richardbeare / calciumcharacterisation

Segmentation and characterisation of cardiac tissue

calciumcharacterisation

Segmentation and characterisation of cardiac tissue

Sample routines in a python package

Assumes data comes in imaris format.

Installation

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]

Command line tools

1. Viewer for single channel time series:

iv imarisfile

1. characterisation

calcium folder_with_imarisfiles

1. Add pyramid levels

pyramid --imarispath file --resolution 0