This package is deprecated!
Please use brainglobe-segmentation instead.
The old README can be found below.
brainreg-segment
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).
brainreg-segment and brainreg were developed by Adam Tyson and Charly Rousseau in the Margrie Lab, based on aMAP by Christian Niedworok. The work was generously supported by the Sainsbury Wellcome Centre.
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.
Contributing
Contributions are very welcome. Please see the developers guide.
Citing brainreg-segment
If you find brainreg-segment 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
3 maintainers
Metadata
3 maintainers
Release files for brainreg-segment 0.2.20
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| brainreg-segment-0.2.20.tar.gz | 13.7 MB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| brainreg_segment-0.2.20-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 13.7 MB
Release files / brainreg-segment-0.2.20.tar.gz
| Download URL | brainreg-segment-0.2.20.tar.gz |
|---|---|
| Size | 13.7 MB |
| Tags | Source |
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Release files / brainreg_segment-0.2.20-py3-none-any.whl
| Download URL | brainreg_segment-0.2.20-py3-none-any.whl |
|---|---|
| Size | 28.7 kB |
| Tags | Python 3 |
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No |
| Uploaded via |
twine/4.0.2 CPython/3.10.12
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