https://github.com/bluebrain/atlas-alignment
Blue Brain multi-modal registration and alignment toolbox
Science Score: 54.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
○.zenodo.json file
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✓DOI references
Found 1 DOI reference(s) in README -
✓Academic publication links
Links to: zenodo.org -
✓Committers with academic emails
2 of 7 committers (28.6%) from academic institutions -
✓Institutional organization owner
Organization bluebrain has institutional domain (portal.bluebrain.epfl.ch) -
○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (14.5%) to scientific vocabulary
Keywords
Keywords from Contributors
Repository
Blue Brain multi-modal registration and alignment toolbox
Basic Info
- Host: GitHub
- Owner: BlueBrain
- License: lgpl-3.0
- Language: Python
- Default Branch: master
- Homepage: https://atlas-alignment.readthedocs.io
- Size: 6.36 MB
Statistics
- Stars: 11
- Watchers: 4
- Forks: 4
- Open Issues: 5
- Releases: 4
Topics
Metadata Files
README.md
Atlas Alignment
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Atlas Alignment is a toolbox to perform multimodal image registration. It includes both traditional and supervised deep learning models.
This project originated from the Blue Brain Project efforts on aligning mouse brain atlases obtained with ISH gene expression and Nissl stains.
Official documentation
All details related to installation and logic are described in the official documentation.
Installation
Installation Requirements
Some of the functionalities of atlalign depend on the TensorFlow implementation
of the Learned Perceptual Image Patch Similarity (LPIPS). Unfortunately, the
package is not available on PyPI and must be installed manually as follows
for full functionality.
shell script
pip install git+http://github.com/alexlee-gk/lpips-tensorflow.git#egg=lpips_tf
You can now move on to installing the actual atlalign package!
Installation from PyPI
The atlalign package can be easily installed from PyPI.
shell script
pip install atlalign
Installation from source
As an alternative to installing from PyPI, if you want to try the latest version
you can also install from source.
shell script
pip install git+https://github.com/BlueBrain/atlas_alignment#egg=atlalign
Installation for development
If you want a dev install, you should install the latest version from source with
all the extra requirements for running test and generating docs.
shell script
git clone https://github.com/BlueBrain/atlas_alignment
cd atlas_alignment
pip install -e .[dev,docs]
Examples
You can find multiple examples in the documentation. Specifically, make sure to read the Building Blocks section of the docs to understand the basics.
Data
You can find example data on Zenodo.
Unzip the files to ~/.atlalign/ folder so that you can use the data.py module
without manual specification of paths.
Allen Brain Institute Database
You can find and download ISH data from Allen Brain Institute thanks to Atlas Download Tools repository.
Funding & Acknowledgment
This project was supported by funding to the Blue Brain Project, a research center of the Ecole polytechnique fédérale de Lausanne, from the Swiss government's ETH Board of the Swiss Federal Institutes of Technology.
COPYRIGHT (c) 2021-2022 Blue Brain Project/EPFL
Owner
- Name: The Blue Brain Project
- Login: BlueBrain
- Kind: organization
- Email: bbp.opensource@epfl.ch
- Location: Geneva, Switzerland
- Website: https://portal.bluebrain.epfl.ch/
- Repositories: 226
- Profile: https://github.com/BlueBrain
Open Source Software produced and used by the Blue Brain Project
GitHub Events
Total
- Fork event: 1
Last Year
- Fork event: 1
Committers
Last synced: 7 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Francesco Casalegno | f****o@g****m | 21 |
| Jan Krepl | j****l@y****m | 12 |
| EmilieDel | 4****l | 8 |
| Stanislav Schmidt | s****t@e****h | 2 |
| bbpgithubaudit | 8****t | 1 |
| Stanislav Schmidt | S****v | 1 |
| Matthias Wolf | m****f@e****h | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 13
- Total pull requests: 32
- Average time to close issues: about 1 month
- Average time to close pull requests: 5 days
- Total issue authors: 5
- Total pull request authors: 7
- Average comments per issue: 1.0
- Average comments per pull request: 0.69
- Merged pull requests: 28
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 0
- Pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- jankrepl (5)
- EmilieDel (3)
- FrancescoCasalegno (3)
- dkeller9 (1)
- pafonta (1)
Pull Request Authors
- FrancescoCasalegno (12)
- EmilieDel (9)
- jankrepl (7)
- Stannislav (2)
- GianlucaFicarelli (1)
- matz-e (1)
- bbpgithubaudit (1)
Top Labels
Issue Labels
Pull Request Labels
Dependencies
- actions/checkout v2 composite
- actions/setup-python v2 composite