an assay panel may not apply its parameters correctly. (#3851)
owl 0.18.288 (2023/07/08)¶
Bug fixes¶
Fix the intensity of the visual stimuli that is tested in the zebrafish assay. It was broken in 0.18.287. (#3844)
owl 0.18.287 (2023/07/08)¶
Bug fixes¶
Address issues where the device illumination may be misrecorded in the dataset’s metadata. (#3816)
owl 0.18.286 (2023/07/05)¶
Improvements¶
Decrease the time required to program vibration motions. (#3812)
owl 0.18.285 (2023/07/04)¶
Improvements¶
Ensure more consistent vibration stimulus response in the zebrafish assay. (#3802) (#3804)
owl 0.18.284 (2023/07/02)¶
Add constraint to avoid pydantic 2 due to its incompatibility with the owl library.
owl 0.18.283 (2023/06/26)¶
Bug fixes¶
Fix opening the web MCAM server from the MCAM GUI. This has been broken since 0.18.282. (#3784) (#3784)
owl 0.18.282 (2023/06/26)¶
New features¶
MCAM Viewer Tool: Best Focus Image Selection. Use this panel to find and specify which images from a stack to save to a “best of” single plane image. (#3324)
WebAPI: The Web MCAM now saves settings related to the configuration of the web server. (#3715)
owl 0.18.281 (2023/06/23)¶
Rename Zoom In and Zoom Out on the Kestrel systems to match the values in the assay files.
Improve error messages in XYZ stacks and well plate stack acquisitions.
owl 0.18.280 (2023/06/22)¶
No significant changes.
owl 0.18.279 (2023/06/20)¶
No significant changes.
owl 0.18.278 (2023/06/20)¶
Address bug in MCAM GUI causing the GUI to crash when the user attempted to close the fluorescence illumination. (#3762)
owl 0.18.277 (2023/06/20)¶
Fix interactions between GUI and fluorescence controller which broke in 0.18.277.
owl 0.18.276 (2023/06/20)¶
Improvements¶
Ensure that
owl.mcam_data.save_videois compatible with stacks where each plane of data is greater than 4GB. (#3742)
Bug fixes¶
Address compatibility with Numpy 1.25. (#3752)
Address inconsistencies in the shutdown of the fluorescence driver preventing it from being reopenned correctly in the case of an error on open. (#3759)
Address compression of monochrome videos that appeared green in standard video players. (#3760)
owl 0.18.275 (2023/06/16)¶
No significant changes.
owl 0.18.274 (2023/06/16)¶
No significant changes.
owl 0.18.273 (2023/06/15)¶
System adjustment
owl 0.18.272 (2023/06/15)¶
System adjustment
owl 0.18.271 (2023/06/15)¶
System adjustment
owl 0.18.270 (2023/06/13)¶
No significant changes.
owl 0.18.269 (2023/06/13)¶
No significant changes.
owl 0.18.268 (2023/06/12)¶
Improvements¶
Add minimum exposure of stack to HDR image created through
get_hdr_dataset(). (#3706)
owl 0.18.267 (2023/06/12)¶
New features¶
Preview: For MCAMs equipped with illumination sources, the MCAM will store the illumination mode as a number within the dataset itself. This number may be used as a unique reference for the purposes of customization of the image filenames. Users may refer to this number as the
illumination_channel_idwithin the datasets returned by the MCAM object in python. (#3683)
owl 0.18.266 (2023/06/10)¶
No significant changes.
owl 0.18.265 (2023/06/09)¶
Bug fixes¶
Fix passing in the metadata to the video acquisition functions. (#3697)
owl 0.18.264 (2023/06/08)¶
New features¶
The WebMCAM Server is now launchable from the MCAM GUI. You can find it in the file menu when the MCAM is not open. (#3659)
Improvements¶
Zebrafish eye analysis is now available in the MCAM GUI. (#3594)
Reduction in the number of calibration constants kept in each dataset. This should make slicing datasets faster as well as reducing the size of the metadata file.
owl 0.18.263 (2023/06/07)¶
Address an edge case that stopped well extraction from working on certain systems built int 2021.
owl 0.18.262 (2023/06/07)¶
No significant changes.
owl 0.18.261 (2023/06/06)¶
Improvements¶
Improve metadata reporting of plane information in multipage TIFF files improving compatibility with scientific image viewers when stacks of monochrome or grayscale images contain exactly 3 or 4 slices. (#3677)
owl 0.18.260 (2023/06/05)¶
Improve detection of GPU encoding capabilities.
owl 0.18.259 (2023/06/05)¶
Improvements¶
Optimize usage of system RAM when acquiring videos for zebrafish assays enabling longer acquisitions at high speed.
Enable Multi-MP4 storage for the zebrafish assay panel. (#3671)
owl 0.18.258 (2023/06/02)¶
Fix labels for well plates broke since 0.18.255.
owl 0.18.257 (2023/06/01)¶
Add webAPI demo configuration file using new features of the Z Stack assay. (#3643)
owl 0.18.256 (2023/06/01)¶
Bug fixes¶
Address self documentations features of the WebAPI. (#3630)
Address errors in the assays GUIs that prevented operation due to the
mcam_state. Introduced in 0.18.255. (#3637)
owl 0.18.255 (2023/06/01)¶
New features¶
Allow users to export and load acquired stacks or videos as a series of single page tiff files. (#3587)
Allow configuration of the image names in the
acquire_and_saveassay and thez_stackassay. (#3625)
Improvements¶
Support writing large image stacks as BigTIFF file formats to support cases where a single
.tiffile is larger than 4GB. (#3577)Simplify the interface for video acquisition to multi MP4 files. (#3592)
Improve consistency in placement and interaction of warning message boxes. (#3597)
A new context manager for MCAM objects exists to help restore the MCAM state after a given experiment. See documentation around
MCAM.hold_state. (#3616)Ensure that image stack metadata is saved in nc format by default reducing overall file size. The behavior has changed for a few image formats:
The option to not save any metadata is now removed. Metadata will always be saved either as a JSON file or as an NC file. We have not observed much usage of this capability and as such we do not expect this to affect many users.
The default metadata extension is now
.ncformulti_mp4andtiledmp4formats.The default metadata extension remains
.jsonforimages,image_stacks, andflat_image_stacks. (#3624)
Bug fixes¶
Ensure that the z-stack assay returns the actually used illumination brightness. (#3607)
Deprecations¶
Deprecation of
owl.mcam_data.save_wells. The datasets now self describe as well datasets with enough information to inform to allow the functionowl.mcam_data.exportto save images with the appropriate file names. (#3626)
owl 0.18.254 (2023/05/25)¶
No significant changes.
owl 0.18.253 (2023/05/25)¶
New features¶
Enable acquisitions faster than 60fps to be saved directly as MP4 files when acquiring videos. (#3523)
Improvements¶
Update Z stack and XYZ stack data so that the leading dimension is
frame_numberinstead ofz_stageto keep in unison with other stack datasets. - Deprecated the following functions inowl.analysis.z_stack_functions:calculate_position_error,get_best_height_for_full_array,get_heights_range_for_subsections,acquire_stack,plot_focus_through_stack,measure_sliceandfind_best_z_position. (#3484)
Bug fixes¶
Fix loading of subset selections in Acquire Video / Acquire Stack panels. This has been broken since 0.18.252. (#3546)
owl 0.18.252 (2023/05/18)¶
Subset selections are now saveable and loadable in assay protocols. (#3544)
owl 0.18.251 (2023/05/18)¶
No significant changes.
owl 0.18.250 (2023/05/17)¶
New features¶
z-stack assay is interruptible through the WebAPI. (null)
Bug fixes¶
Fix bug where video assay would wait twice as long as the requested settle time. (#3535)
owl 0.18.249 (2023/05/17)¶
No significant changes.
owl 0.18.248 (2023/05/17)¶
Hide certain playback controls that don’t apply to to files exported with .tiff or .mp4 extensions.
owl 0.18.247 (2023/05/15)¶
New features¶
Add GUI assay to capture Z stack timalapses. (#3482)
Add GUI assay to capture XYZ stack timalapses. (#3504)
owl 0.18.246 (2023/05/15)¶
Add the ability to save video acquisition settings.
owl 0.18.245 (2023/05/14)¶
New features¶
Preview: New Multi-Animal Tracking analysis panel. (#3501)
owl 0.18.244 (2023/05/12)¶
Improvements¶
Improve speed of acquisition to multi MP4 in high speed acquisition video panel. (#3510)
owl 0.18.243 (2023/05/12)¶
Improvements¶
Hide certain illumination controls when the subcomponents are not available for a given MCAM. (#3502)
owl 0.18.242 (2023/05/12)¶
Improvements¶
Improve encoding speed of multi-mp4 by encoding multiple streams in parallel. (#3945)
owl 0.18.241 (2023/05/11)¶
No significant changes.
owl 0.18.240 (2023/05/11)¶
New features¶
Revise the
imagename_formatin the functionowl.mcam_data.exportto enable the use of more metadata fields in the exported image names. (#2834)
Improvements¶
Ensure that the leading dimension is named
frame_numberin XYZ stacks. (#3486)
owl 0.18.239 (2023/05/10)¶
New features¶
Add the option to save z stacks as minimum or maximum projections instead of the full stack in the GUI. (#3473)
Add the option to save xyz and wellplate stacks as minimum or maximum projections through the z axis instead of the full stack in the GUI. (#3474)
Allow acquisition of high speed video to disk and to MP4. (#3476)
Bug fixes¶
Restore the progress bar update functionality during the preparation for the video buffer. (#3475)
owl 0.18.238 (2023/05/09)¶
System bringup.
owl 0.18.237 (2023/05/08)¶
Bug fixes¶
Fix incompatibility with EXIF Orientation 1 through 4. (#3467)
owl 0.18.236 (2023/05/07)¶
Improvements¶
Ensure that cancelling an xyz stack returns the MCAM to the starting location. (#3463)
owl 0.18.235 (2023/05/06)¶
New features¶
Enable operating the MCAM with sensor regions of interest of size 3136 x 3136. (#3459)
Bug fixes¶
Fix viewing square wells in the MCAM Viewer. (#3458)
owl 0.18.234 (2023/05/05)¶
System bringup.
owl 0.18.233 (2023/05/05)¶
Improvements¶
Multi animal tracking now stitches tracklets to individualize inferences. (#3283)
Improve responsiveness when working with stacks of TIFF images. (#3452)
Bug fixes¶
Fix listing the connected drives and their respective partitions in the
mcam_listcommand. The command was misreporting the partitions and their size since version 0.18.214. (#3447)
owl 0.18.232 (2023/05/03)¶
Improvements¶
Updated the 48 well plate zebrafish tracking model. (#3445)
owl 0.18.231 (2023/05/03)¶
New features¶
Add schema keys for future features of the z-stack assay including a key that specifies allowable projections, high dynamic range acquisitions, and relative position specifications. (#3435)
owl 0.18.230 (2023/05/02)¶
System bringup. (#3436)
owl 0.18.229 (2023/05/01)¶
New features¶
Added assay protocol saving and loading to the XYZ Stack / Well Plate Stack panel. (#3407)
Bug fixes¶
Ensure that the Kestrel0006 loading and unloading positions are within the valid range. (#3432)
owl 0.18.228 (2023/04/28)¶
No significant changes.
owl 0.18.227 (2023/04/28)¶
New features¶
When running assays from the WebAPI, all data is saved within a subfolder. This unifies the behavior no matter if saving in an single .nc file or exporting images as TIFFs. (#3411)
Improvements¶
Tracking composite visualizations now support multi-animal tracking. (#3408)
Bug fixes¶
Fix multithreading bug in the fluorescence driver software. (#3418)
owl 0.18.226 (2023/04/26)¶
New features¶
Preview: Diet stunt and moratlity analysis panel. (#3379)
Add the zebrafish embryonic photomotor response assay to the gui. (#3387)
owl 0.18.225 (2023/04/26)¶
Improvements¶
Unused parameters are removed from single animal tracking model metadata.
Bug fixes¶
Fix applying the correct digital gain in the GUI which was broken between versions 0.18.216 and 0.18.224. (#3412)
owl 0.18.224 (2023/04/24)¶
New features¶
Provide tqdm parameters to monitor the saving progress in
MCAM.acquire_video_to_fileandMCAM.acquire_video_to_tiledmp4. (#3399)
Bug fixes¶
Increase the allowable setup time in
MCAM.acquire_video_to_tiledmp4to account for the larger setup for videos of resolution larger than 4k. (#3399)Fix overestimation in required disk space when saving datasets as
tiledmp4ormulti_mp4image formats. This bug did not affect users of the zebrafish panel that were acquiring videos directly to mp4 compressed formats. (#3400)
Improvements¶
Improved performance during for the zebrafish 8 keypoint tracking.
owl 0.18.223 (2023/04/20)¶
New features¶
WebAPI Asynchronous Preview: Rename the
assay/waitendpoint toassay/result. Removed theassay_nameparameters from theassay/resultandassay/stopendpoint to aid with error recovery. (#3382)
owl 0.18.222 (2023/04/20)¶
New features¶
Preview: WebAPI Asyncrhonous endpoint for assays are being previewed by early adopters. Feedback is welcome regarding any of the behavior. Breaking changes may occur in interactions with the web API in the coming weeks. (#3358)
owl 0.18.221 (2023/04/20)¶
Improvements¶
Ensure compatibility with xarray 2023.4 (#3372)
Bug fixes¶
Ensure correct temporary buffer allocation during video acquisition to MP4 avoiding supurious failures in video acquisition. (#3374)
Ensure that well alignment doesn’t reset upon changing the stitching parameters in the GUI. (#3375)
owl 0.18.220 (2023/04/19)¶
Improvements¶
Increase the maximum recording frame to MP4 files to 60 fps depending on the number of sensors used. Users should be able to capture full wellplates at 60 fps. (#3326)
Bug fixes¶
GUI: Address issues closing the MCAM when no transmission or reflection illumination boards are connected. (#3366)
owl 0.18.219 (2023/04/16)¶
No significant changes.
owl 0.18.218 (2023/04/16)¶
Bug fixes¶
Fix display of the green digital gain when per color digital gains are used. In the previous version, it displayed a value that was twice as large as expected. (#3351)
Update the Zebrafish 24 well plate model.
owl 0.18.216 (2023/04/13)¶
New features¶
GUI: Provide the ability to individually specify the digital gain on a per color level for systems with color image sensors. (#3308)
owl 0.18.215 (2023/04/07)¶
Bug fixes¶
Critical: Datasets previously acquired with the Zebrafish assay with the
"Save To Disk"or"Save as MP4"in conjunction with the the usage of well alignment files at acquisition time have the well row names (AthroughH) mislabled. (#3320)
owl 0.18.214 (2023/04/06)¶
New features¶
Preview: Added Leaf Disk analysis panel (#3215)
Preview: Added Leaf Disk acquisition panel (#3230)
Improvements¶
When re-exporting data with the MCAM Viewer, save the user’s new visualization settings instead of falling back to those selected at acquisition time. (#3289)
Bug fixes¶
Fix calibration data applied to certain datasets taken with fluorescence illumination or white reflection illumination prior to version 0.18.157. These datasets opened without the ability to be stitched, or calibrated in the GUI. (#3284)
Fix restoration of per color digital gain from the MCAM State. (#3313)
owl 0.18.213 (2023/04/03)¶
Improvements¶
Added function to calculate and output fish lengths. (#3257)
Simplify choices in the video compression GUI. (#3268)
Rename MCAM Control application
MCAM(started with the commandmcam) instead ofFalcon GUIto highlight its applicability beyond the Falcon product line. (#3270)Improved error handling when Fluorescence controller and Temperature Monitor experience errors during communication. (#3271)
Bug fixes¶
Address a small memory leak in playing back datasets stored in mp4 format. (#3259)
Fix subset selection in MCAM Viewer when repeatidly opening files with a different number of image tiles. (#3260)
Updated system positioning for sample movement. (#3266)
Improve error handling for failures in setting the MCAM mechanical state in the web interface. (#3267)
Allow users to select sensor regions of interest of shape
3120 x 4096and3136 x 4224in the GUI again. Previously, input validation would have prevented users from selecting these two modes. (#3272)Ensure that MP4 encoder test is valid for very small images. (#3278)
owl 0.18.212 (2023/03/30)¶
Improvements¶
Provide the user with different encoding options when compressing videos and guide them through the different tradeoffs. (#3251)
Allow for fraction of a second stimuli in the Zebrafish assay panel.
Allow for vibration and flash stimulus at the same time. (#3256)
Bug fixes¶
Improve collision detection for Zebrafish / Stimuli assay. Add 0.5 second buffer to allow for previous stimuli to end. (#3256)
owl 0.18.211 (2023/03/28)¶
New features¶
Add activity metric analysis that saves to csv. (#3222)
Address issues saving metadata in Compressed MP4 formats.
owl 0.18.210 (2023/03/27)¶
New features¶
GUI: Stack Projection panel added to the MCAM Viewer. Projections can be exported as Tiff or NetCDF4 and will retain all relevant metadata. Users can install
cupyin order to run projections on their CUDA capable GPU. (#3133)
owl 0.18.209 (2023/03/27)¶
New features¶
Allow compression of monochrome datasets. (#3227)
Enable decompressing monochrome datasets. (#3228)
Improvements¶
Add a feature to use the nona stitcher in the
mcam_stitchcommand line utility. (#3159)
Bug fixes¶
Fix bug where users could not save well images from the MCAM Viewer. Bug since version 0.18.185. (#3216)
Correct issue that prevented created HDR images from well plate extracted images” (#3220)
Fix erroneously returned data that was provided when indexing compressed datasets backed by an MP4 file with negative indexes. (#3228)
Fix bug where extended exposure may be applied incorrectly. Bug since version 0.18.178. (#3225)
owl 0.18.208 (2023/03/17)¶
Improvements¶
Hide the scale bar in the GUI when the data isn’t meaningful. (#3197)
Bug fixes¶
Fixed bug causing a kernel panic and subsequent computer crashes on linux kernel versions 5.19.0 and above.
Ensure that the stage positions passed to
MCAM.set_stateare valid before trying to apply them. Invalid stage positions will be ignored when thestrictparameter is set toFalse. (#3199)GUI: Ensure MCAM retains image adjustment settings when opening the instrument. (#3205)
owl 0.18.207 (2023/03/15)¶
Bug fixes¶
Fix displaying updated image data in the GUI. Bug introduced in 0.18.206. (#3195)
owl 0.18.206 (2023/03/14)¶
Improvements¶
Add the ability to stitch frames of a stack in the gui stitcher. (#3167)
Bug fixes¶
Avoid the appearance of a black border around images when switching resolutions. This bug was introduced in 0.18.205. (#3191)
Ensure buttons are disabled after closing connection to the MCAM or closing the dataset. This bug was introduced in owl version 0.18.205. (#3192)
owl 0.18.205 (2023/03/14)¶
Improvements¶
Prevent MCAM Viewer and Falcon GUI from growing in memory after sustained usage. (#3171)
Bug fixes¶
Fix using custom custom MCAM camera selections with Dual-Kestrel MCAM systems. (#3186)
GUI: Fix bug where the MCAM may not correctly save its state into the users settings. (#3175)
owl 0.18.204 (2023/03/10)¶
GUI: Fix selecting a subset. Broken since 0.18.203. (#3165)
owl 0.18.203 (2023/03/09)¶
Bug fixes¶
GUI: Ensure that the MCAM isn’t streaming during acquire and save assay to ensure validity of data. (#3146)
Improvements¶
New system bringup.
owl 0.18.202 (2023/03/06)¶
Improvements¶
Enable drag and drop of compressed MCAM datasets for activity analysis. (#3139)
Clarify starting and ending temperature during acquisition in the MCAM Viewer. (#3140)
owl 0.18.201 (2023/03/06)¶
Improvements¶
Ensure images are labeled by their well ID during wellplate stacks. (#3121)
owl 0.18.200 (2023/03/06)¶
Fix bug with opening dual channel fluorescence introduced in version 0.18.199. (#3125)
owl 0.18.199 (2023/03/05)¶
Improvements¶
GUI: Display elapsed and remaining time in progress bars. (#3111)
GUI: Simplify XYZ Stack acquisition panel. (#3120)
Bug fixes¶
Address bug where acquiring subsets of video would require a large amount of RAM. (#3112)
owl 0.18.198 (2023/03/03)¶
New features¶
Add function to calculate activity metric while acquiring video straight to mp4s. (#3081)
Add a driver for a temperature monitor peripheral (#3095)
Add temperature metadata to MCAMs that have the hardware feature enabled. (#3097)
Add temperature monitor display to GUI and MCAM Viewer. (#3099)
Improvements¶
Improve interactivity and specificity of the well plate alignment tool. (#3086)
GUI: Well alignment, specify individual well diameters instead of well radii. (#3088)
Zebrafish Assay panel now saves MCAM configuration settings (e.g. exposure, illumination mode)
Zebrafish Assay panel configurations can now load through drag and drop. (#3092)
owl 0.18.197 (2023/03/02)¶
New features¶
Add
acquire_activity_metric_videowhich give the ability to acquire a video to memory while running the activity metric on the frames in parallel. (#3047)
Improvements¶
Allow users to specify zebrafish acquisition duration in minutes.
Provide users with a helpful error message when they select an invalid zebrafish assay file. (#3078)
Bug fixes¶
Fix bug preventing out of bounds error from displaying for 1536 well plate XYZ stack acquisitions.
Fix bug preventing display of the save popup if acquiring XYZ stacks in fluorescence. (#3084)
owl 0.18.196 (2023/03/01)¶
Improvements¶
Improve scene blending for images acquired in high speed mode. (#3075)
Bug fixes¶
Ensure that LED brightness is correctly reported by the zebrafish assay when used in conjunction with a flash stimulus.
Ensure that assays with well plate alignment information can be loaded in the zebrafish panel. (#3076)
owl 0.18.195 (2023/03/01)¶
New features¶
Provide an interface to rapidly compress high speed videos. (#3061)
Improvements¶
Address unresponsiveness of GUI during waiting time of zebrafish acquisition assay. (#3063)
Bug fixes¶
Fix zebrafish assay panel when used in conjunction with flash or vibration stimulus. This was broken in version 0.18.193. (#3064)
owl 0.18.194 (2023/02/27)¶
Improvements¶
Activity can now be analyzed directly from the MCAM Viewer using the activity metric panel. (#3052)
owl 0.18.193 (2023/02/27)¶
Improvements¶
Assay stimulus metadata is now automatically exported with time-series tracking data. (#2896)
PythonAPI: Automatically delay loading of large datasets. Users that desire a specific behavior should specify the delayed parameter in the load function. (#3034)
Bug fixes¶
Fix a bug that resulted in the wrong fluorescence illumination power to be reported in a limited number of cases. (#3045)
owl 0.18.192 (2023/02/23)¶
Improvements¶
Tracking data is now saved in both .csv and MCAM dataset forms by default. (#3019)
owl 0.18.191 (2023/02/22)¶
Improve loading time of multi-MP4 exported data.
owl 0.18.190 (2023/02/21)¶
Improvements¶
Zebrafish tail bend angles are now output by default using the fish frame of reference. (#2969)
Provide a meaningful error message, early on if the users is acquiring images with the MCAM in extended exposure mode during a video acquisition. (#3010)
Improve quality of tracking composite video. (#3012)
owl 0.18.189 (2023/02/17)¶
Ensure that exported image stacks can export in grayscale as well as RGB.
owl 0.18.188 (2023/02/17)¶
Ensure that exported image stacks can export in grayscale as well as RGB.
owl 0.18.187 (2023/02/17)¶
No significant changes.
owl 0.18.186 (2023/02/15)¶
Improvements¶
Tracking skeleton data is now computed directly from the tracking data. (#2952)
Bug fixes¶
Ensure that data stored as RGB (such as the one stored in videos) can be exported by the MCAM. (#2965)
Fix bug introduced in 0.18.184 where the metadata in the Acquisition GUI was not updated upon refreshing the acquired image. (#2967)
Fix the ability to load data exported with owl version 0.18.177 (exactly). This bug was introduced in version 0.18.178. (#2968)
Addressed bug preventing stacks of images containing exactly one 1 image from being displayed in the GUI introduced in 0.18.184. (#2970)
Address a bug where
mcam_data.exportwould mutate the attributes of exported dataset. (#2979)Ensure that MCAM with color sensors that acquire images illuminated with infrared light display the images in grayscale instead of raw. This bug appeared in owl version 0.18.179. (#2992)
owl 0.18.185 (2023/02/14)¶
Improvements¶
Tracking skeleton data is now computed directly from the tracking data. (#2952)
Updated verbiage surrounding well keypoints. Well Extractor panel is now titled Well Alignment. Related files will be referred to as Well Alignment files in the GUI. (#2977)
Bug fixes¶
Ensure that data stored as RGB (such as the one stored in videos) can be exported by the MCAM. (#2965)
Fix bug introduced in 0.18.184 where the metadata in the Acquisition GUI was not updated upon refreshing the acquired image. (#2967)
Fix the ability to load data exported with owl version 0.18.177 (exactly). This bug was introduced in version 0.18.178. (#2968)
Addressed bug preventing stacks of images containing exactly one 1 image from being displayed in the GUI introduced in 0.18.184. (#2970)
Address a bug where
mcam_data.exportwould mutate the attributes of exported dataset. (#2979)
owl 0.18.184 (2023/02/12)¶
Improvements¶
Enable toggling of notes section in the GUI. (#2953)
Added information about the sensor region of interest and binning mode in the MCAM Viewer. (#2956)
Bug fixes¶
Respect user preferences of displaying a popup upon saving a file. (#2949)
WebAPI: Ensure that new style serial numbers are reported by the WebAPI.
WebAPI: Ensure that availability of devices is correctly reported the WebAPI upon disconnecting the device. (#2951)
The central panel in the acquisition GUI now reflects the metadata of the images currently being displayed instead of copying values from the control panel. This ensures that this metadata is related to the data immediately above it. (#2956)
Fix the MCAM Viewer not displaying the image name in the title bar. (#2957)
owl 0.18.183 (2023/02/09)¶
Bug fixes¶
Corrected thigmotaxis assay example for well index sorting and example filepaths. (#2942)
Updated verbiage on some assay panels in response to user feedback. (#2941)
owl 0.18.182 (2023/02/09)¶
No significant changes.
owl 0.18.181 (2023/02/09)¶
Return MCAM to expected state on completion of Z Stack assay. (#2933)
owl 0.18.180 (2023/02/08)¶
New features¶
Added Z Stack panel to GUI with ability to load and save configurations. (#2920)
Added a .csv output for the activity analysis workflow.
Added an example workflow script to allow zebrafish activity analysis. (#2891)
owl 0.18.179 (2023/02/07)¶
New features¶
Enable users to save z-stacks and multiple frames of a time series in a group of TIFF images. (#2900)
Bug fixes¶
Enable well extraction in GUI for dataset subset. (#2871)
Image export will now respect the display mode of the user in the GUI. (#2900)
Enhanced error handling when loading user configurations in the GUI. (#2859)
Fix bug where GUI could crash while streaming video under heavy computer load. (#2918)
owl 0.18.178 (2023/02/02)¶
New features¶
Introduce tap strength modulation to the PlateTapper driver.
PlateTapper methods soft_tap() and hard_tap() are renamed to dampened_tap() and direct_tap(), respectively. (#2870)
Improvements¶
Updated 48 well plate tracking model using 352x352 images. (#2838)
Improve the turn off responsiveness of fluorescence illumination modules. (#2856)
Added a second iteration of the 48 well plate zebrafish tracking model. (#2862)
Create temperature properties for Tokai Hit Thermoplate driver (#2864)
Improved support for RGB images as tiff. (#2868)
owl 0.18.177 (2023/01/26)¶
No significant changes.
owl 0.18.176 (2023/01/26)¶
No significant changes.
owl 0.18.175 (2023/01/26)¶
No significant changes.
owl 0.18.174 (2023/01/25)¶
Improvements¶
Expand the LED control abilities of the fluorescence illumination driver. (#2826)
owl 0.18.173 (2023/01/25)¶
System bringup.
owl 0.18.172 (2023/01/25)¶
Improvements¶
The MCAM serial number is available as a property from the MCAM object.
The MCAM serial will be stored in the dataset if it is defined by the MCAM object. (#2832)
Add system serial number to keypoints files for better system detection. (#2833)
Updated 48 well plate tracking model using 352x352 images. (#2838)
owl 0.18.171 (2023/01/23)¶
Bug fixes¶
Fix bug preventing the WebAPI from correctly listing connected MCAM devices.
Fix bug where the WebAPI was unable to correctly report acquisition brightness. (#2824)
Fix bug where well keypoints may be saved with the incorrect key. (#2827)
owl 0.18.170 (2023/01/23)¶
Improvements¶
Updated tracking workflow example script to use new skeleton labeling and composite video functionality.
Updated tracking workflow example script so that circle masks are no longer automatically applied during well extraction. (#2815)
Bug fixes¶
Address an issue with copying well extracted datasets introduced in 0.18.160. (#2808)
Fix memory accumulation when accessing wellplate slices introduced in 0.18.163.
Fix accessing well plate data when negative indices. (#2810)
Ensure that images obtained from the well extractor are of tif format so that they contain the correct metadata. (#2812)
Corrected typos in well extraction script. (#2816)
owl 0.18.169 (2023/01/19)¶
New features¶
Add well extraction functionality to webAPI. (#2774)
owl 0.18.168 (2023/01/19)¶
Bug fixes¶
Adjust a bug where save video would first copy the data before saving leading to spurious crashes introduced in version 0.18.163. (#2804)
owl 0.18.167 (2023/01/18)¶
New features¶
Add a driver for a plate tapper peripheral. (#2715)
Improvements¶
The video composite function now draws skeletons on fish while combining. (#2781)
Zebrafish tracking: Speedup saving of CSV files. - Zebrafish tracking: Provide a progress bar during saving of CSV files. (#2787)
Removed warning when users are acquiring images at different resolutions. (#2796)
Bug fixes¶
Do not include header in skeleton csv generating during zebrafish tracking if the user does not request it. (#2797)
Documentation¶
Added documentation on the available illumination modes. (#2795)
owl 0.18.166 (2023/01/13)¶
Bug fixes¶
Fix selecting custom keypoints files in the advanced GUI. (#2792)
owl 0.18.165 (2023/01/12)¶
Improvements¶
Make quickstitch the default stitching option in the GUI. (#2789)
Bug fixes¶
Fix a bug that incorrectly sets the maximum power deliverable to single channel fluorescence illumination modules. (#2779)
Enable calibration for
fluorescence_white_5650K_frontandfluorescence_white_5650K_backillumination modes. (#2787)
owl 0.18.164 (2023/01/12)¶
Improvements¶
Speed up well extraction MP4 generation by 20%. (#2761)
Bug fixes¶
Allow the MCAM Viewer to open stacks of data saved in RGB format. (#2783)
owl 0.18.163 (2023/01/10)¶
New features¶
Add a driver for the Tokai Hit stage top incubator. (#2760)
Improvements¶
Integrate a new LED power supply - Add the ability to control front and back fluorescence illumination modules independently. (#2740)
Ensure that subsets of NC files that are larger than the amount of RAM on a given computer can be generated with the GUI. (#2773)
Bug fixes¶
Fix a bug that in some cases incorrectly set the maximum allowable power delivered to the fluorescence illumination module. (#2772)
Fix bug that prevents quick-stitching in
falcon_guiandmcam_viewer. (#2776)
owl 0.18.162 (2022/12/23)¶
New features¶
Allow users to adjust the color of the plotted tracks based on the velocity of the zebrafish. (#2742)
owl 0.18.161 (2022/12/21)¶
Bug fixes¶
Fix bug that prevented usage of custom 6 well plate arrangements (introduced in version 0.18.158). (#2750)
owl 0.18.160 (2022/12/21)¶
Improvements¶
Added progress bars to gui tracking and skeleton data compilation. (#2737)
Tracking metadata will now be saved in netcdf format rather than json. (#2739)
Speed up the generation of the composite videos for zebrafish analysis. (#2745)
The tracking model name will now be saved to the tracking model dataset and output in csv headers. (#2746)
owl 0.18.159 (2022/12/20)¶
Improvements¶
Replace the - character with _ in illumination modes as well as rename calibration metadata to make it more accessible in the dataset. (#2696)
Added demo configurations to the WebMCAM assay “acquire_and_save”. (#2735)
owl 0.18.158 (2022/12/18)¶
New system bringup.
owl 0.18.157 (2022/12/17)¶
Improvements¶
Added progress bar to Export Subset Video panel in the MCAM Viewer. (#2719)
owl 0.18.156 (2022/12/14)¶
Bug fixes¶
Fix bug that prevented the acquisition of videos. (#2720)
owl 0.18.155 (2022/12/13)¶
New features¶
Add Acquire Barcode panel to optimize saving image names with barcodes. (#2711)
Improvements¶
Ensure the progressbar is updated immediately upon starting tracking and well extraction. (#2710)
Ensure that the zebrafish tracking chooses the default wellplate configuration more intelligently. (#2712)
owl 0.18.154 (2022/12/09)¶
Improvements¶
Update 96 wellplate keypoint file for recently recalibrated system. (#2681)
Consolidate zebrafish analysis options during tracking. (#2682)
Bug fixes¶
Fix a bug preventing connection to the temperature sensor interface on single channel fluorescence modules. (#2704)
owl 0.18.153 (2022/11/28)¶
Bug fixes¶
Address slowdowns in zebrafish tracking for head fixed preparations. (#2672)
owl 0.18.152 (2022/11/28)¶
Bug fixes¶
WebMCAM: Fix a bug causing issues with connecting to certain system configurations. (#2670)
owl 0.18.151 (2022/11/28)¶
Improvements¶
Use system serial numbers to open MCAMs from the web interface. (#2667)
Bug fixes¶
WebMCAM: Fix a bug that allowed one to provide any serial number when changing the MCAM’s mechanical state through the web interface. (#2665)
Deprecations¶
Removal of official support for Python 3.8 (#2658)
owl 0.18.150 (2022/11/18)¶
Bug fixes¶
Ensure that early datasets acquired with monochrome sensors display in grayscale in the GUI. (#2649)
owl 0.18.149 (2022/11/18)¶
No significant changes.
owl 0.18.148 (2022/11/17)¶
Fix bug causing bin mode and exposure to desync with the GUI (#2644)
owl 0.18.147 (2022/11/15)¶
Improvements¶
Modify the maximum output power of fluorescence illumination modules. (#2573)
Bug fixes¶
Fix a bug in the fluorescence temperature control firmware wherein a register was not being set correctly. (#2636)
owl 0.18.146 (2022/11/13)¶
New features¶
Retain the last used settings in the GUI settings. Re-opening the MCAM will start it in the same bin mode. (#2625)
Added options to remove excess tracking output files. (#2623)
Added support for tracking skeleton analysis. (#2623)
Bug fixes¶
Ensure that the displayed images in high frame rate operating modes are correctly cropped to the rectangular field of view. (#2624)
Ensure that the right sidebar is always opened to a minimum width. (#2626)
Disable the stage and resolution from accidentally changing upon scroll. (#2628)
Fix bug that would cause zebrafish analysis to crash if run twice sequentially. (#2629)
owl 0.18.145 (2022/11/10)¶
Improvements¶
Provide MCAM Viewer with the ability to specify a playback speed for videos of the MCAM (Linux only).
Remove defunct zebrafish model as options in the tracking assay. (#2610)
Bug fix¶
Fix bug where erroneous binning settings would not be reported back to the end user. This bug affected users of version 0.18.143 and 0.18.144.
owl 0.18.144 (2022/11/09)¶
Bug fixes¶
Solve bug that prevented calibration from being done for fluorescence on monochrome systems. (#2615)
owl 0.18.143 (2022/11/09)¶
Improvements¶
Uncalibrated systems will no longer issue a warning for uncalibrated LED boards. A “best effort” will be made to ensure color accurate visualizations.
The transmission and reflection illumination modes from the MCAM will apply the appropriate red, green, and blue ratios from the LEDs to ensure that the collected image appears white. (#2593)
Ensure that the first image displayed on the MCAM acquisition GUI has the correct corrections applied. (#2594)
Transferal of metadata from coordinate to variable within the mcam dataset. This should come with some mild performance improvements for users. (#2600)
The MCAM datasets now include a property
'illumination_brightness'that records the current illumination mode’s brightness. (#2609)MCAM Viewer and Acquisition will now report the brightness of the illumination controller. (#2611)
Enable generation of composite videos for 6-well plate acquisitions. (#2612)
Bug fixes¶
Ensure that the illumination mode is correctly defined in the dataset on Kestrel devices. This bug was introduced in 0.18.142. (#2597)
WebMCAM: Ensure that the
illumination_modeandillumination_brightnessare correctly returned after an acquire and save assay. (#2598)Ensure that the automatic model selection in the Zebrafish assay detects the chosen wellplate. (#2612)
Help mitigate errors in generating zebrafish composite video on systems with smaller amounts of GPU memory (#2613)
owl 0.18.142 (2022/11/07)¶
New features¶
Provide the ability to the GUI to add a sample stage in the x direction.
Provide the ability to the GUI to automatically detect peripherals based on the detected serial number of the system.
owl 0.18.141 (2022/11/04)¶
Bug fixes¶
Allow users to save z stack with “.” in the file name through the GUI. (#2581)
Fix bug that prevented the generation of the video composite during zebrafish tracking.
owl 0.18.140 (2022/11/03)¶
Fix bug causing the GUI to incorrectly display the currently selected bin mode
owl 0.18.139 (2022/11/03)¶
New features¶
Allow users to select the center of the region of interest when selecting pixels within an image sensor. (#2574)
Allow users to customize whether or not the GUI should automatically open the MCAM upon startup. (#2575)
owl 0.18.138 (2022/11/02)¶
Deprecations¶
MCAM Web API no longer returns mcam state in the endpoint
GET /v1/mcam/{serial_number}. (#2556)
owl 0.18.137 (2022/11/01)¶
Bug fixes¶
Ensure that the Acquire Video is enabled after successful completion of acquired extended zebrafish videos. (#2564)
owl 0.18.136 (2022/11/01)¶
New features¶
Improvements for virtual MCAM devices used for testing. (#2530)
Preview of setting the MCAM in different mechanical states. For the MCAMs that support it, a dropdown menu should appear next to the stage control in the GUI. (#2554)
Improvements¶
Improve opening time of MCAM device. (#2534)
Stage metadata is now stored inside variables in the dataset as opposed to coordinates. This should provide users with minor performance benefits when manipulating the dataset. (#2544)
Fix the location of the save panel vertically within the MCAM acquisition window. (#2549)
Bug fixes¶
Ensure a faster load time MCAM even when working offline. (#2533)
Deprecations¶
Formally deprecate the undocumentaed attribute
MCAM.data. (#2537)Formally deprecate passing non-datasets to the
owl.mcam_data.exportfunction. (#2541)Remove
save_one_as_bmpfrom public API. (#2543)
owl 0.18.135 (2022/10/26)¶
Bug fixes¶
Fix the ability of the GUI to specify user defined stages. Broken since 0.18.130. (#2504)
owl 0.18.134 (2022/10/26)¶
New features¶
Add gui support for switching between fluorescence illumination modes. (#2470)
Improvements¶
Add brightness, available illumination modes, and current illumination mode of illumination devices to the dataset’s metadata. (#2464)
owl 0.18.133 (2022/10/26)¶
Improvements¶
Improve display, blending and startup, of picture in picture in the GUI. (#2485)
Ensure that the images show in the PIP are always consistent with the latest acquired images. (#2486)
Bug fixes¶
Ensure that subselection indication is always on top of the images. (null)
Set the illumination device’s illumination mode when using the expanded illumination modes for the MCAM introduced in 0.18.130. (#2467)
Address the ability to open and use images with xyz stacks acquired using owl version 0.18.123. (#2488)
Addressed some slowdowns involved in loading datasets and opening the MCAM introduced in version 0.18.130.
owl 0.18.132 (2022/10/21)¶
No significant changes.
owl 0.18.131 (2022/10/20)¶
Improvements¶
Add backend support for dual channel fluorescence (#2436)
New stage added to the system settings. (#2462)
owl 0.18.130 (2022/10/17)¶
New features¶
Allow simulated peripheral devices such as stages and illumination devices to be connected to real MCAMs. - Allow real peripheral devices to be connected to simulated MCAMs. (#2414)
Improvements¶
Avoid slight shifts in the GUI when changing imaging resolutions due to the warning label appearing. (#2445)
Improve import time of
from owl.instruments import MCAM. (#2454)
Bug fixes¶
Ensure well plate stacks are displayed in the correct orientation.
For custom XYZ Scans, ensure that the X and Y starting positions are those specified in the scan, not the current position of the stage. (#2432)
Fix bug stopping users from acquiring a stack without selecting an illumination mode (#2444)
owl 0.18.129 (2022/10/12)¶
New features¶
New system build. (#2438)
Improvements¶
Add a new system to the registry (#2413, #2437)
Improve consolidation of cache directories. (#2428)
Faster Illuminate LED control improving pattern control. Users will have to update the firmware on their LED boards. (#2430)
Relax data type constraints for the coordinates
image_xandimage_ywhen exporting images as tiffs or BMPs. (#2433)Ensure compatibility with libnetcdf 4.9. (#2434)
owl 0.18.128 (2022/10/08)¶
Improvements¶
Return stage to starting position after acquiring a Z stack in gui.
Turn of fluorescence unit after acquiring a Z or XYZ stage in gui. (#2406)
Improved system status reported from the command
mcam_list.
Bug fixes¶
Fix bug allowing both streaming mode buttons to be visually checked at the same time. (#2410)
owl 0.18.127 (2022/10/06)¶
Improvements¶
Refactor of WebAPI to enhance discoverability. (#2415)
owl 0.18.126 (2022/10/03)¶
Preview¶
First preview of the MCAM WebAPI.
owl 0.18.125 (2022/10/03)¶
New features¶
Add
set_brightnessfunction to the MCAM object to allow the control of the brightness of the activated illumination source. (#2374)Users can now double click to move the subset selection in the MCAM Viewer. This is the same behavior as is currently possible in Falcon GUI. (#2393)
Bug fixes¶
Fix bug that prevented Illuminate instances from reporting the correct brightness through
get_brightnessafter brightness was set to 0. (#2375)Fix bug that left FakeFluorescence’s brightness in an undefined state after opening. (#2386)
Fix a bug where the MCAM Viewer could freeze up if the file loading was interrupted by a user loading a second file (#2393)
owl 0.18.124 (2022/09/23)¶
New features¶
The MCAM class can now report the size of one micro camera image using
image_nbytes. This can be useful when trying to estimate the space requirement for assays. (#2330)
Improvements¶
Speed up Acquisition GUI startup sequence. (#2360)
Bug fixes¶
Ensure that XYZ stacks can be taken with different numbers of steps in the X and Y directions. - Ensure that new images acquired with the XYZ panel can be exported as TIFFs and BMPs with the MCAM Viewer. (#2377)
Deprecations¶
Formally deprecate
MCAM.saveandMCAM.export_datain favor of the application managing its own dataset. (#2365)Deprecated the
MCAM.illumination_deviceproperty. (#2372)
owl 0.18.123 (2022/09/19)¶
Improvement¶
Improved support for accessing the MCAM when operating offline.
Documentation¶
Added example script for thigmotaxis assay. (#2347)
owl 0.18.122 (2022/09/16)¶
No significant changes.
owl 0.18.121 (2022/09/16)¶
Improvements¶
Update MCAM Viewer metadata on every frame change. (#2338)
owl 0.18.120 (2022/09/14)¶
Bug fixes¶
Ensure that images acquired with White Reflection Illumination have the correct image adjustment applied in the MCAM Viewer. (#2324)
Fixup XYZ acquisition panels which broke in version 0.18.114.
Fix Z-stack acquisitions in the absence of any LED boards. (#2332)
owl 0.18.119 (2022/09/13)¶
Bug fixes¶
Fix bug preventing the loading of some datasets in the MCAM Viewer. This has been broken since 0.18.118. (#2318)
owl 0.18.118 (2022/09/12)¶
Fixed loading datasets with the correct illumination modes in the GUI.
owl 0.18.117 (2022/09/12)¶
Improvements¶
Speed up image color correction. (#2311)
Bug fixes¶
Avoid automatically opening the dialog to select a well plate configuration in the advanced menu. (#2302)
owl 0.18.116 (2022/09/09)¶
Improvements¶
Simplify the process of starting up a remote help session with Ramona Optics team from the GUI.
Bug fixes¶
Set Fluorescence object’s illumination mode at opening. Previously it was left undefined. (#2305)
owl 0.18.115 (2022/09/07)¶
Improvements¶
Enable finer grained control on which models are used during Zebrafish analysis. (#2297)
owl 0.18.114 (2022/09/06)¶
Improvements¶
Expand allowable sensor shapes from the GUI. (#2295)
Bug fixes¶
Fix bug preventing saving of exposure stacks and subsets. This broke in version 0.18.112. (#2299)
owl 0.18.113 (2022/09/01)¶
Improvements¶
Added a close file button to the MCAM Viewer. (#2276)
GUI: Zebrafish assay will now store information about whether or not a subset is used during the zebrafish assay. The exact subset itself will not be saved. (#2282)
Bug fixes¶
Ensure users can restore default settings in the Falcon GUI. This broke in version 0.18.112. (#2286)
owl 0.18.112 (2022/08/31)¶
New features¶
Add
illumination_deviceproperty to MCAM so that the current illumination device can be accessed. (#2132)Additional user settings are now saved in the dataset to apply expected image settings in the viewer (#2278)
Bug fixes¶
Fix saving subsets of images which was broken in version 0.18.111. In version 0.18.111 saving subsets would save the entire array. (#2282)
owl 0.18.111 (2022/08/30)¶
Improvements¶
Enable the selection of micro-camera region of interest of 384 x 512 and 768 x 1024 pixels in the GUI. (#2280)
Bug fixes¶
Ensure collect colors are displayed when the user changes sensor resolution for non-square image shape in the Falcon GUI. This bug appeared in version 0.18.103. Data integrity was not affected. (#2279)
owl 0.18.110 (2022/08/26)¶
Improvements¶
Unification of XYZ stack aquistion.
Ensure that XYZ stacks can be acquired when the MCAM is in the inverted configuration.
Bug fixes¶
Erroneous MCAM configuration that made certain systems unable to acquire images since version 0.18.103. (#2264)
Stitching without quick stitching now applies color corrections and software white balancing if they are checked. (#2265)
owl 0.18.109 (2022/08/24)¶
Bug fixes¶
Fixed virtual selection registry values for some systems. (#2262)
owl 0.18.108 (2022/08/23)¶
Improvements¶
Remove analysis panel from zebrafish acquisition GUI for more a more focused process. (#2253)
Ensure the starting window size fits within a Full HD monitor with 100% scaling.
Ensure the close assay button is disabled during Video Acquisitions. (#2254)
Bug fixes¶
Fixup High Speed Video acquisition broken since version 0.18.102. (#2251)
Ensure that users can acquire zebrafish assays with both vibration and flash stimuli. Users were unable to do so since version 0.18.106. (#2255)
owl 0.18.106 (2022/08/22)¶
New features¶
Add ability to specify desired lux of flash in Zebrafish Assay Panel (#2165)
owl 0.18.105 (2022/08/21)¶
New features¶
GUI: Enable batch processing of multiple NC files with the zebrafish tracker. (#2244)
Improvements¶
GUI: Ensure that the About Dialog opens up more fluidly. (#2245)
owl 0.18.104 (2022/08/20)¶
Improvements¶
Crop out well plates in video composite generation during final visualization step. (#2241)
Bug fixes¶
Work around errors that can cause the generation of the final well plate composite to fail during zebrafish tracking analysis. (#2241)
owl 0.18.103 (2022/08/19)¶
New features¶
Extend the applicability of the Image Export panel to operate on z_stacks and exposure stacks. (#2227)
Improvements¶
GUI: Enable users to switch to standard resolution (bin x2) more fluidly. (#2235)
Bug fixes¶
Fix z-stack acquisition without any illumination mode or with fluorescence illumination. (#2222)
owl 0.18.102 (2022/08/12)¶
New features¶
Add toggle to
falcon_guito activate software white balancing when acquisitions switch to fluorescence illumination. (#2219)
owl 0.18.101 (2022/08/11)¶
Improvements¶
Fix title in the Zebrafish analysis panel. (#2216)
owl 0.18.100 (2022/08/10)¶
New features¶
Added functionality to compute distance traveled and speed. (#2190)
GUI: Allow the user to customize the output of the zebrafish analysis panel. (#2211)
owl 0.18.99 (2022/08/09)¶
New features¶
Gui: Only apply color corrections to exported images if the user has it enabled. (#2183)
Added functionality to visualize plotted tracks over time on composite well images. (#2189)
Improvements¶
System bringup for 24 well plate mode (#2184)
owl 0.18.98 (2022/08/03)¶
New features¶
Add switch in
falcon_guito allow user to manually control the display mode or allow the software to switch the display mode according to the illumination mode. (#2161)
Improvements¶
Don’t scale down the power of any fluorescence driver (#2170)
Bug fixes¶
Stopped bug that cause the display mode to return to the default display mode for the current illumination mode after every acquisition. (#2161)
owl 0.18.97 (2022/08/03)¶
Bug fixes¶
GUI: Ensure that the fluorescence lighting doesn’t turn on if the Enable checkbox is not set. Since version 0.18.90 the fluorescence illumination could be enabled even without the enable checkbox. (#2167)
owl 0.18.96 (2022/08/01)¶
New system bringup.
owl 0.18.95 (2022/08/01)¶
Bug fixes¶
Address issue that stopped the GUI from starting up in with IR illumination and PWM. (#2156)
Fixup MCAM calibration commandline interface. (#2157)
owl 0.18.94 (2022/08/01)¶
Improvements¶
Enable tracking data to be exported as a CSV file. (#2088)
Bug fixes¶
Fixup IR LED Brightness when used in conjunction with flashes. (#2153)
owl 0.18.93 (2022/07/29)¶
Bug fixes¶
Fix calibration command line application.
Fix the color of the LED flashes.
Fix setting the LED brightness to 0 in analog control modes. (#2141)
Fix z-stack acquisition without any illumination mode or with fluorescence illumination. (#2143)
owl 0.18.92 (2022/07/26)¶
New features¶
GUI: Add an assay to acquire a multiple different exposures. (#2087)
Bug fixes¶
Enable well extraction on datasets that are loaded into the
mcam_viewerfrom exported images.Enable well extraction on color datasets. (#2130)
owl 0.18.91 (2022/07/25)¶
Improvements¶
Save Falcon GUI stitching preference in user settings. (#2126)
Bug fixes¶
Only update
falcon_guidisplay for lighting changes after the following acquisition instead after lighting changes are made. (#2119)
owl 0.18.90 (2022/07/24)¶
New features¶
GUI: Provide option to control which fluorescence illumination unit is enabled for a given MCAM. (#2120)
Improvements¶
Added functionality to convert units within a dataset prior to exporting. (#2100)
Decrease the time required for the MCAM to switch binning modes. (#2118)
Improved tracking data analysis compilation adding skeleton data to dataset. (#2122)
Bug fixes¶
Enable exporting stacks of in-memory videos as collections of video files. (#2090)
Improve robustness of exporting small videos. (#2099)
Fix blending for binned datasets. The bug was introduced in version 0.18.89. (#2113)
Ensure that the serial numbers of the reflection and transmission boards are retained in the GUI settings. (#2120)
Deprecations¶
Formally deprecate the keyword argument
exif_orientationof theMCAMconstructor. If the keyword is provided, a warning will be issued to the user. (#2106)
owl 0.18.89 (2022/07/18)¶
New features¶
Add more metadata about the underlying hardware array in the MCAM dataset. This new information includes the hardware colloquial name
'falcon','eagle', or'kestrel48'as well as the number of cameras in the array. (#2082)
Bug fixes¶
Ensure that images of wells that are exported are done so in the correct orientation when they are acquire with EXIF orientations 5, 6, 7, or 8. Previously, those acquired with EXIF orientation 5, 6, and 7 would be mislabeled. (#2074)
Fix GUI panel to acqurie XYZ and well plate stacks. These panels were broken since version 0.18.85. (#2084)
Ensure that users can provide a custom buffer in the methods
MCAM.acquire_full_field_of_view. (#2084)
owl 0.18.88 (2022/07/16)¶
New features¶
Provide buttons to export as TIF and PNG from the GUI. (#2076)
Bug fixes¶
Ensure that the EXIF orientation mentioned in the GUI matches the exif orientation of the exported TIF images. Previously EXIF orientations
5and7were mislabled. Old datasets loaded with the coordinate'exif_orientation'5will be changed to have a value of7. Old datasets loaded with the coordinate'exif_orientation'7will be changed to have a value of5. There should be no effect on the displayed images in the MCAM viewer GUI. (#2077)
owl 0.18.87 (2022/07/15)¶
Improvements¶
System bringup. (#2072)
owl 0.18.86 (2022/07/14)¶
Flip the axis of z stage 84466.
owl 0.18.85 (2022/07/13)¶
Fix broken GUI.
owl 0.18.84 (2022/07/12)¶
Bug fixes¶
Fix application of advanced settings in the GUI. Bug introduced in 0.18.83. (#2052)
owl 0.18.83 (2022/07/11)¶
New features¶
Provide users with an interface to export stacks of images from the GUI. (#1997)
Improvements¶
Added functionality to allow well extraction of a well subset. (#2030)
Added functionality to save metadata with extracted well data during tracking well extraction. (#2043)
Bug fixes¶
Correct single object tracking when working on cropped and/or binned datasets. (#1800)
owl 0.18.82 (2022/07/08)¶
Improvements¶
GUI: Enable generation of videos with a very large number of frames (>1000). (#2005)
Speed up color corrections for rgb datasets in
owl.calibration.color_correction.get_corrected_dataset()andowl.calibration.color_correction.get_corrected_dataset_stack(). (#2025)Update system information in the registry (#2026)
Remove redundant information about the LED state stored in video datasets acquired before version 0.18.66. (#2029)
Bug fixes¶
Ensure zebrafish assays can be acquired even if no stimulus is specified. (#2023)
owl 0.18.81 (2022/06/29)¶
Bug fixes¶
Fix flashing the LEDs in the stimulus pane and the long zebrafish assay. (#2014)
owl 0.18.80 (2022/06/29)¶
Improvements¶
Allow users to apply circular masks during composite well plate video generation. (#1918)
Bug fixes¶
Enable generation of composite videos of tracked well plates without a progress bar. (#1918)
owl 0.18.79 (2022/06/29)¶
New features¶
Allow users to save and load their stimuli in the zebrafish assay panel. (#1914)
Add function to overlay a Ramona Optics logo to a video. (#2000)
owl 0.18.78 (2022/06/27)¶
Improvements¶
Well Extractor Panel in MCAM Viewer now infers rows/columns from loaded dataset (#1996)
System bringup. (#1999)
owl 0.18.77 (2022/06/18)¶
Improvements¶
Small touchups for zebrafish tracking. (#1991)
System bringup. (#1992)
owl 0.18.76 (2022/06/16)¶
Improvements¶
MCAM Viewer now capable of exporting well plate datasets as BMP (#1980)
Improve accuracy of zebrafish tracking models. (#1988)
owl 0.18.75 (2022/06/13)¶
Improvements¶
Add
set_brightnessfunction to Fluorescence class. (#1956)Enable co-installation of the
owl-basepackage with older cuda installations. (#1982)
Bug fixes¶
Improve GUI compatibility with different versions of Qt. (#1983)
Ensure video generation can occur when ffmpeg is compiled with different versions. (#1984)
owl 0.18.74 (2022/06/13)¶
No significant changes.
owl 0.18.73 (2022/06/13)¶
No significant changes.
owl 0.18.72 (2022/06/13)¶
Improvements¶
Allow users to specify a starting second seconds greater than 60 in zebrafish assays. The start time will be the sum of the start minute and start seconds. (#1971)
System bringup: adjust stage properties. (#1972)
owl 0.18.71 (2022/06/11)¶
New features¶
GUI: Zebrafish assay allow users to specify a delay before which starting their experiments. (#1965)
Improvements¶
Allow creating full resolution composite images from unstitched images such as those created by xy scans within
mcam_viewer. (#1867)Leave the IR lights during a flash for the zebrafish assays. (#1963)
GUI: Allow up to 11 stimuli in the Zebrafish assays. (#1964)
Bug fixes¶
GUI: Ensure that LEDs is turned off instead of very dim when transmission board is turned down in IR mode. (#1960)
owl (2022/06/11)¶
New features¶
GUI: Zebrafish assay allow users to specify a delay before which starting their experiments. (#1965)
Improvements¶
Allow creating full resolution composite images from unstitched images such as those created by xy scans within
mcam_viewer. (#1867)Leave the IR lights during a flash for the zebrafish assays. (#1963)
GUI: Allow up to 11 stimulis in the Zebrafish assays. (#1964)
Bug fixes¶
GUI: Ensure that LEDs is turned off instead of very dim when transmission board is turned down in IR mode. (#1960)
owl 0.18.70 (2022/06/10)¶
New features¶
Feature preview: GUI: Create assay for 10 minute recording times in the GUI. (#1953)
New system bringup. (#1961)
Improvements¶
Improve precision of timing in the zebrafish assay panel. (#1953)
owl 0.18.69 (2022/06/10)¶
Improvements¶
Allow users to reuse video buffer even after changing the MCAM frame size and binning mode. (#1955)
owl 0.18.68 (2022/06/08)¶
Improvements¶
GUI: Avoid applying color corrections to saturated pixels. (#1913)
GUI: The zebrafish stimulus options are now hidden by default. An option to enable them is available in the Advanced Settings. (#1915)
GUI: Subset Video Panel now provides confirmation to the user when saving saving a NetCDF4 file is completed. (#1945)
Bug fixes¶
Revert automatically taking images when turning off or on the fluorescence controller. (#1943)
Feature Preview¶
A new method,
MCAM.acquire_video_to_fileenables acquiring video directly to disk during streaming. (#1944)
owl 0.18.67 (2022/05/31)¶
Bug fixes¶
Address issues with the generation of videos with high resolution screens from the MCAM Viewer. Videos that were previously generated were not centered or scaled according to the viewing window. (#1931)
Ensure that every frame is captured during video acquisition. Previously, during long acquisition, the number of frames returned might be slightly smaller than the number of frames requested. (#1936)
owl 0.18.66 (2022/05/27)¶
New features¶
Add the ability to monitor temperature on rail illumination modules (#1816)
Added button to Zebrafish Assay panels allowing users to provide their own keypoints file. (#1888)
Add a laser diode driver. (#1920)
Improvements¶
Set transmission illumination to flicker free mode when illuminating with IR light and return to flicker mode when illuminating with visible light. (#1908)
Activate software white balancing by default when opening fluorescence illumination. (#1912)
Bug fixes¶
Apply color color corrections and white balancing to images produced by well extraction. (#1910)
Reduce the resolution of 4k square videos and stitched images to 2160 x 2160 pixels and the resolution of Full HD square videos and stitched images to 1080 x 1080 pixels. This solves an issue that prevents video creation for the previous 3840 x 3840 pixel 4k videos. (#1919)
Resolve ability to open reflection illumination devices. This was broken since version
0.18.63. (#1921)Fix bug causing illumination to persist through File>Close MCAM (#1927)
Documentation¶
Add documentation about the
mcam_data.save_videofunction. (#1923)
owl 0.18.65 (2022/05/19)¶
Improvements¶
Acquire new image when opening and closing fluorescence illumination (#1902)
Bug fixes¶
Ensure that default settings can be restored for MCAM systems that do not include built in lighting illumination. (#1901)
owl 0.18.64 (2022/05/19)¶
Improvements¶
Falcon GUI now acquires a new image when new settings are loaded. (#1892)
Video streaming now disabled when saving and loading settings files. (#1893)
Update default settings for a particular MCAM system. (#1897)
Bug fixes¶
Ensure that sensor settings like resolution and extended exposure are retained after the user reopens the advanced settings menu. (#1896)
owl 0.18.63 (2022/05/17)¶
Improvements¶
System bringup. (#1890)
Bug fixes¶
Solve bug that causes illumination board to incorrectly turn on after turning off fluorescence illumination in some cases. (#1884)
owl 0.18.62 (2022/05/16)¶
Bug fixes¶
Solve bug that causes illumination board to incorrectly turn on after turning off fluorescence illumination in some cases. (#1884)
owl 0.18.61 (2022/05/15)¶
Bug fixes¶
Fixed streaming in high frame rate mode when the users change the resolution of the high speed mode. This bug first appeared in 0.18.60. (#1878)
owl 0.18.60 (2022/05/13)¶
Improvements¶
Fluorescence driver monitors temperature on only one interface device. (#1858)
Avoid LED flash in GUI Opening sequence during initial boot-up and settings recall. (#1871)
Bug fixes¶
Address bug that stopped the user from changing the resolution of the MCAM after it had been opened once in the GUI. This occurred in conjunction with external illumination or the fluorescence illumination devices. (#1873)
owl 0.18.59 (2022/05/13)¶
New features¶
Provide users with the ability to get notified just before video acquisition starts through an event when calling
MCAM.high_speed_video_acquisition. (#1869)
Bug fixes¶
Silence warning about loading experimental data. (#1859)
Ensure that the default value for the color limits in the GUI is set between 0 and 1. This was accidentally set to 0.1 and 1.0 in versions 0.18.56 through 0.18.58. (#1861)
Correct bug introduced in 0.18.55 that causes fluorescence calibration data to be overwritten by transmission calibration data when loaded. (#1865)
owl 0.18.58 (2022/05/10)¶
New features¶
Exposure the
chunksparameters in theowl.mcam_data.loadfunction. This allows users to optimize loading of very large datasets. This is only compatible with datasets saved and loaded as.ncfiles This is only compatible with datasets saved and loaded as.ncfiles. (#1855)
Improvements¶
The fluorescence driver no longer supports dual LED drivers. (#1840)
Slightly decrease the time it takes to apply image corrections to images. (#1847)
Update assembled system information to ensure devices automatically open. (#1856)
Bug fixes¶
Ensure that the correct Illumination drivers are used for each illumination module. This error could occur when an MCAM is equipped with multiple illumination modules. (#1848)
Fix how opening fluorescence devices is attempted. Since 0.18.48, specifying a reflection illumination device could conflict with the fluorescence illumination controller. (#1856)
owl 0.18.57 (2022/05/02)¶
System settings for new build.
owl 0.18.56 (2022/05/01)¶
Improvements¶
Ensure that the
X_LSM_Eclass to control the motion stages is thread safe. (#1815)Resolve a warnings about two previously unregistered systems. (#1834)
Bug fixes¶
Fixed bug that prevented stack stitching with reused masks (default). (#1821)
Enhance compatibility with
tifffile2022.4.26. Previously some datasets would store bogus resolution information in resolution field of the tiff image. This caused certain tif image readers and writers to crash.Ensure that the reported LED power in the fluorescence submodule is self consistent. The fluorescence LED module was mis-reporting the LED power since owl version
0.18.9. (#1824)Fix bug where certain GUI elements were accessible when it shouldn’t have been possible. (#1827)
GUI: Ensure images can be exported from uncalibrated MCAMs. This bug was introduced in
0.18.55. (#1835)
owl 0.18.55 (2022/04/25)¶
New features¶
Add the ability to update the fluorescence controller firmware. (#1784)
Improvements¶
Export images from GUI with with white balance corrections if enabled. (#1786)
Make the fluorescence driver thread safe. (#1787)
Add an option to disable timestamp addition to well plate extraction in
owl.analysis.wellplate.save_well_stack. (#1793)Fix multi-threading errors related to the illumination sub-components. (#1795)
Bug fixes¶
Fix menu item installation on windows systems. (#1788)
GUI: Expand the Subset Video extraction to handle z-stacks, timelapses, and other video-like datasets. (#1790)
Avoid garbled frame acquisition in the GUI or repetition of old data. (#1803)
owl 0.18.54 (2022/04/14)¶
Fixed released process for Python 3.9.
owl 0.18.53 (2022/04/14)¶
Bug fixes¶
Fix bug where side panels were not closing when new dataset was loaded. (#1776)
owl 0.18.52 (2022/04/12)¶
New features¶
Add menu option to allow users to save subset selections as NetCDF4 files (#1749)
Improvements¶
Add Falcon0006 to MCAM registry (#1778)
Bug fixes¶
Allow the
owl.mcam_data.save_videoto re-save datasets that were previous acquired and saved in.ncfiles. (#1771)
owl 0.18.51 (2022/04/11)¶
New features¶
Preview: GUI enabled zebrafish tracking in a 24 well plate. (#1714)
Improvements¶
Add additional constraints to ensure that installations contain self-consistent versions of the OWL software. (#1773)
Bug fixes¶
Ensure the registry reflects the current configuration of MCAM system. (#1769)
owl 0.18.50 (2022/04/11)¶
Improvements¶
Add software limits to a particular stage so that it doesn’t interfere with the illumination hardware (#1764)
Increase compatibility with different versions of imageio installed. (#1765)
Bug fixes¶
Ensure that packages required for video exporting are installed with the owl software package. (#1765)
owl 0.18.49 (2022/04/10)¶
Improvements¶
Expand compatibility with different versions of ffmpeg installed. (#1757)
Bug fixes¶
Avoid error when the user presses cancel in the advanced menu. (#1761)
owl 0.18.48 (2022/04/07)¶
New features¶
For MCAM systems with registered x, y and z stages, the MCAM constructor can take two new parameters:
with_x_stageandwith_y_stageto control if the MCAM is opened with those stages by default. (#1689)
Improvements¶
Provide users with a helpful warning message when we detect the use of an unregistered MCAM. (#1689)
Avoid top level import
matplotlib.pyplotto avoid accidentally setting the default matplotlib backend. (#1743)Allow users to provide a custom configuration file when starting the Falcon GUI from the command line. (#1744)
The GUI will retain the image blending settings between sessions. (#1745)
Retain basic information about the last used MCAM in the GUI settings files. (#1747)
Update stage system registry. (#1748)
Provide users with more feedback about ongoing progress during zebrafish assay. (#1751)
Address potential bugs in passing Python Path objects to the zebrafish tracker. (#1752)
Improve video composite generation speed by avoiding unnecessary memory copies. (#1753)
owl 0.18.47 (2022/04/05)¶
Internal change to GUI settings file format.
owl 0.18.45 (2022/04/05)¶
Improvements¶
Help avoid typos when accessing properties of the motorized stages. (#1731)
Increase the output power of a fluorescence system. (#1734)
Bug fixes¶
GUI: Address issue where exposure limits were being reset when the users pressed the Enter key on the keyboard in the Advanced Settings dialog. (#1729)
Help ensure the python interpreter closes if motorized stage devices (
X_LSM_E) are still open at the time of interpreter shutdown. (#1731)
owl 0.18.44 (2022/04/01)¶
Remove numba as a dependency.
owl 0.8.43 (2022/04/01)¶
New features¶
Provide a new function
sleep_fromthat allows the user to specify a reference point from which to sleep from. (#1722)
Improvements¶
Added functionality to extract single well from single well video. (#1716)
Improved accuracy for tracking for 24 and 48 well plates. (#1725)
Bug fixes¶
Fix bug that caused zebrafish tracking to only be able to be run once (#1726)
owl 0.18.42 (2022/03/30)¶
Improvements¶
Add parameter
reuse_masksto allow user to specify if they would like the same stitching masks to be used for all stitched images inhugin_stitching_stack. (#1717)Add the ability to provide a basic progress bar during zebrafish tracking. (#1718)
Ensure GPU memory is released after model inference (#1718)
Allow users to set longer exposures in the GUI. (#1720)
Bug fixes¶
Match workflow of xyz scanning stack and well plate scanning stack to other assays. (#1701)
Allow well extraction for 384 well plates. (#1713)
owl 0.18.41 (2022/03/24)¶
Improvements¶
Update the zebrafish tracking model for square 96 well plates. (#1712)
owl 0.18.40 (2022/03/24)¶
Improvements¶
Support for a new MCAM unit (board 1300. (#1705, #1706)
Bug fixes¶
Ensure that the
exif_orientationis of integer datatype in the MCAM class dataset. (#1697)
owl 0.18.39 (2022/03/13)¶
Improvements¶
Update the mechanical stage settings. (#1688)
Improve image quality for exported videos from zebrafish analysis. (#1692)
owl 0.18.38 (2022/03/07)¶
Bug fixes¶
Fix well extraction broken since 0.18.34 (#1686)
owl 0.18.37 (2022/03/06)¶
GUI: Ensure orientation of scanned well plates is correct in upright configuration.
owl 0.18.36 (2022/03/06)¶
Bug fixes¶
Fix bug that stopped the scanning GUI to open. (#1684)
owl 0.18.35 (2022/03/06)¶
New features¶
Preliminary support for generation of video files from 54 well plates. (#1682)
Improvements¶
GUI: Provide a friendly error message when the user requests an exposure too large for the requested frame rate. (#1681)
Bug fixes¶
Fix well plate extraction for images taken with EXIF 8 orientation. (#1679)
Fix erroneous timestamps in high speed video acquisition. This was broken since version 0.18.31. (#1680)
GUI: Reduce chances of erroneous images appearing after acquiring high speed videos. (#1681)
owl 0.18.34 (2022/03/05)¶
New features¶
Expand usage of Zebrafish assays to 96 well plates in GUI. (#1677)
Improvements¶
Speed up extraction of well plate image from the GUI. (#1678)
Bug fixes¶
GUI: Ensure well extraction can occur with datasets taken in early 2021. (#1674)
Fix orientation in video well plate extraction. (#1677)
owl 0.18.33 (2022/03/04)¶
New features¶
Provide new assay to collect a stack for 94 and 384 well plates with non continuous field of views. (#1660)
Provide new assay to collect a stack with xy scanning. (#1657)
Bug fixes¶
Fix reopening the Illumination module in the GUI. (#1670)
Fixed bug that caused video creation to fail if there was a space in the output filename (#1672)
owl 0.18.32 (2022/03/04)¶
New features¶
Provide a home command for stages. (#1666)
Improvements¶
Open fluorescence illumination with MCAM opening automatically if available. (#1580)
GUI: Increase responsiveness of GUI when changing illumination parameters. - Increase communicate speed between Illuminate boards and software when changing LED patterns. (#1654)
Ensure exported well plate images are always in the right orientation. (#1663)
Bug fixes¶
Users can now export videos with non-integer frame rates from the video exporting GUI. (#1655)
owl 0.18.31 (2022/02/27)¶
New features¶
Added z-stages for new system (#1653)
Improvements¶
Reduction in the size of the metadata for large video acquisition. This slightly reduces the file size and improves the loading time of the datasets in various applications. (#1645)
owl 0.18.30 (2022/02/25)¶
Bug fixes¶
The GUI Splash screen on Windows now shows the logo. (#1643)
Correct well extraction performance for binned datasets in GUI. (#1647)
owl 0.18.28 (2022/02/23)¶
New features¶
A new function
owl.mcam_data.get_bin_modehelps users obtain the binning mode of MCAM dataset. (#1634)
Bug fixes¶
Ensure the falcon GUI can be opened when IR capabilities of an MCAM are removed. (#1639)
owl 0.18.27 (2022/02/23)¶
Improvements¶
Removed the ability to stitch using hugin’s backend
nonaformcam_stitchand useenblendbackend exclusively. (#1629)
Bug fixes¶
Ensure that the tracking dependencies are not needed to use the baseline GUI. (#1630)
owl 0.18.26 (2022/02/22)¶
New features¶
Provide a new method
owl.color.bayer2grayto convert between raw images and grayscale. (#1627)
Improvements¶
Add ability to stitch stacks with
mcam_stitchusing--stackflag. - Present a progress bar in terminal during stitching withmcam_stitch. (#1616)
Bug fixes¶
Save image stitched by
mcam_stitchunder the original filename when using--save-directoryflag. (#1616)
owl 0.18.25 (2022/02/17)¶
New features¶
Feature preview: Integrated Zebrafish tracking within the GUI. (#1622)
Improvements¶
Improve communication speed with transmission illumination boards (C008). (#1617)
Bug fixes¶
Address bug that would prevent one for saving extremely short videos. (#1620)
owl 0.18.24 (2022/02/13)¶
Improvements¶
Enable exporting larger videos of well plates. (#1607)
owl 0.18.23 (2022/02/07)¶
Add a white flash stimulus in the GUI.
owl 0.18.21 (2022/02/07)¶
New features¶
New GUI for high speed video acquisition. (#1585)
Allow users to specify sensor resolutions of
(2048, 2048)and(1536, 1536)in the GUI. (#1598)
Improvements¶
GUI: The GUI is now able to provide controlled stimuli to imaged sample. (#1590)
Increase the speed of saving videos from the GUI. (#1595)
Bug fixes¶
Fix high speed video acquisition. (#1584)
GUI:Ensure lower exposures are attainable in the GUI. (#1587)
GUI: fixed bug which prevented exporting well plate data taken with infrared illumination as images. (#1596)
owl 0.18.20 (2022/01/31)¶
Improvements¶
Allow stitching in
falcon_guifor the current dataset. (#1361)Improved animation for the splash screen. (#1576)
Features preview¶
Preliminary support for all-analog control of the transmission LED boards. API is subject to change without notice. (#1545)
owl 0.18.19 (2022/01/28)¶
Improvements¶
Ensure a more natural choice for the starting directory in the well extractor (#1574)
owl 0.18.18 (2022/01/28)¶
Improvements¶
Improvements in GUI white balance for Kestrel system. (#1567)
owl 0.18.17 (2022/01/27)¶
Updated GUI with modifications for the Kestrel system.
owl 0.18.16 (2022/01/27)¶
Bug fixes¶
Exported well images are no longer exported as raw data but rather converted from bayer to rgb. (#1559)
Correctly reset view in the stitching and video creation GUIs so that the data fits entirely inside the displayed rectangle. (#1562)
owl 0.18.15 (2022/01/25)¶
New features¶
Preview: Provide a
"ramona"backend for writing data that bypasses the system cache when accessing the SSD. This can be beneficial when writing large datasets to disk. (#1549)
Improvements¶
Add square and vertical resolutions for stitching in the GUI. (#1553)
owl.mcam_data.append_netcdfcan now take an open file handle instead of a filename to speed up writing operations. (#1555)
owl 0.18.14 (2022/01/23)¶
Improvements¶
fluorescence_controller.py now has examples for the temperature monitoring interface (#1457)
Add calibration information for Kestrel-24 (#1544)
Allow users to specify xarray engine when loading MCAM data. (#1548)
owl 0.18.13 (2022/01/23)¶
Bug fixes¶
Fix regression in IPython complete introduced in version 0.17.0. (#1543)
owl 0.18.12 (2022/01/18)¶
Improvements¶
Avoid unnecessarily access to metadata variable
__falcon.dna__during file opening procedure. (#1541)
Bug fixes¶
GUI: Fix the PIP when changing the EXIF orientation live. (#1538)
Allow stacks of 1 to be opened in the GUI. (#1542)
owl 0.18.11 (2022/01/13)¶
New features¶
Add ability do detect and extract wells from a well plate into
falcon_guiandmcam_gui. (#1508)Added new
open_deviceparameter toMultiLidarconstructor.Added new property
lidar_counttoMultiLidarclass.Removed unused public method methods of the
MultiLidarclass.MultiLidarclass can now be imported fromowl.instrumentsinstead ofowl.instruments.lidar. (#1535)
Documentation¶
Updated and improved
MultiLidardocumentation. (#1535)
owl 0.18.10 (2022/01/11)¶
Improvements¶
Automatically adjust the chunk size when acquiring z-stacks for larger chunks improving performance for the end user. (#1531)
owl 0.18.9 (2022/01/10)¶
New features¶
Add ability to directly save stacks of wells from dataset stacks. (#1495)
Allow users to specify which backend to use when saving MCAM Datasets. Functions
owl.mcam_data.saveand methodsowl.instruments.MCAM.saveandowl.instruments.MCAM.save_colorhave a new keyword argument allowing users to specify which engine they wish to use. (#1526)
Improvements¶
Improved the uniformity of the fluorescence illumination. (#1524)
Update logo for exporting videos. (#1525)
Deprecate the usage of the
single_fileparameter inowl.mcam_data.save. (#1526)Removed deprecated
owl.mcam_data.get_global_transformsmethod.Removed deprecated
owl.instruments.MCAM.exposure_secondsproperty. (#1527)
owl 0.18.8 (2022/01/04)¶
Bug fixes¶
Fixed bug that prevented color correction to be removed from the display in the gui. (#1513)
Update stage configuration for Kestrel-24 system.
owl 0.18.6 (2021/12/31)¶
New features¶
Added stages for the Kestrel-24 system. (#1516)
Improvements¶
Removal of the
ftd2xxdependency and associated drivers for the Thorlabs APT motors. (#1489)
owl 0.18.5 (2021/12/29)¶
New features¶
Add function
display_keypointsto display well keypoints on vispy image visuals. (#1505)
Improvements¶
Ship the changelog with the source code. The changelog is now contained within the python package directory. (#1510)
owl 0.18.4 (2021/12/27)¶
New features¶
Updated suggested firmware version from 1.20.10 to 1.20.11 for Illumination LED boards (#1473)
GUI: The Kestrel12 and Kestrel24 can now be dynamically changed between high resolution and low resolution. (#1491)
Add function
detect_circular_wellsto find wells of 96 well plates imaged with the 19mm field of view system. (#1492)
Improvements¶
falcon_guican apply calibration data specific for IR illumination. (#1346)Allow calibration for IR 850nm lighting sources. (#1453)
Allow z stack of subsets to be acquired in gui. User must enter subset mode in main gui and then acquire z stack in assay panel. (#1494)
Bumped minimum requirement versions for dependencies to support Kestrel24 boards. (#1500)
Deprecate use of
MCAM.selection_center_12from API. (#1502)
Bug fixes¶
Correctly update the pip window when switching between grayscale, rgb, and raw viewing modes. (#1499)
owl 0.18.3 (2021/12/14)¶
New features¶
New preview of zebrafish tracking in well plates. (#1288)
New example files show how to acquire data and output videos of tracked zebrafish. (#1288)
Bug fixes¶
Avoid incompatibility with
distributedversion 2021.12.01. (#1484)
owl 0.18.2 (2021/12/12)¶
New features¶
New light theme enabled. (#1477)
Improvements¶
Display raw image data for monochrome sensors. (#1478)
Bug fixes¶
Address crashes with dask distributed. (#1476)
Address issues in the GUI where zooming into subsets of data was not behaving as expected. (#1479)
owl 0.18.1 (2021/12/11)¶
New features¶
Added the ability to read fluorescence illumination device serial numbers (#1472)
Updated suggested firmware version from 1.20.10 to 1.20.11 for Illumination LED boards (#1473)
owl 0.18.0 (2021/12/07)¶
New features¶
Add ability to export wells from gui with well plate calibration file. (#1402)
Support specifying
Noneto theMCAM.illumination_modewhich removes the default calibration from the dataset. (#1448)Breaking: The
MCAM.dataandMCAM.datasetcan no longer be accessed after the MCAM is closed. This change was introduced to reduce the possibility of memory leaks and to ensure consistency in the dataset itself. (#1461)
Improvements¶
Allow wells to be extracted from stacked datasets such as videos and z-stacks. (#1409)
Allow pixel corrections to have a color ratio provided. This moves away from illuminating with different channels of the illumination board to just increasing values of LEDs with the same color ratio. (#1455)
Remove alpha channel from exported stitched images using
quick stitchto reduce file size by 25%. (#1456)
Bug fixes¶
Fix the usage of the GUI with no illumination connected. (#1448)
Corrects bug introduced in version 0.17.4 that incorrectly extracts calibration data from the MCAM. Calibration data created during this version may be corrupt and should be remade. (#1455)
Fix taking z-stacks in GUI without any LED board connected. (#1460)
Enable the removal of the last illumination device. (#1461)
Add locations of pixel start and end indices in calibration data to allow created calibration data to be read correctly. (#1467)
GUI: Fix bug where timelapses with periods smaller than 1 minute could not be opened by the MCAM Viewer. (#1468)
owl 0.17.4 (2021/12/01)¶
New features¶
Added temperature sensing
Added automatic detection of fluorescence units
Setting the LED power automatically enables the most recently selected LED (#1323)
Preliminary support for the Kestrel-12 MCAM. (#1436)
Improvements¶
The
Fluorescencecontroller now automatically turns on the LEDs once the power is set withled_electrical_powerorled_power_percentage. (#1272)
Bug fixes¶
Correctly return fluorescence controller serial number (#1323)
Fixed bug that caused filter that shows located wells to be removed when stitching is toggled on and off. (#1414)
Add correct pixel correction metadata to extracted well centric datasets. (#1427)
owl 0.17.3 (2021/11/23)¶
GUI: Fix saving images in the GUI that was broken between versions 0.17.0-0.17.2.
owl 0.17.2 (2021/11/22)¶
GUI: Display more frame numbers on the sidebar in the MCAM GUI.
owl 0.17.1 (2021/11/19)¶
Bug fixes¶
Fixed video acquisition functions from the MCAM class (bug introduced in 0.17.0).
owl 0.17.0 (2021/11/19)¶
Improvements¶
Allow exporting of datasets divided by well rather than camera.
Export images as tif files as default in order to maintain exif orientation, pixel width and description if present in dataset. (#994)
Bug fixes¶
Fixed bug that caused
mcam_viewerto sometimes fail when moving to next frame with subset mode enabled. (#723)Removed erroneously added
__calibration_owl_version__and__calibration.transmission.owl_version__from datasets after update. (#1408)
Deprecations¶
Deprecation:
mcam_data.newhas been deprecated. Users are encouraged to usemcam_data.new_dataset. (#1426)
Breaking changes¶
Removal of support for the
make_squarekeyword argument. (#1415)Datasets now have the image data named
'images'instead of'mcam_data'. The associated dimensions are now'image_y'and'image_x'instead of'camera_y'and'camera_x'respectively. (#1416)Removed options
imagename_format,image_names,output_mode,dtype,make_square,preserve_rangefrommcam_data.load. (#1418)Renamed the
owl.stitcher_reduxsubmodule toowl.stitch. (#1420)
owl 0.16.29 (2021/11/15)¶
New features¶
The
MCAMclass now contains a property,sensor_chromathat describes the chromaticity of the sensor. (#1397)
Improvements¶
Avoid stage constructor crashing if the stage isn’t in the database. (#1394)
Well plate extractor subroutines are now found under
owl.analysis.wellplate_trackerinstead ofowl.analysis.tracker. (#1398)Breaking: Certain datasets from 2018 and early 2019 will no longer be able to be opened with this release of OWL. Please contact Ramona Optics if you experience errors opening your datasets.
owl.mcam_datawill avoid guess the conditions under which the datasets were acquired. (#1404)
Bug fixes¶
Ensure that the exported datasets retain the full metadata. (#1401)
Add back a dummy owl-owl_gui package to help mamba updated to the newest version of owl. (#1403)
owl 0.16.28 (2021/11/11)¶
Bug fixes¶
Ensure high frame rate mode operates in the highest frame rate mode possible. A bug was introduced in version 0.16.27 where the system was operating at half speed.
owl 0.16.27 (2021/11/10)¶
New features¶
Remove the original OWL GUI package. (#1372)
The GUI will now automatically attempt to connect to the MCAM upon startup. (#1381)
Expose various sensor timing parameter limits to the MCAM class including the minimum and maximum frame rate setpoint. (#1384)
Improvements¶
Provide users with an option to calibrate the MCAM in transmission for IR 850 nm illumination. (#1335)
Bug fixes¶
Target correct version for calibration parameter update needed for pixel correction improvements introduced in version 0.16.24. (#1378)
Correctly handle pixel corrections for binned data in the gui. (#1379)
Correct color calibration in MCAM Viewer with many older datasets. (#1385)
Enable Board 9 to fetch calibration from online registry. (#1387)
owl 0.16.26 (2021/11/08)¶
Ensure MCAM Viewer can open certain legacy datasets.
owl 0.16.25 (2021/11/08)¶
Bug fixes¶
Avoid saving extra data when a slice of data is requested to be saved. (#1367)
Ensure that subprocesses do not attempt to use stdout if it is undefined. (#1368)
Ensure that datasets creates before 0.16.22 record the necessary settings for photometric calibrations. (#1370)
owl 0.16.24 (2021/11/08)¶
Bug fixes¶
Correctly apply color corrections to square images in gui. (#1351)
New features¶
Add function
get_crop_binned_pixel_polynomialto create polynomials to get the correctly shifted and scaled color corrections for the given dataset. (#1351)
owl 0.16.23 (2021/11/03)¶
Bug fixes¶
High frame rate videos now report the correct frame rate information. (#1355)
Ensure that the dataset property correctly reflects changes in the illumination mode. This bug was introduced in version 0.16.22. (#1357)
owl 0.16.22 (2021/11/02)¶
New features¶
Feature preview: Ability to take videos at precisely controlled frame rates. (#1353). Note that the API of this feature is set to change without notice.
owl 0.16.21 (2021/11/02)¶
Bug fixes¶
Fixed a bug that caused acquiring video from a subset of sensors to fail. (#1350)
owl 0.16.20 (2021/10/30)¶
Improvements¶
Ensure compatibility with filelock 3.3.2. (#1347)
Bug fixes¶
Ensure that the MCAM can be closed when the python kernel is shutting down. (#1347)
owl 0.16.19 (2021/10/28)¶
Bug fixes¶
Fixed bug that caused stitching calibration to not be saved for transmission illumination. (#1340)
Fixed bug that only showed images with reflection color correction regardless of the used illumination mode in the calibration gui. (#1340)
Fixed a bug that prevented images in downsampled mode from being blending in some situations. (#1342)
Save calibrated pixel width under both
reflection_pixel_widthandtransmission_pixel_width. (#1343)
owl 0.16.17 (2021/10/26)¶
Improvements¶
Limit the scaling of the gui camera to prevent zooming too far out or too far in. (#1338)
Bug fixes¶
Solve issue where partially calibrated systems could have calibration data from the incorrect illumination mode applied. (#1333)
Fixed bug that removed support for setting the
ignore_calibrationparameter inhugin_stitching. (#1334)
owl 0.16.16 (2021/10/21)¶
New features¶
Falcon GUI now saves the illumination mode activated in gui to the dataset metadata under parameter
illumination_mode. (#1321)Provide a method to compute the average frame rate and time difference between frames in a dataset. (#1325)
Improvements¶
Include the illumination mode used to capture the image in the data’s metadata for data that was acquired with standard illumination modalities. (#1305)
MCAM datasets now include calibration data that is split by illumination modes. Current available illumination modes are reflection and transmission in the rgb spectrum. (#1309)
Improve error message in GUI and Python API when no Illumination board is detected. (#1318)
Add information about the frame rate in the MCAM Viewer. (#1328)
Maintain gui view when doing quick stitching of video creation in gui. (#1331)
Bug fixes¶
Ensure compatibility with qdma 0.8.17 and above. (#1315)
Solved bug introduced in 0.16.15 that prevents the frame stitching in
mcam_viewer. (#1320)
owl 0.16.15 (2021/10/12)¶
Improvements¶
Avoid warning due to missing reflection LED board in transmission illumination calibration. (#1311)
Add factory calibration information for serial number 9. (#1313)
Bug fixes¶
Fix the toggle button in the calibration GUI that broke in 0.16.14.
Ensure the toggle button is functional in the calibration GUI for transmission calibration. (#1316)
owl 0.16.14 (2021/10/11)¶
New features¶
Enable users to select more image shape during acquisition. (#1307)
Improvements¶
Ensure that whenever the MCAM opens, it starts in high resolution mode. (#1307)
Ensure that the entirety of each micro camera image is displayed in the MCAM Viewer during playback. (#1308)
Bug fixes¶
Prevent the gui from becoming unresponsive during video acquisitions. (#1302)
Fixed layering to make selected images appear correct when streaming a subset. (#1310)
Documentation¶
Improved documentation for the stage subsystem in the MCAM. (#1303)
owl 0.16.13 (2021/10/06)¶
Bug fixes¶
Remove red box from exported video frames. (#1300)
Ensure calibration data does not contain string arrays that prevent the json files from being loaded. (#1301)
owl 0.16.12 (2021/10/04)¶
New features¶
Provide a context manager for the motion stages. - Provide a pythonic function for making the stages vibrate.
move_sin(#1281)Stitching calibration can now be done with transmission illumination. (#1285)
Allow users to select pixels centered on the sensor. (#1295)
Improvements¶
Update minimum version of qdma to avoid known bugs. (#1293)
Maintain the bin mode when selecting the center pixels. (#1296)
owl 0.16.11 (2021/09/30)¶
New features¶
Experimental support for control for the fluorescence module in the GUI. (#1216)
Introduced function to remove calibration data from datasets. (#1282)
Improvements¶
Ensure that the IR LEDs are labelled as having IR chroma for the (transmission) C008 boards. (#1280)
Correctly handle pixel width calibration metadata during update pipeline. (#1282)
Bug fixes¶
Update stitching calibration metadata through calibration update pipeline. Previously stitching homographies would be updated but if this updated data was re-saved and then reloaded the reloaded dataset would be “corrected” again causing misalignment during stitching. This would happen to any dataset originally acquired before owl version
0.16.0. (#1282)
owl 0.16.10 (2021/09/30)¶
Bug fixes¶
Resolve bug that caused
mcam_viewergui to fail when closing the video creator. (#1278)
owl 0.16.9 (2021/09/30)¶
New features¶
Add ability to create videos from stack in
mcam_viewer. (#1206)Add an option to create a stitched image through the Vispy render called Quick Stitch. This method is much faster but might not produce as seamless results. (#1254)
Enable the well extractor in the MCAM viewer. (#1276)
Improvements¶
The
Fluorescencecontroller now automatically turns on the LEDs once the power is set withled_electrical_powerorled_power_percentage. (#1272)
Bug fixes¶
Avoid divide by zero error when attempting to blend poorly aligned images. (#1257)
Correct check boxes for stitched image display ing GUI to always be accurate to the current state. (#1257)
owl 0.16.8 (2021/09/25)¶
New features¶
Add switch to blend images in the gui. this reduces seams but may introduce artifacts in some cases. (#1249)
A context manager is now available for the
MCAMclass. (#1253)
Improvements¶
Connected stages are listed in the
mcam_listcommand. (#1236)Remove check that automatically adds a time stamp to the output stitched image filename when it would overwrite an existing file. Instead add a new parameter
add_timestampthat defaults to True to control the addition of timestamps to the filename. (#1237)Add ability to specify output shape and view of stitched image when using
render_images(#1255)Stitch and unstitch images more rapidly live in the MCAM Viewer and Falcon GUI. (#1258)
Bug fixes¶
Fix bug that caused well masks to distort when using 3120 x 4096 images. (#1238)
Fixed bug that cause z stage to move to bottom position instead of top during transmission calibration. (#1241)
owl 0.16.7 (2021/09/12)¶
Bug fixes¶
Fix stitching sidebar that was broken in 0.16.4. (#1233)
owl 0.16.6 (2021/09/09)¶
Bug fixes¶
Fix bug where GUI would crash if well extractor was open without extracting any wells. (#1223)
Solved bug introduced in 0.16.4 that prevents
mcam_calibratefrom completing. (#1229)
owl 0.16.5 (2021/09/08)¶
Improvements¶
Video save location text is now selectable. (#1221)
Bug fixes¶
Ensure each video acquisition gets saved to a new file. (#1221)
owl 0.16.4 (2021/09/08)¶
Bug fixes¶
Ensure that the exploded view in the 4:3 acquisition mode shows the images with the correct border. (#1220)
owl 0.16.3 (2021/09/04)¶
Improvements¶
Speed up video memory allocation when a user configures their system to take advantage of HugePages. (#1214)
Compatibility with qdma version
0.8.9.
owl 0.16.2 (2021/09/03)¶
Improvements¶
Silence the output of
create_video()by default. (#1199)Minimize the chance of extra images being acquired during high frame rate acquisitions in the GUI. (#1209)
Update the
--x_overlapdefault value for the new 19mm FOV standard withinmcam_calibrate. (#1210)
Bug fixes¶
Solved bug introduced in owl version 0.15.22 that prevented calibration results from being visible in pop up window. (#652)
owl 0.16.1 (2021/08/31)¶
New features¶
Allow users to select subsets of cameras when acquiring z-stacks. (#1153)
Improvements¶
Reduce time required to prepare the video buffer for video acquisition. (#1197)
Improve the speed of loading stack dataset into
mcam_viewer. (#1200)
Bug fixes¶
Resolve bug that caused
create_video()to fail whenadd_scalebar=Falseandadd_logo=True. (#1183)GUI: Fix GUI erroneously setting x and y stages to 50 mm of travel range. (#1201)
owl 0.16.0 (2021/08/26)¶
New features¶
Provide functions to easily change between popular pixel selections in the imaging sensor (#1189)
GUI: Enable users to reduce the size of the acquired images by capture the center region of each micro camera. (#1192)
Improvements¶
The pixel coordinates included in the metadata now reflect the location within the sensor where the data was acquired from. Before this update, the standard image of shape
3120 x 4096used to start at pixel location(0, 0). With this update, the location of the same pixel is reported as(8, 64).Previously saved data data that is loaded with the MCAM Software will reflect the changes mentioned above. Both the pixel coordinates and the stitching parameters will be updated to reflect the changes mentioned above. (#967)
Ensure more consistent use of fonts in the GUI. (#1168)
Bug fixes¶
Fixed drag and drop capabilities on Windows. (#1190)
Fix bug that prevented the stitching window from opening in the MCAM viewer in version 0.15.25. (#1191)
owl 0.15.25 (2021/08/23)¶
Bug fixes¶
Ensure compatibility with pooch version 1.5.0. (#1185)
owl 0.15.24 (2021/08/22)¶
Bug fixes¶
Fix
mcam_data.saveandmcam_data.exportfunctions. They failed to save the dataset in version 0.15.23. (#1184)
owl 0.15.23 (2021/08/20)¶
New features¶
MCAM data file will update its version once it is updated enable it to be saved again. Version history is now kept in a new separate variable called
__owl_previous_version__in the dataset. (#1177)
Improvements¶
Ensure that all loaded datasets have the variables
start_pixel_y,start_pixel_x,end_pixel_y, andend_pixel_x. Best efforts are made to correctly guess the value for standard image shapes otherwise, a valid value is inserted. (#1169)Update to OWL repository to support qdma version 0.8 in order to to support newer firmware versions. (#1175)
Bug fixes¶
Ensure minimum version requirements for
pyilluminateare specified. (#1174)Ensure minimum version requirements for
tifffileare specified. (#1179 and #1180)
owl 0.15.22 (2021/08/17)¶
New features¶
Add functions for saving images from a subset of sensors in the GUI (#1017)
Integrate a driver for fluorescence illumination control (#1064)
Improvements¶
Depreciate parameters
z_stageandilluminatein functionacquire_stack. Thez_stageandilluminateinstances are now taken from the providedMCAMinstance. (#1008)Add a progress bar to the Stitching GUI. (#1089)
GUI: Reorganize layout. - Add descriptive images to LED settings (#1099) - Video and stack acquisition windows are now located in the right sidebar enabling users to modify all acquisition parameters before starting the lengthy acquisitions. (#1130) - Display loading cursor when switching between high and low resolution images (#1135) - Prompt user to select a file location when saving an image, if one has not been selected previously. (#1137) - Update help information with support phone numbers (#1138) - Flash the screen when saving a screenshot. Optionally display a popup when a screenshot is saved (#1140) - Add a warning label when streaming in low-resolution mode (#1102) - Ensure that read only text describing various imaging parameters is selectable. (#1108)
GUI: Improved default settings and usability changes: - Allow the user to double click when streaming from a subset to change the center of the region of interest. - Decrease the default brightness value in the GUI. This does not affect existing users of the MCAM who have already customized their brightness settings. (#1113) - Lower default analog gain maximum limit to 2.0 (#1116) - Ensure that the up button makes the z-stage move upward (against gravity) in the GUI.(#1122) - Infrared (IR) illumination will now only utilize the 850nm LEDs. (#1133)
API: Remove the ability of users to select different pixel selections on a per-sensor level. (#1144)
Speed up loading data in the python API and in the GUI. (#1123)
Avoid deprecation warning in use of TiffFile. (#1158)
Provide warnings to users using the function
owl.mcam_data.savewith the keyword argumentdirectory. That argument has meantfilenamefor many versions now. (#1166)
Bug fixes¶
GUI: Ensure the subset selection for streaming is always rectangular (#1120)
GUI: Ensure color corrections are correctly applied as soon as the MCAM opens. (#1133)
Fixed bug that prevents stitching through stitching GUI. (#1139)
GUI: Ensure all the images being streamed in a subset are updated correctly when streaming is switched or turned off. (#1147)
GUI: Ensure “negative zero” never appears in the stage text box. (#1149)
GUI: Hide loading bar and ensure GUI stays enabled after failing to load a dataset. (#1150)
Deprecations¶
Using output_mode with
mcam_data.loadis deprecated and will be removed in a later version. If you rely on this feature, contact Ramona Optics atinfo@ramonaoptics.comto discuss your use-case. (#1123)
owl 0.15.21 (2021/07/24)¶
New features¶
Add the ability to stitch the currently targeted frame in a stack from within
mcam_viewer. (#1084)
Improvements¶
Check to make sure there is room in disk before beginning any acquisition including z stacks and videos. (#965)
Allow downsampling of the masks generated through
owl.analysis.wellplate.create_wellplate_roi(). (#1046)
Bug fixes¶
Append
.tifsuffix to the filename of image stitched through the stitching GUI if no valid TIFF suffix is provided. (#1084)GUI: Ensure GUI can open stages connected to the same serial port (#1098)
owl 0.15.20 (2021/07/19)¶
Improvements¶
Add support for new Z-stage. (#1085)
owl 0.15.19 (2021/07/19)¶
Improvements¶
Reset the speed and acceleration of managed stages whenever they are reopened. This can be disabled by providing the parameter
set_default_parameters=Falseto theX_LSM_Econstructor. (#1047)
Bug fixes¶
GUI: Remove discoloration around edges of image when streaming from a subset of cameras (#1075)
Corrected
owl.analysis.z_stack_functions.calculate_position_errorto only return position error and to calculate it correctly. (#1082)
owl 0.15.18 (2021/07/10)¶
Improvements¶
Add information about machine’s hostname in the metadata. (#889)
Enable users to call
MCAM.saveafter the connection to the physicalMCAMhas been closed. (#1072)
Bug fixes¶
Ensure x and y pixel information metadata is stored correctly for binned videos.
Ensure that one can display video data correctly for previously acquired binned videos. (#1062)
Documentation¶
Add example for timelapse acquisitions. (#1049)
owl 0.15.17 (2021/07/09)¶
Improvements¶
Removal of
maximum_speed,maximum_position, andenable_ledparameters during X_LSM_E stage initialization.New
led_enableproperty for turning X_LSM_E stage LED on and off.New
busyproperty for the X_LSM_E class returningTrueif the stage is moving. (#1056)GUI: Increase step size precision of the stages to allow 1 µm movements. (#1061)
Bug fixes¶
Ensure stages opened through the
StageSystemclass do not home when theensure_homedargument is False. (#1056)Fixed bug that did not allow the MCAM to be opened if it did not have a factory calibration file available. (#1067)
Get current calibration data from the mcam during pixel width calibration to prevent pixel width calibration from deleting previous calibration data. (#1068)
owl 0.15.16 (2021/07/04)¶
New features¶
Enable setting exif orientation from the GUI (#1039)
Bug fixes¶
Ensure view range is set correctly in GUI and quickview for images with any exif orientation
Ensure view is reset correctly in GUI for non-square images (#1039)
Remove the
MCAM.update_firmwarefunction. (#1059)Ensure compatibility with modern versions of Vispy up to 0.7.0. (#1063)
owl 0.15.15 (2021/06/24)¶
Improvements¶
Provide better instructions on how to request missing factory calibration settings for each MCAM. (#973)
Update
z_stack_analysis.pyexample. (#996)Improve pattern drawing speed for perimeter LEDs. (#1024)
Add backend ability to turn off coordinated arrival times for stage system (#1031)
Add the Eagle stages to the stage database providing better defaults. (#1036)
Bug fixes¶
Correct resolution for Full HD stitched imaged exporting. (#1011)
Ensure
BADDATAerrors are not generated when moving a single stage within aStageSystem. (#1033)GUI: Ensure x and y stage widgets visibility is set correctly (#1041)
GUI: Ensure contrast limit levels are properly shown in the settings bar when an image is first opened in the viewer. (#1042)
Correctly load datasets that were acquired with the incorrect
15.9.0version tag. (#1044)Ensure that videos can be exported with the Ramona Optics logo (this is the default setting). (#1050)
Ensure that users can download the calibration files the first time they connect to any MCAM. (#1052)
owl 0.15.14 (2021/06/10)¶
Improvements¶
Decrease delay time when opening an X_LSM_E stage (#1030)
Add backend ability to turn off coordinating arrival times when moving the stage system (#1031)
Add the Eagle stages to the stage database (#1036)
Bug fixes¶
Ensure BADDATA errors are not generated when moving a single stage within a StageSystem (#1033)
owl 0.15.13 (2021/06/09)¶
Improvements¶
Home stages opened as a system simultaneously
Add an “acceleration” property to the X_LSM_E class
Speed up the process for opening a system of stages
owl 0.15.12 (2021/06/07)¶
New features¶
GUI: Add a mode for controlling a 3 stage system (#1002)
Improvements¶
Add functions for easily managing systems of stages that may share serial ports or Zaber devices (#1001)
Bug fixes¶
Enable users of the MCAM to change the
exif_orientationin the saved dataset. Previously, changing theexif_propertyof the instrument did not propagate the change to the acquired datasets. (#1019)
owl 0.15.11 (2021/06/06)¶
New features¶
Integrate a multi-lidar driver for large system scanning. (#1009)
Allow user to specify whether a given X_LSM_E object uses a controller type of “axis” or “lockstep”, and to specify the controller id.
Allow multiple stages using different axes or locksteps to be opened on the same Zaber device.
Allow the user to set a “maximum_speed” for each X_LSM_E object.
Improvements¶
Add database of Zaber stages.
Add function for opening a Zaber stage on a given axis (‘z’, ‘y’, or ‘x’) (#983)
Add functions for easily managing systems of stages that may share serial ports or Zaber devices.
Add a class for simultaneously controlling a system of stages.
Add property to the X_LSM_E class for getting and setting the approach (homing) speed (#1001)
Bug fixes¶
GUI: Ensure the PIP and view sizes correctly for any camera configuration (#1016)
owl 0.15.10 (2021/06/02)¶
New features¶
Add an option to calibrate
pixel_widththroughmcam_calibrate. (#999)
Improvements¶
Default stitched image filename now mimics the given dataset’s name with
_stitchedappended. (#984)Add calibration information for Falcon Board 8. (#989)
Removed outdated example calibration scripts. (#995)
quickviewnow attempts to readstitch_global_homographies,exif_orientation, andbayer_patternfrom the given dataset’s metadata if they are not provided as parameters. This feature can be disabled by passingignore_metadata=Trueas a parameter. (#998)Add flag to set estimated overlap of images in the x dimension. (#1006)
Bug fixes¶
Ensure video buffer is reallocated if the image shape changes (due to binning or pixel selection). (#991)
owl 0.15.9 (2021/05/20)¶
New features¶
Incorporate functions for adding y-stage and x-stage information to the MCAM metadata. (#961)
Add function for finding the composite corner coordinates of an inscribed rectangle within a full stitched image. (#979)
Improvements¶
GUI: Improve label formatting on the settings bar.
GUI: Ensure arrow keys can be consistently used to control sliders on the settings bar. (#978)
GUI: Only display inscribed rectangle within a full image. (#988)
Bug fixes¶
GUI: Ensure exposure and gamma line edits accept user input to desired level of precision. (#978)
Fixed a bug introduced in 0.15.8 that prevented stitching calibration from performing correctly. (#982)
owl 0.15.8 (2021/05/14)¶
New features¶
GUI: Export images as uncompressed BMPs to ensure no loss in image quality in the GUI. (#909)
Improvements¶
Locating best images in a z stack through
find_best_z_position_arrayandfind_best_z_positionno longer requires loading in the entire z stack into memory. (#500)Removed hardcoded font filename, improving robustness and allowing the user more control over what font is used in
owl.io.video.create_video. (#918)Windows: Ensure that application executables files have the appropriate icon. (#953)
Automatically format directory name that holds a generated calibration report. (#969)
Bug fixes¶
Corrected bug introduced in version 0.15.4 that caused stitched images to be misaligned after the exif orientation was applied. (#955)
Correctly display white light image during illumination board calibration. (#969)
owl 0.15.7 (2021/05/02)¶
New features¶
Add ability to generate output file to give a record of the calibration process. (#813)
Add
bbox_indicesparameter tohugin_stitchingto define a subsection of the full composite to stitch. (#888)GUI: Add option to play video from a subset of cameras in the Image Viewer (#904)
Provide users with an option to specify the output directory when using the
mcam_stitchcommand. (#935)
Improvements¶
Add firmware release 20210414 to the list of supported firmware versions. (#922)
GUI: The viewer screen and loading bar will now be visible when while loading a NC file directly from the directory into the viewer. (#927)
GUI: Zooming in and out now centers around the mouse location, rather than the center of the screen (#938)
GUI: Users can now take videos with more than 200 frames for subsets of cameras. (#949)
Keep GUI layout fixed when the loading bar is active (#946).
Bug fixes¶
GUI: Ensure GUI only allocates enough buffer for the size of video actually being captured. (#879)
Normalize the white light vector created by
define_white_lightinowl.calibration.color_corrections.pyto return a vector with unit norm. (#917)Fixed fatal bug that didn’t allow video datasets collected with owl version 0.14.0 and earlier from being loaded with updated metadata. (#923)
Correctly center composite when generating stitched images with
hugin_stitching. Previous versions would create stitched images with the composites less than about 100 pixels off center. (#926)GUI: Disable buttons while loading a file or opening the MCAM, to prevent erroneous signals (#927)
Fix bug sometime generating errors in “find_clean_number” (#931)
GUI: Fix bug where the “Reset View” button cut off the top and bottom of tall images (#936)
Fix
mcam_calibrationreturning results that were erroneously rotated by 90 degrees. (#937)GUI: Ensure default settings in Advanced Settings window are always set correctly (#948).
owl 0.15.6 (2021/04/19)¶
New features¶
GUI: Add a button to return view to original zoom level. (#897)
GUI: Add a “Clear Screen” button in the acquisition GUI that will set the images to black. (#910)
Improvements¶
Add ability to overlay frame specific labels to videos created with
create_video. (#862)Fully update calibration data when designated during loading. (#875)
Add ability to place the Ramona Optics logo on encoded videos. (#900)
Added ability to change the primary seam generator used when blending images with
enblendduringhugin_stitching. (#908)Added ability to extract the camera index and pixel location within a camera array from a given point in a vispy view. (#911)
Bug fixes¶
Solved fatal bug that occurred when trying to create a video without a scale bar. (#862)
Fixed bug that prevented selecting a subsection of a dataset that was saved without camera index
(0, 0)when stitching withhugin_stitching. (#884)Fixed bug that cause images that are rotated due to EXIF orientation tags to have their stitch composite incorrectly calculated. (#899)
GUI: Fix bug that was causing the GUI to crash or freeze when using the calibration graphs. (#901)
Solved fatal bug that occurs with with
template_pto_filenameset and blender=’none’ when callinghugin_stitching. (#914)Fix bugs in the
find_rowandfind_nearestIlluminate functions that caused them to throw errors. (#916)
Documentation¶
Fixed documentation generation for the
mcam_calibratecommand line program. (#907)
Deprecations¶
Removal of
hardware_triggerkeyword argument to theowl.instruments.MCAMconstructor. If hardware trigger functionality is desired, utilize the theuse_hardware_triggerproperty of theMCAMobject instead. (#905)
owl 0.15.5 (2021/04/05)¶
New features¶
GUI: Allow user to specify serial numbers for subcomponents. (#805)
A new function,
owl.stitcher_redux.hugin_stitching_stack, can be used to simplify stitching of stacks of MCAM datasets. (#823)Provide a function
mcam_data.get_color_datasetto extract 3 channel color datasets (containing all metadata) from a given bayered dataset.Provide a function
mcam_data.get_color_datato extract 3 channel color data from a given bayered data. (#863)
Improvements¶
Add
output_shapeparameter tomcam_stitchto control the shape or the produced composite image. (#825)Save tiffs from
hugin_stitchingwith LZW compression.Stitched images are saved with alpha channel to highlight what is actual camera data and what is not. (#865)
Modify
draw_squareanddraw_circleIlluminate functions to accept"ir"as an LED type. (#867)GUI: Reset the zoom level for the picture-in-picture when changing the image transform mode. (#871)
GUI: Reset the exposure limits as necessary when after changing the binning level. (#880)
Add relevant titles to all dialog menus in the Falcon GUI. (#894)
Bug fixes¶
Firmware: Include ability to update firmware to 202103029 which addresses overheating issues with the FPGA by better utilizing the built-in cooling fans. (#870)
GUI: Fix bug preventing the Image Viewer from playing videos. (#877)
GUI: Ensure Image Viewer displays correct frame number when loading a new video. (#878)
GUI: Ensure transmission and reflection mode buttons get re-enabled if the subcomponent is disabled and re-enabled. (#885)
GUI: Ensure LED settings are only changed once each time a new value is typed in. (#886)
GUI: Avoid crashes associated with opening datasets that only include a single micro-camera. (#890)
MCAM Viewer: Avoid crashes associated with opening images of stacks. (#891)
Fixed focus score calculation when a region of interest is provided. (#894)
Avoid potential error when stitching large files on Windows with hugin due to not detecting the correct encoding for the PTO file. (#895)
owl 0.15.4 (2021/03/28)¶
New features¶
GUI: Enable streaming from a selected subset of adjacent cameras (#808)
Report the start pixel and end pixel offset on the sensor as part of the
MCAM.datasetacquisition asstart_pixel_x,end_pixel_x,start_pixel_y, andend_pixel_y. For now, thexandycoordinates still start at index0. It is anticipated that in future versions, thexandycoordinates will match the physical coordinates where the image is being acquired on the sensor. (#827)GUI: Enable video and zstack acquisition from subset of cameras. (#838)
Separately control RGB and IR LEDs in rev4 c-008-falcon-transmission boards
GUI: Enable control of UV and IR LEDs in the GUI. (#851)
Introduced the update menu to update the firmware version of the LED boards. (#864)
Improvements¶
Ensure compatibility of the
owl.instruments.MCAMclass with qdma version 0.7.0. (#827)Stitched images rotated saved to disk always have their EXIF orientation set to 1 ensuring they are displayed in the correct orientation on a wider variety of platforms. (#841)
Bug fixes¶
GUI: Show the RGB values in the viewer display (#830)
Return
all_ledsandrgb_ledsIlluminate properties as lists (#851)Reverted the ability to specify output shape of composite images generated through hugin since it caused the
mcam_stitchcommand to fail. (#797)
owl 0.15.3 (2021/03/24)¶
Improvements¶
Video acquisition functions in the MCAM API now require explicitly defining the number of frames to be acquired. (#849)
Bugfix¶
Hotfix: Removed update menu since it would cause the GUI to get locked up.
owl 0.15.2 (2021/03/23)¶
New features¶
GUI: Add a dialog menu to update the illumination boards. (#785)
Created function
create_videolocated atowl.io.videoto encode a video file from a list of image filenames. (#822)
Improvements¶
Add the ability to update the image acquisition hardware firmware through an internet connection. (#756)
GUI: Hide the “Stream All Sensors” button when the GUI is in high frame rate mode since it was never functional. (#818)
Bug fixes¶
GUI: MCAM viewer can open files with whitespace in the file path. (#832)
GUI: Disable z-stack functionality when the MCAM is opened without a z-stage. (#839)
Users can now acquire videos of selections of micro cameras with correct calibration data. (#840)
Documentation¶
Add documentation describing that the
mcam_data.load(..., update=False)is not supported by laterowlfunctions. (#834)Add documentation about available command line functions. (#835)
owl 0.15.1 (2021/03/17)¶
Bugfix¶
Ensure image orientation in the acquisition GUI is correctly set compared to the orientation of the MCAM.
owl 0.15.0 (2021/03/17)¶
New features¶
Enable full array streaming in the GUI.
Give user option to switch between high resolution and high frame rate modes of operation (#725)
GUI: New experimental play video button for z-stacks and time stacks. (#759)
Added the ability to specify output shape of composite images generated through hugin. (#797)
Add ability to dynamically add and remove sub-components to the MCAM (#799)
Provide higher precision in the MCAM viewer regarding the stage position. (#803)
Improvements¶
When dealing with downsampled or binned data
hugin_stitchingproduces a composite image with an output shape reduced by the same factor. (#776)GUI: buttons for enabling/disabling sub-components are moved to the advanced settings window (#786)
Provided serial numbers will now be used when opening an Illuminate board using the
by_device_namefunction, and an error will be raised if the provided serial number does not match a known board of the given device name. (#806)
Bug fixes¶
Fixed fatal bug in
mcam_calibrate. (#807)Linux GUI: Ensure that the Applications are associated with the correct desktop files. (#809)
owl 0.14.3 (2021/03/08)¶
New features¶
New a parameter
set_ledsfor theowl.instruments.Illuminate.draw_edgemethod enabling users to obtain the list of LEDs that would be set by the command without affecting the physical LED pattern. (#736)Introduce experimental command line function
mcam_calibrateto simplify the calibration process for stitching alignment and transmission/reflection color corrections. (#740)Enable separate control of daisy chained X-LSM-E Zaber stages (#746)
Improvements¶
GUI: Ensure the brightness control sliders can access the full range of the LED brightness for a particular LED board and LED lighting configuration. (#736)
Tightened the bounds for matching control points when refining stitching with Hugin for more precise stitching. (#740)
Added ability to download factory calibration for Falcons with sensor boards 4 and 5 from remote directory. (#766)
Track owl versions for stitching, reflection and transmission calibration separately within the mcam dataset.” (#771)
GUI: Avoid LED reflections on specular samples in reflection illumination mode by only turn on a single LED instead of 4 around edge of the board in perimeter illumination mode. (#790)
Bug fixes¶
GUI: Ensure that the brightness is always changed when the user types in the brightness via the text entry box. (#736)
Solved bug in
owl.calibration.calibration.add_photometric_to_dataintroduced in owl version0.14.0that would cause this function to raise an error.GUI: Open MCAM data in correct orientation in case the user set the orientation to be non-standard (
exif_orientationnot set to8). (#740)Enable users to stitch MCAM datasets that contain spaces in their filenames using the hugin backend. (#757)
Functions
add_stitch_to_dataandadd_photometric_to_databoth add specified timestamps and owl version for their particular calibration type.” (#783)GUI: Hide the loading bar when after there is an error opening the MCAM. (#787)
Documentation¶
Document the existence of the
exif_orientationcoordinate in the MCAM dataset. (#775)
owl 0.14.2 (2021/02/26)¶
New features¶
Provide a function
mcam_data.bayer_dataset_to_single_channelto extract a single channel from images taken with color filter array sensors. (#747)
Improvements¶
The location of the python executable is now included in the image metadata. (#694)
Added ability to separate images into individual wells based on a template image. The separated well images can be displayed through
quickviewbut cannot yet be exported or saved. (#708)GUI: change the default to showing a popup message whenever an image is saved (#735)
Reduce setup speed when acquiring multiple videos in the GUI with the same imaging parameters. (#737)
Ensure all images have at least one control point pair between them and all of their neighboring images (excluding diagonally neighboring images). This improves performance of
hugin_stitchingwithattempt_custom_alignmentset toTruewhen compared to the previous method of only adding control point pairs to images that were disconnected from the full array. (#739)Removal of the unused
'trigger'variable in theMCAM.dataset. (#749)Remove the data variable
'best_heights'from theMCAM.datasetsince it was never used. (#751)Address NumPy deprecation warnings from version 1.20.
Address
xarray.Dataset.dropdeprecation warning from loadingmcam_data.load. (#754)Ensure screen displays recently saved image while the “Image Saved” popup is open (#762)
Bug fixes¶
Return correct value for Falcon unique identifier (DNA). DNA identifier should have the least significant bit set to 1. Users using the
mcam_data.loadfunction will automatically be returned the correct DNA. Users that are required to use their own functions to load the DNA can check if they have the correct DNA by testing the least significant bit. If it is 0, they should multiply the DNA by 2 and add 1 to obtain the correct DNA value. (#715)Fixed issue that prevented calibrated datasets from being aligned based on features within the given dataset. Prior to this fix setting
attempt_custom_alignment=Truewould have no effect and the final alignment would be exactly the same as the initial alignment. (#726)Ensure the MCAM doesn’t immediately re-open after closing it from the GUI (#733)
Avoid system crashes when users acquire videos multiple times in the GUI. (#737)
Ensure GUI doesn’t crash in environments where different versions of Qt are installed. (#738)
Ensure that the bayer_pattern is removed from
MCAM.blue_dataset,MCAM.green_dataset,MCAM.red_datasetto avoid confusion with color filter array datasets. (#747)Return the acquisition parameters for the function
MCAM.acquire_image_from_sensorandMCAM.acquire_new_image. (#753)
Documentation¶
Add developer documentation explaining how to acquire gigapixel videos with the MCAM. (#737)
Add more information about the variables available as part of the
MCAM.dataset. (#750)Add documentation for the function
MCAM.acquire_full_field_of_viewreturn value. (#753)Updated formatting for documentation regarding the
owl.instruments.MCAMclass.
owl 0.14.1 (2021/02/15)¶
New features¶
Add support for MCAM Eagle. (#710)
To help users debug analysis pipelines,
mcam_stitchcommand now has a--dry-runargument to allow printing the files to be stitched without actually stitching them. (#727)GUI: Add option to display a popup when a new image is saved. The default is to not display the popup; this can be changed in the advanced settings window. (#724)
Improvements¶
Add orientation, software, and resolution to hugin composites. (#646)
Add options “Save Frame” and “Export Frame” when a video or z-stack is open in the Image Viewer. (#675)
Increase percentage of useful screen space for the MCAM Viewer GUI. (#680)
Add ability to switch between rgb, grayscale, and raw images in the acquisition GUI
Remove camera number overlays which were causing slowdowns
Add functionality to viewer exit button
Ensure toolbar buttons do not cause errors when pressed before opening the mcam or image file
Rearrange toolbars for Acquisition GUI and Image Viewer to match each other (#681)
Enable
hugin_stitchingto handle datasets cropped to not include camera(0, 0). (#686)Flash the GUI screen when saving an image (#690)
Allow datasets with
nanvalue metadata to be exported. (#703)Allow users to leverage their GPU to speed up nona’s performance in
hugin_stitchingusing the variableuse_gpu. This improves stitching time by about 30% when using the nona stitcher, but is insignificant when using the enblend stitcher. In some edge cases enabling the gpu for nona improves the stitched results from enblend. (#706)Streamline the output of the
mcam_listcommand.Enable the
mcam_listcommand to list Falcon Devices. (#709)Enable the Falcon to print firmware build information through the
mcam_listcommand. (#710)mcam_stitchhelp information now prints the version of the stitching software. (#727)
Bug fixes¶
Ensure loaded color images are squared correctly for display in the viewer (#683)
Update coordinates for photometric calibration data so that it does not cause exported single channel images to fail when loaded. (#685)
Ensure binned images can be properly opened in the Image Viewer (#687)
Ensure histogram is generated and labeled correctly (#699)
Ensure images exported from the Image Viewer will re-open as color images (#700)
Ensure settings bar text boxes can accept the full range of values after the slider max and min values are changed using the advanced settings window. (#718)
Ensure minimum version of vispy dependency is met when end users install
owlpackages through conda. (#729)
owl 0.14.0 (2021/01/07)¶
New features¶
Added conda packages for Python 3.9 compatibility. (#586)
Render images to memory from array of vispy ImageVisuals with
owl.visualize.quickview.render_images. (#601)Allow users to save image as ‘.nc’ file form the Image Viewer (#616)
Add functionality to export data as jpgs from the Image Viewer (#617)
Introduce a grayscale option to the Image Viewer.
Introduce pixel corrections to the Image Viewer.
Avoid erroneous color corrections when the user adds and removes color corrections from the GUI
Speed up adding and removing color corrections from the GUI (#656)
Improvements¶
Fix syntax error warning in
owl/stitch. The warning did not affect any results. (#331)Updated the save format for the calibration data to save homographies and the image shape of the dataset when the image was acquired. (#611)
Added
attempt_custom_alignmenttohugin_stitchingfor users to stitch images based only on the calibrated homographies for alignment. This parameter is True by default so that the default behavior does not change. (#624)Use bicubic interpolation for displaying debayered images which can be turned on and off in the GUI, or enabled/disabled when initializing a BayerImageVisual. (#636)
Improved shortcuts in Falcon acquisition GUI. (#638)
Ensure that the scale bar in the GUI shows the calibrated scale. (#641)
Fix slightly misaligned images in the MCAM image viewer and MCAM acquisition GUI. (#642)
Updated calibration scripts to enable them to report their progress. (#644)
Improved layout of user facing documentation. (#651)
Wider compatibility with different OpenGL implementations by explicitly clamping the output of different filters applied to the images. (#654)
Provide correct stack level for warnings emitted from
acquire_stack.Provide more appropriate stack level warning when adding photometric calibration. (#655)
Add the option to specify led type (
'uv','rgb', or'all') for the'draw_square'and'draw_circle'illumination board functions. (#666)Added two new sample images of 3 day old zebrafish larvae. (#669)
Make pixel corrections available in the Acquisition GUI. (#673)
Bug fixes¶
Restore the ability of the mcam_viewer to open an image by name from the commandline. (#627)
Decoupled the
'rgb'coordinate for the image color channels from the'rgb'coordinate of the photometric correction. This bug was preventing exported single channel images from being able to be loaded. For legacy single channel exported data you must make the following changes in themetadata.jsonfile to be able to load them:transmission_pixel_response_coefficient,transmission_pixel_response_offset,reflection_pixel_response_coefficient,reflection_pixel_response_offsetchanged their dimension fromrgbtophoto_rgb.(transmission/reflection)_pixel_response_offset-> changed its dimension (#631)Fix using the hardware trigger mode for the MCAM Falcon. (#644)
Ensure sensor corrections are applied correctly in the Image Viewer GUI. (#645)
GUI: Fix erroneously labeled gamma slider minimum value. The previous value was labeled as
0, but should have always been labeled as0.25. (#668)Correctly open a few legacy formats where images are stored in individual files. (#671)
Deprecations¶
Remove function
find_infocus_indicesas it was deprecated.Remove
soldered_boardparameter from theowl.instruments.mcam.Change default keyword argument
preserve_range=Falseinrgb2grayfunction.Remove usage of
from owl.mcam_data import mcam_data.Removal of
estimated_overlapparameter inStitcherFourierin accordance to deprecation warning.Removal of parameter
single_fileas well as associated parameters inowl.mcam_data.savein accordance to warning.Removal of
LEDColorclass. (#655)
owl 0.13.12 (2020/12/09)¶
New features¶
Can leverage GPU to apply pixel corrections to images. (#581)
Introduce a command line stitching option. (#593)
Add a loading bar to the Acquisition GUI for opening the MCAM. (#610)
Allow users to save image as
'.nc'file form the Image Viewer. (#616)
Improvements¶
Cleanup top bar when loading the MCAM. (#605)
Change how the loading bar is managed. This should prevent crashes in Windows. (#608)
Bug fix¶
Ensure Image Viewer works in development mode on Windows. (#604)
Poorly handled input variable in
pto_file_from_calibrated_imagesnow handled correctly. (#613)Image Viewer handles
Cancelbutton on file dialog correctly. (#614)Restore ability to open exported image in the Image Viewer. (#618)
owl 0.13.11 (2020/12/04)¶
Bug fix¶
Fix crash on MCAM Viewer occurring when opening an image on Windows. (#602)
owl 0.13.10 (2020/12/04)¶
Improvements¶
Incorporate loading bars for the Acquisition GUI and Image Viewer (#591)
owl 0.13.9 (2020/12/03)¶
Bug fix¶
Fix system installation for Linux applications. (#595)
owl 0.13.8 (2020/12/03)¶
Bug fix¶
GUI: Fix crash on windows when displaying the license information. (#589)
owl 0.13.7 (2020/12/02)¶
Release windows packages with the correct version information.
owl 0.13.6 (2020/12/01)¶
New features¶
Preliminary support for “drag and drop” to open files in the MCAM Viewer. (#583)
Improvements¶
MCAM Viewer: Remember last used directory for finding images to open. (#583)
Bug fix¶
Fix MCAM Viewer crash upon opening image. (#589)
Fix opening legacy exported datasets.
owl 0.13.5 (2020/12/01)¶
New features¶
Add the ability to view video or z-stacks of multiple frames in the Image Viewer. (#551)
GUI: Slider maximum imaging parameters can be configured in an advanced menu. (#576)
Improvements¶
Individual installers now exist for the MCAM Viewer and Control application. (#548)
Windows MCAM Viewer is functional without the command prompt. (#548)
Include all metadata in exported images. (#564)
Exported images can be exported and reloaded without any loss of metadata. (#564)
Improve loading time of sample datasets when they are already downloaded onto the system. (#575)
Added an example using XYZ stages for acquisition. (#578)
Save the timestamp in the file and folder names for videos and z-stacks acquired from the GUI. (#580)
Bug fix¶
owl.mcam_data.falcon_samples.color_calibration_chartnow returns the fullDatasetas opposed to aDataArray. (#548)Remove appended
'nc'from z-stack folder names saved from the GUI (#577)
Deprecation¶
The application
mcam_guihas been removed and replaced byowl_guiavailable with the conda packageowl-owl_gui. (#548)
owl 0.13.4 (2020/11/18)¶
New features¶
Add gamma filters to the Image Viewer and Acquisition GUI (#560)
Add new C-008 board (serial number
7562120). (#566)
Improvements¶
Improve theme colors to make greyed out buttons more obvious. (#549)
Add settings bar to the Image Viewer GUI (#555)
Add keyboard shorts to the MCAM Viewer application. (#557)
GUI: Improve MCAM Viewer System Information sidebar. (#558)
Save contrast limit values used in the acquisition GUI to the mcam dataset, and reopen these values in the Image Viewer (#562)
Add known stages to the KDC101 database. (#567)
Disable setting sliders in Image Viewer prior to an image being opened (#571)
Bug fix¶
Flip Y led positions by default when using transmission illumination board so that the indexed sensor is lit up. (#554)
Fix bug so GUI displays location of most recently saved image (#561)
Documentation¶
Document properties related to image resolution and shape. (#507)
Document MCAM methods related to image acquisition. (#521)
owl 0.13.2 (2020/11/11)¶
Improvements¶
Added support for non~blocking move for the Thorlabs KDC101 stages. (#443)
Fix video acquisition example. (#539)
Reorganize GUI files to enable using the Image Viewer in Windows (#542)
Display About information in the Image Viewer GUI. (#546)
Bug fix¶
Fixed windows package upload to anaconda.org. (#540)
Ensure z~stacks occur in the correct range (#545)
owl 0.13.1 (2020/11/10)¶
New features¶
Toggleable option to apply calibrated sensor corrections to image within gui. (#504)
Add z~stack acquisition to the GUI (#535)
Improvements¶
GUI: A new image is taken with the previously saved settings as soon the MCAM is open. (#537)
Bug fix¶
Ensure Image Viewer GUI can open and display binned images (#534)
Check for adequate disk space before acquiring video (#536)
owl 0.13.0 (2020/11/09)¶
Bug fix¶
Temporarily hide the ‘stream full array’ button (#531)
Improvement¶
Unified function argument names.
owl 0.12.10 (2020/11/09)¶
New features¶
The MCAM Viewer can now open a file from the command line. (#520)
GUI: Can now acquire video time slices in the acquisition GUI. (#522)
Improvements¶
Added
make_timestampto the__all__list inowl.utils. (#523)GUI: Saving custom settings no longer starts the user in the application specific directory. (#527)
Bug fix¶
GUI: The image viewer background goes dark when choosing a file.
GUI: The legacy MCAM OWL gui can start again.
GUI: Contrast sliders on the MCAM viewer now start at the correct values. (#520)
Ensure that
MCAM.acquire_full_field_of_viewreturns the acquisition parameters. (#524)
owl 0.12.9 (2020/11/05)¶
Improvements¶
GUI: Displayed imaged region stays fixed even upon changing which camera is being streamed from in single camera mode. (#519)
owl 0.12.8 (2020/11/05)¶
Improvements¶
Added ability to extract the individual rgb channels from raw bayered mcam dataset including it as the
mcam_datain a shallow copy of the original mcam metadata.Added ability to save rgb data as a single file through a
MCAMmethod. (#495)Enable users to program
Illuminatefirmware on previously unregistered illumination devices. (#513)Improve warning for missing calibration file. (#516)
Bug fix¶
GUI: Export images as JPEG instead of BMP. (#515)
owl 0.12.7 (2020/11/04)¶
Bug fix¶
Illuminate boards camera orientation more closely matches the MCAM Falcon orientation.
owl 0.12.6 (2020/11/03)¶
Bug fix¶
GUI: MCAM viewer can be opened again
New features¶
GUI: Enable the user to select a workspace and add additional information about the imaged sample. (#490)
owl 0.12.5 (2020/11/03)¶
Bug fix¶
GUI: The gui is able to be opened again. (#508)
owl 0.12.4 (2020/11/02)¶
Bug fix¶
Unpin python~qdma dependency to enable correct installation. (#502)
Deprecation¶
Deprecation: Remove
Stitcher,normalize_smooth_rawandnormalize_smooth_rgbfrom the top level package. (#498)Drop support for Python 3.6. (#500)
owl 0.12.3 (2020/11/01)¶
Improvements¶
Add best_heights and pixel_width scaled by images scaling actor to the falcon metadata. (#475)
Allow for portions of the calibration file to be updated or new parameters appended without recreating the whole file. (#483)
GUI: z~stage controls are now on the left hand side bar. (#487)
save calibration report in calibration example (#489)
owl 0.12.2 (2020/10/23)¶
Restored histogram plotting functionality in the GUI.
owl 0.12.1 (2020/10/22)¶
Improvements¶
Created example for multi-resolution searching.
Squashed bug occurring when appending focus scores during z_stack acquisitions. (#446)
Include a timestamp and the version of the owl module in saved calibration data. (#448)
Cleaned up z_stack_functions api for more clarity. (#462)
Provide method to generate pixel level corrections during calibration and apply those corrects offline.
Photometric corrections are included in calibration file and saved onto every image collected with a calibrated device. (#467)
Connect images that are not connected to the stitched array by control points by adding a control point based on initial positioning. (#468)
owl 0.12.0 (2020/10/18)¶
New features¶
Add sensor response to leds to calibration file to enable streamlined photometric corrections.
Provide known LED values that provide white light as imaged by the sensor. (#395)
Change the display layout for the Image Viewer
Add histogram to display color value information for the Image Viewer
Add contrast control to the Image Viewer (#455)
Add ability to illuminate squares or circles of LEDs or illuminate a border around the perimeter on the transmission illumination board. (#463)
Improvements¶
allows user to save z_stacks in a single netcdf file
best_imagesare exported as rgb (#399)Screenshots are automatically saved in users’
Picturedirectory with timestamp. (#438)Focus scores are now held in xarray DataArrays.
Removed legacy focus analysis method
contrast_search. (#440)hugin_stitching handles both paths to exported mcam_data and single file mcam_data. (#447)
The user can now specify the path of the template pto file and also specify the location to save the created pto file. (#451)
MCAM Falcon now documented in PDF. (#457)
Deprecation¶
BREAKING change:
MCAM.datais now a pure numpy array.MCAM.datasetcontains the metadata of the instrument. (#452)A few debugging parameters have been removed from the MCAM Falcon object. (#457)
owl 0.11.4 (2020/09/30)¶
Improvements¶
Improve initial positioning for hugin alignment to be based on calibration and expected overlap.
Control point trimming is now based on distance from initial position. (#385)
EXIF Orientation is now saved alongside MCAM data.
Image viewer will now correctly orient MCAM data according to
exif_orientation. (#404)Add a package called
owl~basefor GUI~free installation. (#411)By default,
Illuminate.fill_arraywill only turn on the RGB LEDs for the reflection board on the Falcon. (#413)GUI: Exposure slide now enables finer grained control at both low and high exposures. (#414)
GUI: Add option to make the y axis of the color histogram logarithmic (#416)
GUI: Falcon no longer opens up automatically making the GUI appear more responsive at startup. (#420)
GUI: A pause streaming button has been added to the GUI to stop the acquisition at the last acquired data. (#421)
GUI: Remember last camera used when streaming.
GUI: The first camera use when streaming is now the middle camera. (#422)
GUI: Histogram limits are now fixed between 0 and 255. (#424)
GUI: Enable opening the focus graph even without a z~stage present. (#426)
GUI: Complete license information added to the About dialog. (#428)
Bug fix¶
GUI: Setting the motor absolute position is functioning correctly again. (#418)
owl 0.11.3 (2020/09/22)¶
Dependencies on the Ramona Optics OWL unit are not longer necessary to import the
owlpackage.
owl 0.11.2 (2020/09/21)¶
Slight tweaks in the GUI layout.
owl 0.11.1 (2020/09/20)¶
New features¶
Live image viewer can adjust image contrast of acquired images. (#394)
Improvements¶
Fixed a typo in the
expanding_dataset.pyfile. (#378)Step size box has the correct value when the focus GUI is first opened.
Sliders now show the correct value upon GUI opening.
Make sure picture~in~picture disappears when the mcam closes. (#380)
MCAM GUI will automatically open the instrument.
A file menu has been added to consolidate many of the buttons that were crowding the GUI. (#382)
GUI can now be used in full screen mode.
GUI can now be used in light background mode. (#383)
Ensure the scale bar is visible in light mode, and remove bugs with textual overlays (#384)
Zaber cache now located in a central directory with other MCAM cache information. (#393)
Prove an error message when the user tries to use the
Illuminate.draw_holefunction for unsupported devices.
Bug fix¶
Fix a bug where both the save and export button were not working on the GUI. (#387)
Correct color orientation in GUI histogram. (#388)
scale,rotation,x_translationandy_translationadded back to theMCAM.data.mcam_data.get_global_transformsworks with both new styleMCAM.datasetand old styleMCAM.data. (#390)
owl 0.11.0 (2020/09/07)¶
New features¶
Add ability to stream from single camera, 3x4 array, or full 54 camera array (#350)
Use xarray dataset to expand on the capabilities of storing the experiment data. (#368)
added function to quantify and visualize stitching errors (#370)
Improvements¶
The multi~image file format for saving data has been deprecated and will now issue a warning. In future versions of
owl, the export function will have to be used to obtain a multi~image file format. This file format will help in the acquisition of z~stacks and the acquisition of time lapses. (#353)New layout for GUI increasing image space.
Added color histogram and focus score to the GUI. (#367)
Hugin is now a dependency when installing on windows enabling better stitching. (#369)
Bug fix¶
falcon can now read calibration file with system specific naming (#357)
when using a template, now allows the user to use a different blender than the one used to generate the template instead of silently using the template’s blender
One can now select a single row or column to stitch (#358)
Fix the setting the digital gain attribute.
Fix the reported value of the exposure to the correct one. (#371)
Deprecations¶
The
daskkeyword will now cause a full error to be raised instead of warnings in functions where a deprecation warning used to be issued.
owl 0.10.3 (2020/08/30)¶
Bug fix¶
Remove desktop file after uninstallation. (#366)
owl 0.10.2 (2020/08/30)¶
New features¶
mcam_data.loadnow supports loading single file formats. (#347)Add ability to toggle between stitched and unstitched images in GUI (#349)
Added a new function to plot histograms of MCAM data more readily. (#354)
Improvements¶
Properties are added to the
owl.instruments.MCAMobject to make selecting all sensors, and the center 12 sensors easier. (#345)A desktop entry is added to the installer for easy startup. (#364)
Deprecation¶
mcam_data.load_netcdfhas been deprecated. (#347)
owl 0.10.1 (2020/08/17)¶
Improvements¶
Bump qdma version requirement for Linux to avoid circular imports. (#344)
owl 0.10.0 (2020/08/17)¶
New features¶
First addition of the MCAM Falcon to the instruments submodule. (#340)
owl 0.9.60 (2020/08/17)¶
New features¶
Add ability to create a pto file for mcam_data using its
global_transforms(#337)
Improvements¶
Allows images to be downsampled in
simple_mergeto create a composite image at a lower resolution (#334)Calibration file path can now be provided so that the user may have better control over calibration. (#338)
owl 0.9.59 (2020/08/12)¶
New features¶
Save stitching transforms in a calibration file to be used by other image sets (#322)
Improvements¶
Compile program with numpy 1.16 as opposed to numpy 1.14. (#329)
Zaber Motion
X_LSM_Edriver now reports the FTDI serial number used. (#330)
owl 0.9.58 (2020/08/05)¶
Improvements¶
Illumination boards now open faster due to caching of LED positions. (#327)
owl 0.9.57 (2020/07/31)¶
New features¶
X_LSM_E driver can now return stage serial number. (#303)
added ability to select the best plane to bring the most cameras to their peak focus (#316)
Avoid accidental image rotations in 3D when viewing MCAM images. (#323)
Bug fix¶
Illumination boards that do not include UV lights will fail when asked to turn them on. (#311)
owl 0.9.56 (2020/07/22)¶
New features¶
Added ability to extract homography matrix from hugin’s pto files within the hugin module. (#297)
owl 0.9.55 (2020/07/19)¶
New features¶
Motors step sizes can now be controlled in MCAM GUI. (#294)
- X_LSM_E motors from Zaber are automatically found regardless of what serial
port they appear as on the operating system. (#301)
Illuminate devices can now be open by name for simplified connection to reflection and transmission boards. (#302)
Illuminate board firmwares can now be updated programmatically. (#306)
Bug fix¶
Fixed display of debayering images with
grbgandgbrgpatterns. (#299)ensure
_fake_maximum_positionis consistently used for the fake motor (#304)Better stability for the c007 and c008 fill array commands (#305)
owl 0.9.54 (2020/07/14)¶
New features¶
hugin_stitchingcan now select a subsection rectangle of images to stitch. This can be any portion and does not need to start at camera (0,0) (#287)Better support for use of Z-stage without internet access. (#289)
allows user to specify a region of interest to calculate focus of (#290)
A loading progress bar is now added to the image viewer. (#293)
API Change:
owl.analysis.acquire_stacknow return the paths where data was saved. (#295)
owl 0.9.53 (2020/06/30)¶
New features¶
Improved
mcam_viewerapplication that displays metadata about the images. (#276)Hugin is now integrated with Ramona Optics’ software for seamless stitching. (#240)
Created function in illuminate for lighting up the edge leds around the perimeter of the c007 board. (#249)
acquire_stackadded to facilitate acquisition of z~stack while cherry-picking the “in focus” images (#271)Enable users to select the chromaticity of the LEDs in the
draw_edgemethod. (#278)A new software timestamp has been added to the metadata. (#279)
Improvements¶
The version of qdma is now printed as part of owl.sys_info(). (#259)
0.9.52 (2020/05/18)¶
Fixed¶
Compatibility with scikit~image 0.17.2
0.9.51 (2020/05/12)¶
Added¶
Preliminary support for Zaber X~LSM~E linear stage.
Fixed¶
Compatibility with scikit~image 0.17.1
Allowed
SimpleStitcherto have negative offsets (add gaps between cameras).Touched up Simulation Compositor to avoid shadows at edges.
0.9.50 (2020/04/14)¶
Added¶
Experimental feature save_netcdf that saves array of images and metadata in one netcdf file
Experimental feature load_netcdf that loads array of images and metadata from one netcdf file
0.9.49 (2020/01/19)¶
Added¶
Added a new very basic MCAM image viewer.
0.9.48 (2020/01/17)¶
Fixed¶
Metadata:
exposure_secondsandgainare now floating point numbers.
Added¶
Software compatibility with Illuminate board.
0.9.47 (2020/01/13)¶
Added¶
Distribution compatible with Python 3.8.
0.9.46 (2020/01/03)¶
Added¶
Documentation for the
owl.simulation.MCAMSimulator.A new method
owl.simulation.create_stitching_paramsto create stitching parameters from simulated datasets.
Changed¶
owl.simulation.Simulatoris now deprecated in favor ofowl.simulation.MCAMSimulator.
Fixed¶
Setting the rotation in
quickvieworview_large_imagenow works as expected.
0.9.45 (2020/01/01)¶
Fixed¶
GUI no longer crashes with Python 3.7.4 and above.
Added¶
owl.visualize.quickviewandowl.visualize.view_large_imagecan now rotate images.GUI live view can be rotated using the middle mouse button.
0.9.44 (2019/12/12)¶
Fixed¶
Importing
owl.visualizeno longer issuesQSocketNotifierwarnings.GUI Crashes related to the fluorescence module.
Added¶
The serial number for the Illumination unit can now be specified in the GUI.
0.9.43 (2019/12/10)¶
Added¶
A basic example on how to stitch images.
0.9.42 (2019/12/08)¶
Fixed¶
Add the splash screen back to the GUI.
0.9.41 (2019/12/08)¶
Fixed¶
GUI no longer randomly crashes after prolonged usage.
0.9.39 (2019/12/07)¶
Added¶
macOS Experimental support. Requires OS X Sierra (10.12).
Fixed¶
Max Levelis now correctly labeled on the GUI.The
Board IDselector text has been updated to be more descriptive.
0.9.37 (2019/11/30)¶
Added¶
New release of system independent package for installation on Apple OSX computers.
Fixed¶
Removed accidentally added button to the GUI.
0.9.36 (2019/11/25)¶
Fixed¶
GUI LED Controller now automatically collapses when not in use.
GUI now remembers the last directory used to save the data.
GUI now has a button and shortcut for enabling full screen mode.
0.9.35 (2019/11/23)¶
Fixed¶
The command line application
mcam_listdoesn’t crash when no TeensyPowers are found.In the
GUI, theVideo OnandVideo Offbuttons now get greyed out after being pressed.array_scanning_acquisition.pyno longer assumes it is using theIlluminateboard.
Changed¶
Generating the composite can now be done with a subset of the data starting from the top left corner of the acquisition.
Added¶
Graphical User Interface now zoom’s to the newly selected camera in single camera mode.
Graphical User Interface now has a button to save all the data, and a single image.
Graphical User Interface now uses a dropdown to select the control board ID.
Graphical User Interface now has a option to display the center square region of an image.
0.9.34 (2019/11/18)¶
Fixed¶
Closing the fluorescence LED from the GUI no longer crashes the GUI.
0.9.31 (2019/11/17)¶
Added¶
Command line utility
mcam_listto list the available Ramona Optics devices.schedulerparameter toowl.mcam_data.loadto specify the dask scheduler used. Default scheduler is now'threading'.GUI now has a button to set the mock device
owl.instruments.mcamnow has two additional properties:micro_camera_separationandsensor_pixel_size.GPU Debayering can now be enabled and disabled in a menu drop down in the GUI.
0.9.30 (2019/11/12)¶
Changed¶
Added a button to turn on the fluorescence module.
Added¶
Added documentation about how to analyze z stacks
Added documentation on how to turn on the fluorescence module in Python
0.9.29 (2019/11/11)¶
Changed¶
Removed the Pyside2 constraint on the package to enable downgrade with Qt 5.9.
0.9.28 (2019/11/10)¶
Added¶
Documentation for
find_in_focus_indicesfunctions.
Fixed¶
slice_in_focus_indicesnow works if the leading dimension isn’t called ‘z’.
Changed¶
owl.mcam_data.resize_as_squareshould now be a little faster.
0.9.27 (2019/10/26)¶
Fixed¶
GUI no longer uses GPU accelerated debayer due to memory leak that would cause crashes.
A memory leak has potentially been fixed in the GPU debayering code but needs to be tested in the field before deploying as the default behavior for the GUI.
0.9.26 (2019/10/22)¶
Fixed¶
Pixel based stitcher had a bug and would not output images.
0.9.25 (2019/10/21)¶
Added¶
owl.visualize.view_large_imagewill now automatically chunk large images to allow one to display true gigapixel images.Provide new methods to convert between the layout in
owl.stitcher_reduxandowl.stitcher.Layout.New methods
owl.stitcher_redux.save_stitching_paramsandowl.stitcher_redux.load_stitching_paramsexist to load and save stitching parameters.
Fixed¶
Fixed docstring for
owl.stitcher_redux.translation.
0.9.24 (2019/10/19)¶
This released focused on improving usability, both in terms of compatibility with Spyder and Jupyter notebooks, as well as making hacking finding global transforms easier.
Added¶
Users can now select the control board year in the GUI.
An experimental
owl.analysis.equalize_intensityattempts to equalize the intensity of images across the entire MCAM array after stitching is completed.
Changed¶
Updated examples to use GPU demosaicing for live viewing.
Single camera mode GUI is now more in line with the array mode GUI.
Better detection for Vispy when running within Spyder.
0.9.23 (2019/10/13)¶
Added¶
The GUI can now specify basic options for how to display data.
Documentation on how to modify the stitching parameters has been added.
Changed¶
The GUI’s single and array mode interfaces have been merged into one.
GUI performance improvement: GPU now used to render color images in the GUI. this greatly increases the performance of live viewing images.
0.9.22 (2019/09/23)¶
Added¶
A splash screen has been added to GUI to show the loading progress of the application.
0.9.21 (2019/09/21)¶
Changed¶
Updated branding.
0.9.20 (2019/09/20)¶
Changed¶
Updated example files.
Fixed¶
mcam.acquire_full_field_of_viewwas broken on windows internally. It is now fixed.
0.9.19 (2019/09/20)¶
Changed¶
mcam.acquire_full_field_of_viewerror message now lists the missing cameras.The default border size of
mcam.visualize.quickviewis now 5% of the image instead of 0.
Added¶
mcam.acquire_full_field_of_viewnow enables ignoring a subset of cameras from raising an error if images cannot be acquired.
0.9.18 (2019/09/19)¶
Fixed¶
GUI: LED controls would be broken once the instrument mode was changed from array to single camera mode.
0.9.17 (2019/09/19)¶
Added¶
owl.instruments.KDC101now has a propertyposition_mm.The Graphical User Interface (GUI) now saves most of the last used parameters for the next sessions.
The GUI now has basic control of the motors.
Fixed¶
owl.instruments.KDC101could not open devices due to missing import statement on Linux operating systems.GUI will not crash when acquiring the full field of view fails, but rather it will show a warning.
0.9.16 (2019/09/18)¶
Fixed¶
Gui now actually opens a device instead of opening a fake one.
owl.color.rgb2grayandowl.color.rgba2grayused to automatically convert integer types to floating point types without changing the image scale. This now issues a warning unless the user specifies the explicitly desired behavior. In future versions, this will be changed to automatically convert the scale of the images.
Changed¶
owl.mcam.gray_datanow returns an image scaled between 0 and 1.owl.mcam_data.loadnow defaults topreserve_range=False. Old behavior ofpreserve_range=True(which gave unpredictable results) can be obtained by specifying the desired outcome.owl.mcamwill now check if the image is exactly the same as before by randomly sampling 100 points across the entire FOV and testing that they are not identical instead of checking that they are simply zero.
0.9.15 (2019/08/27)¶
Changed¶
pyilluminate requirement now bumped to version 0.4.0. While we do subclass the
pyilluminate.Illuminateit was decided that this the changes in version 0.4.0, mainly associated to device discovery are relatively minor and do not warrant a full minor version bump for the owl package.thorlabs_aptcontroller now usesftd2xxbackend on windows for increased stability.
Added¶
Basic support for 777 LED MCAM illuminate board (8x6 hole configuration).
New dependency on
ftd2xxwhen installingowlon Windows. This dependency is installed automatically.
0.9.14 (2019/08/20)¶
Please note that the KDC101 driver is still considered experimental and subject to change without warning. Let us know if any of the functionality is useful to you.
Added¶
Data is now partially checked to ensure that zero data isn’t returned from the MCAM.
KDC101 motors can now check if they were homed and other status bits.
KDC101 motors can now ensure it was homed during initialization.
KDC101 motors now check the newly set absolute position of the motor before actuating the motors.
KDC101 motor controllers can now set the motor velocity.
Fixed¶
Avoided spurious warnings in
mcam_guiaboutexposurebeing used instead ofexposure_arb_units.Usage of Illuminate in MCAM GUI single camera mode is restored.
owl.visualize.illuminate.draw_ledsnow uses the updated xarray property for the LED chromaticity.
0.9.13 (2019/08/11)¶
Added¶
owl.instruments.mcam.acquire_full_field_of_viewnow takes a new parametern_tries.
mcam_sdk ~- 0.8.1 (2019/08/10)¶
Fixed¶
fake_device=Trueis now more stable when acquiring multiple images withacquire_full_field_of_view
0.9.12 (2019/08/07)¶
Added¶
Com ports can now be used to specify which KDC101 motor is open. This is useful in Windows where serial numbers might all appear to be the same. For Linux you can search
/dev/tty.
0.9.11 (2019/08/07)¶
Added¶
A new function
mcam_data.from_large_imagetakes a large image and chunks it up into smaller ones and stores it in anmcam_datacontainer. This function can be useful for storing images for post~processing with other software that may not be able to open the large MCAM images all at once.A new function
KDC101.list_available_serial_numbershelps identify which KDC101 drivers from Thorlabs are currently attached to a computer.
Fixed¶
mcam_data.newnow respectarrayparameter generated the expected output.
Changed¶
owl.util.sys_infonow returns a dictionary that contains information about the version of even more packages.
0.9.10 (2019/06/12)¶
Added¶
Modified
quickviewmoduleAdded
border_sizeparameter, allows an exploded view by placing a borderborder_sizepixels around each camera’s imageAdded
bgcolorparameter to allow configuration of the background color of thequickviewwindowAdded
blendviewinowl.visualize.blendviewBlendview allows the interactive blending of two images of the same shape.
Added
multiviewinowl.visualize.multiviewMultiview allows the viewing of a grid of multiple mcam_data sets, large images, or a mix of the two
owl.instruments.mcamandowl.instruments.mcam_2x2now have a__slots__attribute to help avoid typos in scripts.owl.instruments.KDC101has now been added to control the KDC101 motor from Thorlabs. At this stage, this should still be considered experimental.
Fixed¶
owl.mcam_data.savenow respects theinclude_timestampparameter.mcam_data.save_allnow includes a single timestamp instead of two.
0.9.9 (2019/05/30)¶
Fixed¶
owl.instruments.mcam_2x2now correctly sets the propertyexposure_seconds.
0.9.8 (2019/05/28)¶
Added¶
The
forceparameter inowl.instruments.mcamnow gets passed to the C++ driver. Requiresmcam_sdkversion0.8.owl.mcam_data.loadnow takes a new parameterimage_namesallowing precise definition of each of the images to load in the dataset.
Fixed¶
Docstrings of the
owl.visualizemodule is now added to the official documentation.
0.9.7 (2019/05/21)¶
Fixed¶
Removed an error that would stop
owl.colorfrom being imported twice on occasion.
0.9.6 (2019/05/12)¶
Added¶
owl.instruments.mcamcan now set the exposure of the camera in seconds.owl.mcam_data.load: documented that theoutput_mode'gray'is valid.The python examples section in the documentation now describes where to find the examples.
Information in the documentation about how to use metadata with xarray.
Information about how to use delayed objects with dask for parallelization.
owl.mcam_dataobjects now have__owl_version__and__sys_version__coordinates.Much more documentation on pyilluminate.
Changed¶
owlnow requirespyilluminate>=0.3.0due to changes in howled_positionsis defined.
Deprecated¶
owl.instruments.Illuminate.positions_as_xarray()is deprecated in favor ofowl.instruments.Illuminate.led_positions.
Fixed¶
The
exposure_secondsmetadata now has adtypeofnp.float64to store fraction of seconds correctly. Previously it always held a values of0as the value would be rounded down.
0.9.5 (2019/05/07)¶
Added¶
The ability to see a rudimentary progress bar has been added to many functions that could be delayed.
The executable
mcam_guinow takes the command line argument--helpwhich displays the version number of the interface.
Changed¶
Many functions that would return delayed objects now return imperatively by default.
The owl python package now depends on
wabisabi, a pure python library to handle deprecations.
Deprecated¶
The
daskkeyword has been deprecated in favour of thedelayedkeyword for functions where the computation can be delayed.
Fixed¶
owl.__version__now returns a valid version instead of'unknown'.
0.9.4 (2019/05/06)¶
Added¶
The control board year can now be specified in the
mcamandmcam_2x2constructor.
0.9.3 (2019/05/02)¶
Added¶
The
mcamandmcam_2x2now have parameters ofexposure_secondsthat return the current exposure in units of seconds.
0.9.0 (2019/04/11)¶
Changed¶
Packages
owl_instrumentsandramonaoptics_guiare now defunct and have been included in theowlpackage.