Range Expansion Image Analysis in Fiji

Preprocessing routines for the python based "Range Expansion Analysis" program.

I personally find that programming user input in Python is quite difficult. In contrast, user input is extremely easy to accept in Fiji. Consequently, for our imperfect biological data, I use Fiji to preprocess the images and create binary masks. The masks are then analyzed in the Range Expansion Python package.

Installation

Clone this git repository into the "plugins" folder of your Fiji installation. So, just use

cd PATH/TO/FIJI/plugins/
git clone https://github.com/btweinstein/range_expansion_analysis_fiji.git

Usage

0. Extract all images using the bioformats plugin to a folder called "tif"
1. Test