podocytes

For users

Install the dependencies

• Legacy Java SE 6 runtime

Install Podo

• Download Podo.app.zip (currently available only for MacOS Mojave)

Unzip the file, then move the app to /Applications/

Running the program

Be patient, the app takes several seconds to open.

Also, when opening the app for the first time, make sure to hold down Control while clicking on the app, and then select 'Open'. Then confirm you want to open this app from an unidentified developer. See here for step by step screenshots.

Notes:

• Currently, you must be connected to the internet to run the app. Pims relies on the Bioformats loci_tools.jar and downloads this at program runtime.
• The output directory location must not include any spaces in the path. Eg: /Documents/path/to/output/ is fine, but Documents/folder with spaces/to/output/ is not.

For developers

Setup development environment

conda env create -f environment.yml
conda activate podo
git clone https://github.com/monashmicroimaging/podocytes.git
cd podocytes
pip install -e .

Running python scripts directly

Run the main program:

pythonw podocytes/main.py

Compare existing CellCounter marker files to the Podo app results:

pythonw podocytes/validate.py

Quickly count the number of markers in a directory of CellCounter files:

pythonw podocytes/cellcounter_xml.py

Running PyInstaller to create macOS build

pip install -e .
pyinstaller Podo.spec -w -F -y