https://github.com/brainglobe/cellfinder

Automated 3D cell detection in very large images
https://github.com/brainglobe/cellfinder

cell-detection deep-learning image-analysis imaging microscopy neuroanatomy neuroscience python

Last synced: 5 months ago
JSON representation

Automated 3D cell detection in very large images

• Host: GitHub
• URL: https://github.com/brainglobe/cellfinder
• Owner: brainglobe
• License: bsd-3-clause
• Created: 2020-01-17T14:14:12.000Z (over 6 years ago)
• Default Branch: main
• Last Pushed: 2026-01-22T18:27:51.000Z (5 months ago)
• Last Synced: 2026-01-23T10:31:31.897Z (5 months ago)
• Topics: cell-detection, deep-learning, image-analysis, imaging, microscopy, neuroanatomy, neuroscience, python
• Language: Python
• Homepage: https://brainglobe.info/documentation/cellfinder/index.html
• Size: 167 MB
• Stars: 223
• Watchers: 15
• Forks: 67
• Open Issues: 67
• Metadata Files:
  • Readme: README.md
  • License: LICENSE
  • Citation: CITATION.cff

Awesome Lists containing this project

• awesome-biological-image-analysis - Cellfinder - Automated 3D cell detection and registration of whole-brain images. (Neuroscience)

README

          
[![Python Version](https://img.shields.io/pypi/pyversions/cellfinder.svg)](https://pypi.org/project/cellfinder)

[![PyPI](https://img.shields.io/pypi/v/cellfinder.svg)](https://pypi.org/project/cellfinder)

[![Anaconda version](https://anaconda.org/conda-forge/cellfinder/badges/version.svg)](https://anaconda.org/conda-forge/cellfinder)

[![Napari hub](https://img.shields.io/endpoint?url=https://npe2api-git-add-shields-napari.vercel.app/api/shields/cellfinder)](https://napari-hub.org/plugins/cellfinder.html)

[![PyPI Downloads](https://pepy.tech/badge/cellfinder)](https://pepy.tech/project/cellfinder)

[![Wheel](https://img.shields.io/pypi/wheel/cellfinder.svg)](https://pypi.org/project/cellfinder)

[![Development Status](https://img.shields.io/pypi/status/cellfinder.svg)](https://github.com/brainglobe/cellfinder)

[![Tests](https://img.shields.io/github/actions/workflow/status/brainglobe/cellfinder/test_and_deploy.yml?branch=main)](https://github.com/brainglobe/cellfinder/actions)

[![codecov](https://codecov.io/gh/brainglobe/cellfinder/branch/main/graph/badge.svg?token=nx1lhNI7ox)](https://codecov.io/gh/brainglobe/cellfinder)

[![Code style: Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/format.json)](https://github.com/astral-sh/ruff)[![Imports: isort](https://img.shields.io/badge/%20imports-isort-%231674b1?style=flat&labelColor=ef8336)](https://pycqa.github.io/isort/)

[![pre-commit](https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit&logoColor=white)](https://github.com/pre-commit/pre-commit)

[![Contributions](https://img.shields.io/badge/Contributions-Welcome-brightgreen.svg)](https://brainglobe.info/community/developers/index.html)

[![image.sc forum](https://img.shields.io/badge/dynamic/json.svg?label=forum&url=https%3A%2F%2Fforum.image.sc%2Ftags%2Fbrainglobe.json&query=%24.topic_list.tags.0.topic_count&colorB=brightgreen&suffix=%20topics&logo=data:image/png;base64,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)](https://forum.image.sc/tag/brainglobe)

[![Bluesky](https://img.shields.io/badge/Bluesky-0285FF?logo=bluesky&logoColor=fff)](https://bsky.app/profile/brainglobe.info)

[![Mastodon](https://img.shields.io/badge/Mastodon-6364FF?logo=mastodon&logoColor=fff)](https://mastodon.online/@brainglobe)

# cellfinder

cellfinder is software for automated 3D cell detection in very large 3D images (e.g., serial two-photon or lightsheet volumes of whole mouse brains).

There are three different ways to interact and use it, each with different user interfaces and objectives in mind.

For more details, head over to [the documentation website](https://brainglobe.info/documentation/cellfinder/index.html).

At a glance:

- There is a command-line interface called [brainmapper](https://brainglobe.info/documentation/brainglobe-workflows/brainmapper/index.html) that integrates [with `brainreg`](https://github.com/brainglobe/brainreg) for automated cell detection and classification. You can install it through [`brainglobe-workflows`](https://brainglobe.info/documentation/brainglobe-workflows/index.html).

- There is a [napari plugin](https://brainglobe.info/documentation/cellfinder/user-guide/napari-plugin/index.html) for interacting graphically with the cellfinder tool.

- There is a [Python API](https://brainglobe.info/documentation/cellfinder/user-guide/cellfinder-core.html) to allow users to integrate BrainGlobe tools into their custom workflows.

## Installation

You can find [the installation instructions](https://brainglobe.info/documentation/cellfinder/installation.html#installation) on the BrainGlobe website, which will go into more detail about the installation process if you want to minimise your installation to suit your needs.

However, we recommend that users install `cellfinder` either through installing BrainGlobe version 1, or (if you also want the command-line interface) installing `brainglobe-workflows`.

```bash

# If you want to install all BrainGlobe tools, including cellfinder, in a consistent manner with one command:

pip install brainglobe>=1.0.0

# If you want to install the brainmapper CLI tool as well:

pip install brainglobe-workflows>=1.0.0

```

If you only want the `cellfinder` package by itself, you can `pip install` it alone:

```bash

pip install cellfinder>=1.0.0

```

Be sure to specify a version greater than version `v1.0.0` - prior to this version the `cellfinder` package had a very different structure that is incompatible with BrainGlobe version 1 and the other tools in the BrainGlobe suite.

See [our blog posts](https://brainglobe.info/blog/) for more information on the release of BrainGlobe version 1.

## Seeking help or contributing

We are always happy to help users of our tools, and welcome any contributions. If you would like to get in contact with us for any reason, please see the [contact page of our website](https://brainglobe.info/contact.html).

## Citation

If you find this package useful, and use it in your research, please cite the following paper:

> Tyson, A. L., Rousseau, C. V., Niedworok, C. J., Keshavarzi, S., Tsitoura, C., Cossell, L., Strom, M. and Margrie, T. W. (2021) “A deep learning algorithm for 3D cell detection in whole mouse brain image datasets’ PLOS Computational Biology, 17(5), e1009074

[https://doi.org/10.1371/journal.pcbi.1009074](https://doi.org/10.1371/journal.pcbi.1009074)

**If you use this, or any other tools in the brainglobe suite, please

 [let us know](https://brainglobe.info/contact.html), and

 we'd be happy to promote your paper/talk etc.**