Segmentation and characterisation of cardiac tissue
Sample routines in a python package
Assumes data comes in imaris format.
Using miniconda
conda create --name napari python=3.7 ipython
conda activate napari
pip install git+https://github.com/richardbeare/calciumcharacterisation.git@master
pip install napari[all]
- Viewer for single channel time series:
iv imarisfile
- characterisation
calcium folder_with_imarisfiles
- Add pyramid levels
pyramid --imarispath file --resolution 0