Semi-automated processing of autoradiography (ARG) images from mouse brain tissue. This project includes a Napari-based user interface where ARG slides can be preprocessed and registered to Allen Brain Atlas regions.
The user manual is found here.
We use the mamba or conda package manager. If there are any changes in the environment.yml, please update your environment using one of the following lines:
mamba env update -f environment.yml --prune
conda env update -f environment.yml --prune
Activate the environment:
mamba activate mouse-brain-alignment-tool
We use PyInstaller *.spec files for the build process. In the local environment pip install pyinstaller.
pyinstaller preprocess.spec
pyinstaller analyze.spec
This will generate two single-file executables preprocess-0.2.2.exe and analyze-0.2.2.exe. Released builds are found in here.
Funding for this project was provided by the Integrated Services for Infectious Disease Outbreak Research (ISIDORe) project of Euro-BioImaging.