8. OWL Schemas

These are the following settings files used in the MCAM.

MCAM State

This model describes an MCAM at its resting state. Only light field validation is performed when creating a model. However, upon attempting to restore the settings from the model for an active MCAM, more extensive model validation is performed. Most field are optional and if not provided, it is assumed that they should be left in their previous values, if possible. As such, we encourgae users to specify the state of the MCAM as much as possible if they are attempting to restore the MCAM to a particular state.
type	object
properties
__owl_version__	Owl Version
	type	string
	default	0.19.173
__owl_settings_type__	Owl Settings Type
	type	string
	default	mcam_state
exposure	Exposure
	The exposure of the MCAM in seconds. Typical values range between 1E-3 and 1.0.
	default	None
	anyOf		type	number
			exclusiveMinimum	0.0
			type	null
exposure2	Exposure2
	The exposure of the MCAM in seconds. Typical values range between 1E-3 and 1.0. This is only valid for acquisitions taken with iHDR enabled.
	default	None
	anyOf		type	number
			exclusiveMinimum	0.0
			type	null
interlaced_hdr	Interlaced Hdr
	Whether or not the MCAM is using interlaced HDR (iHDR).
	default	None
	anyOf		type	boolean
			type	null
analog_gain	Analog Gain
	The anlaog gain used with the image sensor. Typical values range between 1 and 7.75.
	default	None
	anyOf		type	number
			exclusiveMinimum	0.0
			type	null
digital_gain	Digital Gain
	The analog gain of the sensors used for the image acquisition. Typical values range between 0.015625 and 7.984375, however, Ramona Optics suggests values of 1, 2, or 4.
	default	None
	anyOf		type	number
			exclusiveMinimum	0.0
			type	null
digital_gain_color	Per Color Digital Gain
	The image sensors support setting the digital gain on a per color level allowing for individual adjustment of the red, green adjacent to the red pixel, blue, and green adjacent to the blue pixel channels.
	default	None
	anyOf		type	array
			items
				type	number
			type	null
illumination_mode	Illumination Mode
	The illumination modality of the MCAM. Allowed values depend on the hardware capabilities of the MCAM. If this value is specified, the illumination_birghtness should bespecified, otherwise, it is assumed that the illumination brightness is 0. Contact Ramona Optics at help@ramonaoptics.com for more information about your available illumination modes with a screenshot of your screen including this error message.
	default	None
	anyOf		type	string
			type	null
illumination_brightness	Illumination Brightness
	The illumination brightness. Values between 0. and 1. are allowed. This value in this field is unused if illumination_mode is None.If illumination_mode is specified, this value must be specified otherwise it is assumed that the brightness is 0.
	default	None
	anyOf		type	number
			type	null
illumination_brightness_kwargs	Illumination Brightness Kwargs
	Additional keyword arguments to the illumination mode. Note that the key value pairs in this field are very experimental and subject to change without notice. Please consult Ramona Optics at help@ramonaoptics.com with a screenshot of your screen including this error message before making any changes to this field.
	default	None
	anyOf		type	object
			type	null
bin_mode	Bin Mode
	The bin mode of the image acquisition.The bin mode must take a value of 1, 2, or 4.
	default	None
	anyOf		type	integer
			enum	1, 2, 4
			type	null
start_pixel	Start Pixel Within Each Micro Camera
	The starting pixel for image acquisition within each micro camera.
	default	None
	anyOf		type	array
			items
				type	integer
			type	null
end_pixel	The Ending Pixel Within Each Micro Camera
	The ending pixel for image acquisition within each micro camera.
	default	None
	anyOf		type	array
			items
				type	integer
			type	null
exif_orientation	Display Orientation of the Captured Images
	The display orientation of the captured images.
	default	None
	anyOf		type	integer
			enum	1, 2, 3, 4, 5, 6, 7, 8
			type	null
frame_rate_setpoint	Frame Rate Setpoint
	Frame rate setpoint for the sensors. The actual frame rate is determined by whether or not the sensors are optimized for high speed acquisition and the preset exposure.
	default	None
	anyOf		type	number
			exclusiveMinimum	0.0
			type	null
sensor_timing_settings	Sensor Timing Settings
	Whether or not the sensors are optimized for stability or high frame acquisition. This field must take a value of ‘stability’ or ‘frame_rate’. If the frame rate is specified, this field must be specified. This feature is still experimental. Please contact Ramona Optics at help@ramonaoptics.com with a screenshot of your screen including this error message before changing this.
	default	None
	anyOf		type	string
			enum	stability, frame_rate
			type	null
use_hardware_trigger	Use Hardware Trigger
	Internal setting that describes how the image sensors are controlled. If set to true, the image sensors acquire images using an internally generate trigger. This trigger determines both the frame rate and the exposure, thus making it is impossible to decouple the two.
	default	None
	anyOf		type	boolean
			type	null
virtual_selection	Virtual Selection
	The named subset of sensors from which the acquisition is occurring. Not all MCAMs support this feature. Contact us at help@ramonaoptics.com with a screenshot of your screen including this error message if you have any questions.
	default	None
	anyOf		type	string
			type	null
acquisition_mode	Acquisition Mode
	This field is used to set the acquisition mode of the MCAM.
	default	None
	anyOf		type	string
			type	null
z_stage_position	Z Stage Position
	The position of the Z stage in the MCAM. The position of the stage is set after the mechanical state is set.
	default	None
	anyOf		type	number
			type	null
y_stage_position	Y Stage Position
	The position of the Y stage in the MCAM. The position of the stage is set after the mechanical state is set.
	default	None
	anyOf		type	number
			type	null
x_stage_position	X Stage Position
	The position of the X stage in the MCAM. The position of the stage is set after the mechanical state is set.
	default	None
	anyOf		type	number
			type	null
x_sample_stage_position	X Sample Stage Position
	The position of the X sample stage in the MCAM. The position of the stage is set after the mechanical state is set.
	default	None
	anyOf		type	number
			type	null
mechanical_state	Mechanical State
	The named mechanical state of the MCAM. This the MCAM will move this state prior to setting any stage the positions settings specified here.
	default	None
	anyOf		type	string
			type	null
serial_number	Serial Number
	The serial number of the MCAM. This field can be used to verify that the given settings apply to the presently connected MCAM.
	default	None
	anyOf		type	string
			type	null
falcon_dna	Falcon Dna
	The DNA of the Falcon frame grabber.This field can be used to verify that the given settings apply to the presently connected MCAM.
	default	None
	anyOf		type	string
			type	null
sensor_board_serial_number	Sensor Board Serial Number
	The serial number of the sensor board.This field can be used to verify that the given settings apply to the presently connected MCAM.
	default	None
	anyOf		type	string
			type	null
sensor_chroma	Sensor Chroma
	The sensor chroma of the MCAM.This field can be used to verify that the given settings apply to the presently connected MCAM.
	default	None
	anyOf		type	string
			type	null
sensor_board	Sensor Board
	The sensor family of the MCAM.This field can be used to verify that the given settings apply to the presently connected MCAM.
	default	None
	anyOf		type	string
			enum	falcon, eagle, kestrel48
			type	null
with_z_stage	With Z Stage
	Whether or not the MCAM has a Z stage connected to it.If a boolean values is provided, the MCAM only verifies for the presence of the subcomponent. If a serial number is provided as a string validation can be performed on the basis of an exact match. This field can be used to verify that the given settings apply to the presently connected MCAM.
	default	None
	anyOf		type	boolean
			type	string
			type	null
with_y_stage	With Y Stage
	Whether or not the MCAM has a Y stage connected to it.If a boolean values is provided, the MCAM only verifies for the presence of the subcomponent. If a serial number is provided as a string validation can be performed on the basis of an exact match. This field can be used to verify that the given settings apply to the presently connected MCAM.
	default	None
	anyOf		type	boolean
			type	string
			type	null
with_x_stage	With X Stage
	Whether or not the MCAM has a X stage connected to it.If a boolean values is provided, the MCAM only verifies for the presence of the subcomponent. If a serial number is provided as a string validation can be performed on the basis of an exact match. This field can be used to verify that the given settings apply to the presently connected MCAM.
	default	None
	anyOf		type	boolean
			type	string
			type	null
with_x_sample_stage	With X Sample Stage
	Whether or not the MCAM has a X sample stage connected to it.If a boolean values is provided, the MCAM only verifies for the presence of the subcomponent. If a serial number is provided as a string validation can be performed on the basis of an exact match. This field can be used to verify that the given settings apply to the presently connected MCAM.
	default	None
	anyOf		type	boolean
			type	string
			type	null
with_transmission_illumination	With Transmission Illumination
	Whether or not the MCAM has a transmission illumination module connected to it.If a boolean values is provided, the MCAM only verifies for the presence of the subcomponent. If a serial number is provided as a string validation can be performed on the basis of an exact match. This field can be used to verify that the given settings apply to the presently connected MCAM.
	default	None
	anyOf		type	boolean
			type	string
			type	null
with_reflection_illumination	With Reflection Illumination
	Whether or not the MCAM has a reflection illumination module connected to it.If a boolean values is provided, the MCAM only verifies for the presence of the subcomponent. If a serial number is provided as a string validation can be performed on the basis of an exact match. This field can be used to verify that the given settings apply to the presently connected MCAM.
	default	None
	anyOf		type	boolean
			type	string
			type	null
with_fluorescence_illumination	With Fluorescence Illumination
	Whether or not the MCAM has a fluorescence illumination module connected to it.If a boolean values is provided, the MCAM only verifies for the presence of the subcomponent. If a serial number is provided as a string validation can be performed on the basis of an exact match. This field can be used to verify that the given settings apply to the presently connected MCAM.
	default	None
	anyOf		type	boolean
			type	string
			type	null
with_temperature_monitor	With Temperature Monitor
	Whether or not the MCAM has a temperature monitor module connected to it.If a boolean values is provided, the MCAM only verifies for the presence of the subcomponent. If a serial number is provided as a string validation can be performed on the basis of an exact match. This field can be used to verify that the given settings apply to the presently connected MCAM.
	default	None
	anyOf		type	boolean
			type	string
			type	null
with_plate_tapper	With Plate Tapper
	Whether or not the MCAM has a plate tapper connected to it.If a boolean values is provided, the MCAM only verifies for the presence of the subcomponent. If a serial number is provided as a string validation can be performed on the basis of an exact match. This field can be used to verify that the given settings apply to the presently connected MCAM.
	default	None
	anyOf		type	boolean
			type	string
			type	null

Acquire And Save Assay

Parameters provided to the acquire and save assay.
properties
Final Mcam State	final_mcam_state
	State of MCAM after acquisition. If specified, the assay will call MCAM.set_state with the parameters specified here. If None or undefined, the state at the end of the acquisition is defined by the assay.
	type	MCAMState
	default	None
Well Keypoints	well_keypoints
	Well Plate Keypoints. If provided the acquired images will be extracted and interpreted as images of a well plate on a per wellbasis.
	type	WellPlateKeypointState
	default	None
High Dynamic Range	high_dynamic_range
	If true, this option will enable will use a combination of multiple exposure times and tone mapping to create an high dynamic range (HDR) composite suitable for human review. Compared to a standard image, an HDR, composite can enable faster human review for images with both bright and dark regions.
	type	bool
	default	False
Start Delay	start_delay
	Amount of time in seconds to wait before beginning assay.
	type	float
	default	0

Z Stack Assay

Parameters provided to the Z stack assay.
properties
Well Keypoints	well_keypoints
	Well Plate Keypoints. If provided the acquired images will be extracted and interpreted as images of a well plate on a per wellbasis.
	type	WellPlateKeypointState
	default	None
Start Delay	start_delay
	Amount of time in seconds to wait before beginning assay.
	type	float
	default	0.0
Z Start	z_start
	Starting Z position.
	type	Optional
	default	None
Z Step Size	z_step_size
	Step size between Z positions.
	type	Optional
	default	None
Z Num Steps	z_num_steps
	Number of Z positions to acquire.
	type	Optional
	default	None
Z Position Origin	z_position_origin
	If ‘absolute’ is specified, then the parameter ‘z_positions’ specifies the absolute position of the stage at the time of image capture. If ‘mcam_state’ is specified, then the parameter ‘z_position’ specifies the position of the stage, with respect the initial ‘z_stage_position’ specified in the ‘mcam_state’.
	type	Literal
	default	absolute
Final Mcam State	final_mcam_state
	State of MCAM after acquisition. If specified, the assay will call MCAM.set_state with the parameters specified here. If None or undefined, the state at the end of the acquisition is defined by the assay.
	type	MCAMState
	default	None
Projection	projection
	If specified a projection of the data will be returned instead of the complete stack. If None (or null) is specified, the full stack is returned. If ‘minimum’ is specified, a composite image is returned where each pixel takes the value of the minimum measured value in the stack. The ‘minimum’ projection is often useful when acquiring images acquired with brightfield transmission illumination. If ‘maximum’ is specified, a composite image is returned where each pixel takes the value of the maximum measured value in the stack. The ‘maximum’ projection is often useful when acquiring images acquired with fluorescence illumination.If ‘mean’ is specified, a composite image is returned where each pixel takes the value of the mean measured value in the stack. If ‘sum’ is specified, a composite image is returned where each pixel takes the value of the sum of the measured values in the stack. If ‘zebrafish’ is specified, best focus zebrafish will be found in the stack.
	type	Literal
	default	None
High Dynamic Range	high_dynamic_range
	If true, this option will enable will use a combination of multiple exposure times and tone mapping to create an high dynamic range (HDR) composite suitable for human review. Compared to a standard image, an HDR, composite can enable faster human review for images with both bright and dark regions.
	type	bool
	default	False