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Tool for labs · Fiji plugin

OrganoidsPlugin

Measures early brain organoids from images.

An ImageJ/Fiji plugin (Java) for automated analysis of early cerebral organoids from brightfield images.

Code and instructions on GitHub
EB
Diagram: an embryoid body, its outline and measurements

Features

What it does

  • Segmentation

    Finds embryoid bodies in a brightfield image.

  • Size

    The perimeter and area of each body.

  • Batch processing

    Every image in a folder in a single run.

  • CSV export

    One table for R, Python or Excel.

Installation

Build from source

You need Fiji/ImageJ 1.53 or newer and Java 8 or newer. There is no ready-made build yet — the plugin is built from the source code:

  1. Download OrganoidsPlugin.java from the repository.
  2. In Fiji, open Plugins → Compile and Run… and choose this file — the plugin compiles and starts.
  3. Choose the folder with your images and the folder for the CSV table.

Link to the lecture

Organoids from episode 1

The organoid growth data in episode 1 were measured with this plugin.

About the research

Licence

Free to use with credit to the author. The licence text from the repository README:

© 2025 Evgenii Kachkin

This plugin is provided free of charge for any use—academic, commercial, or personal. You are welcome to:

  • Use it in your own work.
  • Modify the source code.
  • Distribute copies, including your modified versions.

In return, please:

  1. Credit the original author (Evgenii Kachkin) in your documentation or code headers.
  2. Contribute back any bug fixes or enhancements via pull requests to https://github.com/puerhmaster/OrganoidsPlugin.