Getting started with diff_classifier

Pip install

Currently, diff_classifier is not on PyPi, but the next version of diff_classifer will be uploaded to PyPi.

Git clone

Users can clone a copy of diff_classifier with the command

git clone https://github.com/ccurtis7/diff_classifier.git

Running the setup file will install needed dependencies, including Fiji:

python3 setup.py develop

You can install diff_classifier from the Github repository. This will install diff_classifier and its Python dependencies. Users will also need to have downloaded Fiji in order to implement the Trackmate functionality.

Checking Fiji installation

The tracking portion of diff_classifier relies on the Fiji plugin Trackmate. The setup.py file should do this automatically.

Otherwise, users can install Fiji manually at here. An example installation using the shell:

wget https://downloads.imagej.net/fiji/latest/fiji-linux64.zip
unzip fiji-linux64.zip

When using the diff_classifier.imagej module, default behavior looks for Fiji at ~/Fiji.app/ImageJ-linux64.exe for Linux users or /Applications/Fiji.app/Contents/MacOS/ImageJ-macosx.exe for Apple users. Otherwise, users must manually specify the location using the fiji_bin variable.

Note: Python2/Python3 compatibility

Diff_classifier is not guaranteed to run on Python2.

Examples

You can find example implementations of diff_classifier in the notebooks directory on Github.