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https://github.com/brainglobe/brainreg-napari

Automated 3D brain registration in napari with support for multiple species and atlases.

https://github.com/brainglobe/brainreg-napari

Science Score: 51.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ○
    codemeta.json file
  • ○
    .zenodo.json file
  • ✓
    DOI references
    Found 8 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: nature.com
  • ✓
    Committers with academic emails
    1 of 6 committers (16.7%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (15.3%) to scientific vocabulary

Keywords

anatomy atlases brain microscopy napari neuroscience registration

Keywords from Contributors

imaging cell-detection image-analysis neuroanatomy napari-plugin brainreg cellfinder loading nifti saving
Last synced: 4 months ago · JSON representation ·

Repository

Automated 3D brain registration in napari with support for multiple species and atlases.

Basic Info
Statistics
  • Stars: 16
  • Watchers: 4
  • Forks: 6
  • Open Issues: 0
  • Releases: 4
Archived
Topics
anatomy atlases brain microscopy napari neuroscience registration
Created over 4 years ago · Last pushed about 2 years ago
Metadata Files
Readme License Citation

README.md

THIS PACKAGE HAS MOVED

As of the release of brainreg version 1.0.0, brainreg-napari is now a part of 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 or repository. 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.

Python Version PyPI Wheel Development Status Code style: black codecov

brainreg-napari

Napari plugin to run brainreg, developed by Stephen Lenzi.

Installation

bash pip install brainreg-napari

Usage

Documentation and tutorials for the plugin can be found here.

For segmentation of bulk structures in 3D space (e.g. injection sites, Neuropixels probes), please see 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 or by raising an issue.

Details

brainreg is an update to amap (itself a port of the original Java software) to include multiple registration backends, and to support the many atlases provided by bg-atlasapi.

The aim of brainreg is to register the template brain (e.g. from the Allen Reference 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. reg_process Overview of the registration process

Contributing

Contributions to brainreg-napari are more than welcome. Please see the developers guide.

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

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)!

Owner

  • Name: BrainGlobe
  • Login: brainglobe
  • Kind: organization
  • Location: London/Munich

Open python tools for morphological analyses in systems neuroscience

Citation (CITATION.CFF) 

cff-version: 1.2.0
message: If you use this software, please cite it using these metadata.
title: brainreg-napari
authors:
- family-names: "Tyson"
  given-names: "A."
- family-names: "Vélez-Fort"
  given-names: "M."
- family-names: "Rousseau"
  given-names: "C."
- family-names: "Cossell"
  given-names: "L."
- family-names: "Tsitoura"
  given-names: " C."
- family-names: "Lenzi"
  given-names: " S."
- family-names: "Obenhaus"
  given-names: "H."
- family-names: "Claudi"
  given-names: "F."
- family-names: "Branco"
  given-names: "T."
- family-names: "Margrie"
  given-names: "T."
url: https://github.com/brainglobe/brainreg-napari
preferred-citation:
    type: article
    title: Accurate determination of marker location within whole-brain microscopy images
    journal: Scientific Reports
    volume: 12
    pages: 867
    doi: 10.1038/s41598-021-04676-9
    year: 2022
    date-published: 2022-01-18
    authors:
      - family-names: "Tyson"
        given-names: "A."
      - family-names: "Vélez-Fort"
        given-names: "M."
      - family-names: "Rousseau"
        given-names: "C."
      - family-names: "Cossell"
        given-names: "L."
      - family-names: "Tsitoura"
        given-names: " C."
      - family-names: "Lenzi"
        given-names: "S."
      - family-names: "Obenhaus"
        given-names: "H."
      - family-names: "Claudi"
        given-names: "F."
      - family-names: "Branco"
        given-names: "T."
      - family-names: "Margrie"
        given-names: "T."
references:
  - type: article
    title: AMAP is a validated pipeline for registration and segmentation of high-resolution mouse brain data
    journal: Nature Communications
    volume: 7
    pages: 1-9
    doi: 10.1038/ncomms11879
    year: 2016
    date-published: 2016-07-07
    authors:
      - family-names: "Niedworok"
        given-names: "C."
      - family-names: "Brown"
        given-names: "A."
      - family-names: "Jorge"
        given-names: "M."
      - family-names: "Osten"
        given-names: "P."
      - family-names: "Ourselin"
        given-names: "S."
      - family-names: "Modat"
        given-names: "M."
      - family-names: "Margrie"
        given-names: "T."
references:
  - type: article
    title: BrainGlobe Atlas API a common interface for neuroanatomical atlases
    journal: Journal of Open Source Software
    volume: 5
    pages: 2668
    doi: 10.21105/joss.02668
    year: 2020
    date-published: 2020-09-04
    authors:
      - family-names: "Claudi"
        given-names: "F."
      - family-names: "Petrucco"
        given-names: "L."
      - family-names: "Tyson"
        given-names: "A."
      - family-names: "Branco"
        given-names: "T."
      - family-names: "Margrie"
        given-names: "T."
      - family-names: "Portugues"
        given-names: "R."

GitHub Events

Total
  • Watch event: 1
Last Year
  • Watch event: 1

Committers

Last synced: almost 3 years ago

All Time
  • Total Commits: 82
  • Total Committers: 6
  • Avg Commits per committer: 13.667
  • Development Distribution Score (DDS): 0.634
Top Committers
Name Email Commits
David Stansby d****y@g****m 30
stephen s****i@g****m 29
Adam Tyson c****e@a****m 20
Adam Tyson a****n@u****k 1
Justin Kiggins j****s@g****m 1
Simão Bolota 9****l@u****m 1
Committer Domains (Top 20 + Academic)
ucl.ac.uk: 1 adamltyson.com: 1

Packages

  • Total packages: 2
  • Total downloads:
    • pypi 93 last-month
  • Total dependent packages: 2
    (may contain duplicates)
  • Total dependent repositories: 0
    (may contain duplicates)
  • Total versions: 17
  • Total maintainers: 1
proxy.golang.org: github.com/brainglobe/brainreg-napari
  • Versions: 5
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent packages count: 9.0%
Average: 9.6%
Dependent repos count: 10.2%
Last synced: 5 months ago
pypi.org: brainreg-napari

Multi-atlas whole-brain microscopy registration

  • Versions: 12
  • Dependent Packages: 2
  • Dependent Repositories: 0
  • Downloads: 93 Last month
Rankings
Dependent packages count: 3.1%
Downloads: 21.0%
Average: 30.7%
Dependent repos count: 67.9%
Maintainers (1)
adamltyson
Last synced: 5 months ago

Dependencies

.github/workflows/plugin_preview.yml actions
  • actions/checkout v2 composite
  • chanzuckerberg/napari-hub-preview-action v0.1 composite
.github/workflows/test_and_deploy.yml actions
  • GabrielBB/xvfb-action v1 composite
  • actions/checkout v3 composite
  • actions/download-artifact v3 composite
  • actions/setup-python v4 composite
  • codecov/codecov-action v2 composite
  • neuroinformatics-unit/actions/build_sdist_wheels main composite
  • neuroinformatics-unit/actions/check_manifest v1.2.0 composite
  • neuroinformatics-unit/actions/lint v1.2.0 composite
  • pypa/gh-action-pypi-publish v1.5.0 composite
  • tlambert03/setup-qt-libs v1 composite