Brian's Image Processing Toolbox

This is home to a suite of scripts for image processing using python & imageJ(Fiji). The repo hosts tutorials for:

• image registration
• basic ImageJ utilities
• videography analysis with DeepLabCut

Quickstart

Follow the instructions below to configure a Python environment for the desired project.

1. Install an Anaconda distribution for your operating system.
2. Git clone the repo
3. In the Anaconda terminal, cd to the example project
4. conda env create -f environment.yml
5. conda activate <env>
6. ipython kernel install --user --name <kernel>
7. Open Jupyter Notebook, navigate to envs, upload the .ipynb file from the project and run it on the new kernel.

Follow the instructions below to set up Fiji image-processing software.

1. Install the Fiji application for your operating system.
2. To follow the tutorials, install any auxiliary plugins by navigating to Help > Update... > Manage Update Sites. Alternatively, navigate to the Fiji.app directory and copy/paste the .jar file into the plugins folder.