This repository and the quantiuspipeline repository contain all of the code for the organoids project.
Follow these steps to run an experiment from fixed organoids to feature measurements.
Starting an Experiment
2D Segmentation of Some of the Slices (Quantius Job)
You will need to complete these steps for BOTH the XY and XZ (orthogonal) slices.
2D Segmentation of All of the Slices (Mixed Mode)
Reviewing 2D Segmentations
Note that you can actually start this once the Quantius Job has been preprocessed (you do not need to wait for the Quantius results to come in). Only the last step (Review Nuclear Segmentations) cannot be started until the Mixed Mode step is complete.
Convert Segmentations to 3D
This step will collect all the formatted features from all experiments and run analysis like PCA, correlations, etc. It will also plot the data. Unlike all the previous steps, these commands should be run from within Dropbox (RajLab) --> LEB_Organoids --> Final_Analysis --> (organoid type).