| Name | brainreg-napari JSON |
| Version |
0.1.3
JSON |
| download |
| home_page | |
| Summary | Multi-atlas whole-brain microscopy registration |
| upload_time | 2023-11-06 12:48:54 |
| maintainer | |
| docs_url | None |
| author | |
| requires_python | >=3.9.0 |
| license | BSD-3-Clause |
| keywords |
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| VCS |
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| bugtrack_url |
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| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
# THIS PACKAGE HAS MOVED
As of the release of `brainreg` version `1.0.0`, `brainreg-napari` is now a part of [`brainreg`](https://github.com/brainglobe/brainreg).
If you are looking to install the `brainglobe-napari` plugin, please install `brainreg` with it's optional `napari` dependency as detailed in the installation instructions on the [website](https://brainglobe.info/documentation/brainreg/index.html) or [repository](https://github.com/brainglobe/brainreg).
Before you update, you should also remove the old `brainreg-napari` package from your environment using either
```bash
python -m pip uninstall brainreg-napari # If you installed via pip
conda remove brainreg-napari # If you installed via conda
```
You can find the old documentation and installation instructions below, but please note this version of the package should be considered unmaintained.
---
[](https://pypi.org/project/brainreg-napari)
[](https://pypi.org/project/brainreg-napari)
[](https://pypi.org/project/brainreg-napari)
[](https://github.com/brainglobe/brainreg-napari)
[](https://github.com/python/black)
[](https://codecov.io/gh/brainglobe/brainreg-napari)
# brainreg-napari
Napari plugin to run [brainreg](https://github.com/brainglobe/brainreg),
developed by [Stephen Lenzi](https://github.com/stephenlenzi).
## Installation
```bash
pip install brainreg-napari
```
## Usage
Documentation and tutorials for the plugin can be found [here](https://brainglobe.info/documentation/brainreg/index.html).
For segmentation of bulk structures in 3D space
(e.g. injection sites, Neuropixels probes), please see
[brainreg-segment](https://github.com/brainglobe/brainreg-segment).
This software is at a very early stage, and was written with our data in mind.
Over time we hope to support other data types/formats. If you have any issues, please get in touch [on the forum](https://forum.image.sc/tag/brainglobe) or by
[raising an issue](https://github.com/brainglobe/brainreg/issues).
## Details
brainreg is an update to
[amap](https://github.com/SainsburyWellcomeCentre/amap-python) (itself a port
of the [original Java software](https://www.nature.com/articles/ncomms11879))
to include multiple registration backends, and to support the many atlases
provided by [bg-atlasapi](https://github.com/brainglobe/bg-atlasapi).
The aim of brainreg is to register the template brain
(e.g. from the [Allen Reference Atlas](https://mouse.brain-map.org/static/atlas))
to the sample image. Once this is complete, any other image in the template
space can be aligned with the sample (such as region annotations, for
segmentation of the sample image). The template to sample transformation
can also be inverted, allowing sample images to be aligned in a common
coordinate space.
To do this, the template and sample images are filtered, and then registered in
a three step process (reorientation, affine registration, and freeform
registration.) The resulting transform from template to standard space is then
applied to the atlas.
Full details of the process are in the
[original aMAP paper](https://www.nature.com/articles/ncomms11879).
**Overview of the registration process**
## Contributing
Contributions to brainreg-napari are more than welcome. Please see the [developers guide](https://brainglobe.info/developers/index.html).
### Citing brainreg
If you find brainreg 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](https://doi.org/10.1038/s41598-021-04676-9)
Please also cite aMAP (the original pipeline from which this software is based):
>Niedworok, C.J., Brown, A.P.Y., Jorge Cardoso, M., Osten, P., Ourselin, S., Modat, M. and Margrie, T.W., (2016). AMAP is a validated pipeline for registration and segmentation of high-resolution mouse brain data. Nature Communications. 7, 1–9. https://doi.org/10.1038/ncomms11879
Lastly, if you can, please cite the BrainGlobe Atlas API that provided the atlas:
>Claudi, F., Petrucco, L., Tyson, A. L., Branco, T., Margrie, T. W. and Portugues, R. (2020). BrainGlobe Atlas API: a common interface for neuroanatomical atlases. Journal of Open Source Software, 5(54), 2668, https://doi.org/10.21105/joss.02668
**Don't forget to cite the developers of the atlas that you used (e.g. the Allen Brain Atlas)!**
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"description": "# THIS PACKAGE HAS MOVED\n\nAs of the release of `brainreg` version `1.0.0`, `brainreg-napari` is now a part of [`brainreg`](https://github.com/brainglobe/brainreg).\nIf you are looking to install the `brainglobe-napari` plugin, please install `brainreg` with it's optional `napari` dependency as detailed in the installation instructions on the [website](https://brainglobe.info/documentation/brainreg/index.html) or [repository](https://github.com/brainglobe/brainreg).\nBefore you update, you should also remove the old `brainreg-napari` package from your environment using either\n\n```bash\npython -m pip uninstall brainreg-napari # If you installed via pip\nconda remove brainreg-napari # If you installed via conda\n```\n\nYou can find the old documentation and installation instructions below, but please note this version of the package should be considered unmaintained.\n\n---\n\n[](https://pypi.org/project/brainreg-napari)\n[](https://pypi.org/project/brainreg-napari)\n[](https://pypi.org/project/brainreg-napari)\n[](https://github.com/brainglobe/brainreg-napari)\n[](https://github.com/python/black)\n[](https://codecov.io/gh/brainglobe/brainreg-napari)\n\n# brainreg-napari\nNapari plugin to run [brainreg](https://github.com/brainglobe/brainreg),\ndeveloped by [Stephen Lenzi](https://github.com/stephenlenzi).\n\n## Installation\n```bash\npip install brainreg-napari\n```\n\n## Usage\nDocumentation and tutorials for the plugin can be found [here](https://brainglobe.info/documentation/brainreg/index.html).\n\nFor segmentation of bulk structures in 3D space\n(e.g. injection sites, Neuropixels probes), please see\n[brainreg-segment](https://github.com/brainglobe/brainreg-segment).\n\nThis software is at a very early stage, and was written with our data in mind.\nOver time we hope to support other data types/formats. If you have any issues, please get in touch [on the forum](https://forum.image.sc/tag/brainglobe) or by\n[raising an issue](https://github.com/brainglobe/brainreg/issues).\n\n## Details\nbrainreg is an update to\n[amap](https://github.com/SainsburyWellcomeCentre/amap-python) (itself a port\nof the [original Java software](https://www.nature.com/articles/ncomms11879))\nto include multiple registration backends, and to support the many atlases\nprovided by [bg-atlasapi](https://github.com/brainglobe/bg-atlasapi).\n\nThe aim of brainreg is to register the template brain\n (e.g. from the [Allen Reference Atlas](https://mouse.brain-map.org/static/atlas))\n to the sample image. Once this is complete, any other image in the template\n space can be aligned with the sample (such as region annotations, for\n segmentation of the sample image). The template to sample transformation\n can also be inverted, allowing sample images to be aligned in a common\n coordinate space.\n\nTo do this, the template and sample images are filtered, and then registered in\na three step process (reorientation, affine registration, and freeform\nregistration.) The resulting transform from template to standard space is then\napplied to the atlas.\n\nFull details of the process are in the\n[original aMAP paper](https://www.nature.com/articles/ncomms11879).\n\n**Overview of the registration process**\n\n## Contributing\nContributions to brainreg-napari are more than welcome. Please see the [developers guide](https://brainglobe.info/developers/index.html).\n\n### Citing brainreg\n\nIf you find brainreg useful, and use it in your research, please let us know and also cite the paper:\n\n> 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](https://doi.org/10.1038/s41598-021-04676-9)\n\nPlease also cite aMAP (the original pipeline from which this software is based):\n\n>Niedworok, C.J., Brown, A.P.Y., Jorge Cardoso, M., Osten, P., Ourselin, S., Modat, M. and Margrie, T.W., (2016). AMAP is a validated pipeline for registration and segmentation of high-resolution mouse brain data. Nature Communications. 7, 1\u20139. https://doi.org/10.1038/ncomms11879\n\nLastly, if you can, please cite the BrainGlobe Atlas API that provided the atlas:\n\n>Claudi, F., Petrucco, L., Tyson, A. L., Branco, T., Margrie, T. W. and Portugues, R. (2020). BrainGlobe Atlas API: a common interface for neuroanatomical atlases. Journal of Open Source Software, 5(54), 2668, https://doi.org/10.21105/joss.02668\n\n**Don't forget to cite the developers of the atlas that you used (e.g. the Allen Brain Atlas)!**\n",
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