ichapy
An tool for analysis of immunohistochemical images that using Python bindings for OpenCV (computer vision) library to extract quantitative information from microscopy data. Given a set of stained tissue images, this software allows an automated and efficient extraction of data on colocalization, toplogy, and volume of cell clusters of different phenotype (e.g., distribution of B-Cells in a slice of cardiac tissue). While originally intended to be used in the context of heart tissue, this tool may be used for arbitrary physiological images.
Motivation
The contents of this repository reflect a subset of tools salvaged from prior use in research I contributed to in Cardiac Immunology. While that project has been deprecated, I hope to eventually repurpose this tool in a manner that is generalized in applicability, safe, and easy to use for anyone who is interested in learning more about medical image data.
Tests
Unit tests are included in the test.py file.
> pip install pytest # use the installation manager of your choosing
> pytest test.py
Dataset
A new, unrestricted dataset is now included (source). The dataset originally used to calibrate this program is not available for reasons relating to patient privacy.
Future
- Interface ideas: data querying language, graphic user interface, command line interface
- Fix distance method to slide class in image processing module
- Misc custodial work (addressing several todos)