ca2roi 0.1.3

Calcium imaging automatic ROI selection and analysis tool

MiV-Ca2 Intensity Analysis Toolbox

A CLI tool for calcium imaging video post-processing: bleaching analysis, ROI selection, and trace extraction.

The package is developed to provide light-weight and easy-to-use tools for calcium imaging video analysis. Data can be saved in csv format for further analysis. (Please note in issue if you have desired format other than csv).

Easy installation

pip install ca2roi

Recommend python3.10+.

Easy launch

ca2roi-gui

CLI usage (for batch processing)

ca2roi <video_path> [--workspace <output_folder>]

• video_path: Path to the calcium imaging video (e.g., AVI file)
• --workspace: Output directory (default: result)

The tool will:

• Compute and save bleaching info
• Compute and overlay fluctuation map
• Allow interactive ROI selection (or load existing ROIs)
• Save ROI traces, ROI images, and ROI locations

Python-package ca2roi

import ca2roi

Project Structure

Project uses Python3 as a main backend language. It uses FastAPI to connect frontend and backend. Frontend is developed with Vue3 and TypeScript.

The tool is not yet supported to be launched in a server.

All the core source code is in src folder.

• ca2roi: Python package for analysis functions.
• frontend: Vue3 frontend for GUI development
• commands: CLI command scripts, written with Python with click.

Contribution / Development

Makefile includes useful commands for development.

Support

This project is mainly developed by @skim0119 as part of the support for Mind-in-vitro project.