ImageJ-Lysosome-Transport-Density

ImageJ Jython Pipeline to calculate Lysosome Transport Densities

Prerequisites

Python 3.10.0, with Pandas module installed If you do not have pandas already, install it using python -m pip install pandas

Installation and setup

1. Clone the repository
2. Open Fiji ImageJ
3. Drag and drop the Lysosome_transport_density_pipeline.py file into the window
4. Modify the settings dict with your source folder path, thresholding settings, and complete filepath to the lysosome_density_csv_merge_script.py
5. Click Run