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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

Acquiring the Images

Preparing the Images

Segmenting Nuclei

2D Segmentation of Some of the Slices (Quantius Job)

You will need to complete these steps for BOTH the XY and XZ (orthogonal) slices.

Preprocessing the Quantius Job

Submitting the Quantius Job

Postprocessing the Quantius Job

2D Segmentation of All of the Slices (Mixed Mode)

Running 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.

Collect Other Channels

Format Nuclear Segmentations from fastER

Guess Other Segmentations

Review Segmentations

Convert Segmentations to 3D

Creating 3D Segmentation

Measuring Features

Combine All Segmentations

Measure Manual Features

Measure Automatic Features

Format Features Data

Run Analysis

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).

Collect All Experiments

Combine All Images

Analyze Features