Automated 3D cell detection in large microscopy images


Keywords
cell-detection, deep-learning, image-analysis, imaging, microscopy, neuroanatomy, neuroscience, python, registration
License
BSD-3-Clause
Install
pip install cellfinder==1.1.1

Documentation

Python Version PyPI Downloads Wheel Development Status Tests codecov Code style: black Imports: isort pre-commit Contributions Twitter

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.

At a glance:

Installation

You can find the installation instructions 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:

pip install cellfinder>=1.0.0 # If you just want the napari plugin and Python API
pip install brainglobe>=1.0.0 # If you want to install all BrainGlobe tools, including cellfinder, in a consistent manner with one command
pip install brainglobe-workflows>=1.0.0 # If you want to include the CLI

Contributing

If you have encountered a bug whilst using cellfinder, please open an issue on GitHub.

If you are interested in contributing to cellfinder (thank you!) - please head over to our developer documentation.