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MCAM Workflows Manual
Overview
Introduction
Acquire an Image
Acquire a Z Stack
Acquire an XYZ Stack
Acquire a Video
Tools
Color Picker
Length Tool
Rectangle Tool
Circle Tool
Ellipse Tool
Region of Interest (ROI) Extraction Tool
Stack Projection
Stack Reduction
Select the GFP Channel Corresponding to the Brightfield Best Focus Slice
Labeling Tool
Binary Mask Labeling Tool
Recommended Model Organism Video Acquisition Parameters
Create a Well Alignment File
Compressing .nc Dataset Files
Single File Compression
Batch File Compression
Zebrafish Tracking
Acquire a Zebrafish Assay Video
Acquire a Zebrafish Visual Motor Response (VMR) Dataset
Acquire a Zebrafish Timelapse Stimulus Dataset for Acoustic Startle Response
Tracking Analysis
Animal Behavior Analysis
Dynamic Visual Display Module
Zebrafish Segmentation - Fluorescence
Zebrafish Morphology and Segmentation - BrightField
Diffuser Riser for Zebrafish Morphology and Segmentation
Activity Metric
Zebrafish Embryonic Photomotor Response (EPMR) Assay
Zebrafish Tail Coiling Assay
Best Focus Panel
Full Well Scan
Analysis
Cell Counting Analysis
Channel Threshold Analysis
Confluence Analysis - 4x Magnification
Confluence Analysis - 10x Magnification
Single Point Segmentation
Runtime Single Point Segmentation Analysis
Segmentation
Fluorescent Nuclei Segmentation
Runtime Segmentation Analysis
Tiny Organoid Segmentation and Coordinate Calculation
Stitching Multi-Image Well Datasets
Transfection Assay (Beta*)
Live/Dead Assay (Beta*)
Machine Learning
Model Training - Object Detection
Appendix A
Working with Nuclear Stains
MCAM Workflows Manual
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Ramona MCAMDocumentation
Ramona MCAMDocumentation