Installation ------------------------------ `Install MATLAB `_ Clone the `Github repository `_ and run ``HCRprocess.mlapp`` ImageJ in MATLAB ~~~~~~~~~~~~~~~~~~~~~~~ Required for stitching and final processing `Install Fiji `_ `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 `Install Anaconda Distribution `_ 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: .. code-block:: python 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.