Installation
Clone the Github repository and run HCRprocess.mlapp
ImageJ in MATLAB
Required for stitching and final processing
Add the ImageJ-MATLAB update site in ImageJ and increase your Java heap memory size in MATLAB
How to increase Java heap memory size beyond the default maximum allowed value A minimum of at least two to three times the size of the largest image you intend to work with is recommended.
Set fijiSciptsDir in params.m to the correct Fiji scripts directory on your system. If you don’t know where this is, you can use File -> Show Folder -> ImageJ in Fiji.
Python in MATLAB
Required for registration and segmentation
Create an environment using Anaconda Navigator. The environment can be named whatever you want, but if you don’t use the default name of HCRprocess, be sure to change HCRprocessEnv in params.m to the correct name.
In Anaconda Prompt, activate the environment, and then install the required packages:
conda activate HCRprocess
pip install itk
pip install itk-elastix
pip install cellpose[gui]
Make sure you have added your Anaconda scripts directory to your Path, and that you have run conda init in your terminal at least once. HCRprocess calls Python using MATLAB’s system function and the python command line invocation.