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Since October 1, 2024, this version is no longer actively maintained and will not be updated. New plugins and plugin updates will continue to be listed.

brainglobe-segmentation

brainglobe-segmentation

Segmentation of anatomical structures in a common coordinate space

Python Version PyPI Wheel Development Status Tests codecov Code style: black Twitter

Segmentation of anatomical structures in a common coordinate space

Installation

PyPI

pip install brainglobe-segmentation

conda

conda install -c conda-forge brainglobe-segmentation

N.B. Your data will need to be registered to an anatomical atlas first.

Usage

See user guide.

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.

Citing brainglobe-segmentation

If you find brainglobe-segmentation useful, and use it in your research, please let us know and also cite the paper:

Tyson, A. L., Vélez-Fort, M., Rousseau, C. V., Cossell, L., Tsitoura, C., Lenzi, S. C., Obenhaus, H. A., Claudi, F., Branco, T., Margrie, T. W. (2022). Accurate determination of marker location within whole-brain microscopy images. Scientific Reports, 12, 867 doi.org/10.1038/s41598-021-04676-9

Version:

  • 1.2.6

Last updated:

  • 17 September 2024

First released:

  • 06 November 2023

License:

Supported data:

  • Information not submitted

Plugin type:

GitHub activity:

  • Stars: 28
  • Forks: 10
  • Issues + PRs: 11

Python versions supported:

Operating system:

Requirements:

  • brainglobe-atlasapi>=2.0.1
  • brainglobe-napari-io>=0.3.0
  • brainglobe-utils>=0.5.0
  • napari>=0.4.5
  • numpy
  • pandas[hdf5]
  • qtpy
  • scikit-image
  • scipy
  • tifffile