Version:

  • 0.2.13

Release date:

  • 26 August 2021

First released:

  • 26 August 2020

License:

  • BSD-3-Clause

GitHub activity:

  • Stars: 10
  • Forks: 4
  • Issues + PRs: 13

Python versions supported:

  • >=3.7

Operating system:

  • Microsoft :: Windows :: Windows 10
  • POSIX :: Linux

Requirements:

  • numpy
  • tables
  • scikit-image
  • pandas
  • napari (>=0.4.5)
  • napari-plugin-engine (>=0.1.4)
  • imlib (>=0.0.26)
  • dask (>=2.15.0)
  • imio
  • brainglobe-napari-io

brainreg-segment

Manual segmentation of 3D brain structures in a common anatomical space

Authors:

  • Adam Tyson, Horst Obenhaus

Source code:

Authors:

  • Adam Tyson, Horst Obenhaus

Source code:

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

Segmentation of 1/2/3D brain structures in a common anatomical space

brainreg-segment is a companion to brainreg allowing manual segmentation of regions/objects within the brain (e.g. injection sites, probes etc.) allowing for automated analysis of brain region distribution, and visualisation (e.g. in brainrender).

Installation

brainreg-segment comes bundled with brainreg, so see the brainreg installation instructions.

brainreg-segment can be installed on it's own (pip install brainreg-segment), but you will need to register your data with brainreg first.

Usage

See user guide.

If you have any questions, head over to the image.sc forum.

Citing brainreg-segment

If you find brainreg-segment useful, and use it in your research, please let us know and also cite the preprint:

Tyson, A. L., Vélez-Fort, M., Rousseau, C. V., Cossell, L., Tsitoura, C., Obenhaus, H. A., Claudi, F., Lenzi, S. C., Branco, T., Margrie, T. W. (2021) “Tools for accurate post hoc determination of marker location within whole-brain microscopy images’ bioRxiv, doi.org/10.1101/2021.05.21.445133

Version:

  • 0.2.13

Release date:

  • 26 August 2021

First released:

  • 26 August 2020

License:

  • BSD-3-Clause

GitHub activity:

  • Stars: 10
  • Forks: 4
  • Issues + PRs: 13

Python versions supported:

  • >=3.7

Operating system:

  • Microsoft :: Windows :: Windows 10
  • POSIX :: Linux

Requirements:

  • numpy
  • tables
  • scikit-image
  • pandas
  • napari (>=0.4.5)
  • napari-plugin-engine (>=0.1.4)
  • imlib (>=0.0.26)
  • dask (>=2.15.0)
  • imio
  • brainglobe-napari-io

Version:

  • 0.2.13

Release date:

  • 26 August 2021

First released:

  • 26 August 2020

License:

  • BSD-3-Clause

GitHub activity:

  • Stars: 10
  • Forks: 4
  • Issues + PRs: 13

Python versions supported:

  • >=3.7

Operating system:

  • Microsoft :: Windows :: Windows 10
  • POSIX :: Linux

Requirements:

  • numpy
  • tables
  • scikit-image
  • pandas
  • napari (>=0.4.5)
  • napari-plugin-engine (>=0.1.4)
  • imlib (>=0.0.26)
  • dask (>=2.15.0)
  • imio
  • brainglobe-napari-io

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