https://github.com/alleninstitute/asap-modules
Shared repo for EM connectomics and Array Tomography render based image processing modules
Science Score: 36.0%
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
Found .zenodo.json file -
○DOI references
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○Academic publication links
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✓Committers with academic emails
7 of 12 committers (58.3%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (14.0%) to scientific vocabulary
Repository
Shared repo for EM connectomics and Array Tomography render based image processing modules
Basic Info
- Host: GitHub
- Owner: AllenInstitute
- License: bsd-2-clause
- Language: Python
- Default Branch: master
- Homepage: https://asap-modules.readthedocs.io/
- Size: 113 MB
Statistics
- Stars: 15
- Watchers: 12
- Forks: 5
- Open Issues: 15
- Releases: 0
Metadata Files
README.md
ASAP-modules
ASAP is a set of modules to perform stitching and alignment of EM and Array tomography data. It is suitable for processing large-scale datasets and supports multiple computational environments.
Documentation
The complete documentation is available here
Installation
Please refer the documentation Installation. on how to install and use ASAP modules
How to run
The order of processing is as follows;
Other Modules
A few other modules are included in ASAP to do the following.
- Materialization - render intermediate/final aligned volume to disk for further processing
- Fusion - Fuse global 3D non-linear aligned chunks together to make a complete volume
- Point match filter - A module that performs point match filtering of an existing point match collection
- Point match optimization - Performs a parameter sweep from a given set of ranges on a random sample of tilepairs to identify the optimal set of parameters
- Registration - Register individual sections in an already aligned volume (useful in cases of aligning missing/reimaged sections)
Support
We are planning on occasional updating this tool with no fixed schedule. Community involvement is encouraged through both issues and pull requests. Please make pull requests against the dev branch, as we will test changes there before merging into master.
Acknowledgments
This project is supported by the Intelligence Advanced Research Projects Activity (IARPA) via Department of Interior / Interior Business Center (DoI/IBC) contract number D16PC00004. The U.S. Government is authorized to reproduce and distribute reprints for Governmental purposes notwithstanding any copyright annotation theron.
Disclaimer: The views and conclusions contained herein are those of the authors and should not be interpreted as necessarily representing the official policies or endorsements, either expressed or implied, of IARPA, DoI/IBC, or the U.S. Government.
Owner
- Name: Allen Institute
- Login: AllenInstitute
- Kind: organization
- Location: Seattle, WA
- Website: https://alleninstitute.org
- Repositories: 184
- Profile: https://github.com/AllenInstitute
Please visit http://alleninstitute.github.io/ for more information.
GitHub Events
Total
- Issues event: 13
- Watch event: 2
- Delete event: 3
- Issue comment event: 4
- Push event: 18
- Pull request review event: 2
- Pull request event: 20
- Fork event: 1
- Create event: 9
Last Year
- Issues event: 13
- Watch event: 2
- Delete event: 3
- Issue comment event: 4
- Push event: 18
- Pull request review event: 2
- Pull request event: 20
- Fork event: 1
- Create event: 9
Committers
Last synced: about 1 year ago
Top Committers
| Name | Commits | |
|---|---|---|
| forrest collman | f****n@g****m | 365 |
| RussTorres | r****s@g****m | 221 |
| Dan Kapner | d****k@.****g | 140 |
| Gayathri Mahalingam | m****g@u****u | 119 |
| Gayathri Mahalingam | m****g@u****u | 87 |
| Sam K | s****k@a****g | 38 |
| Dan Kapner | 3****r | 29 |
| Sharmi | s****a@g****m | 15 |
| rathsidd | s****h@a****g | 12 |
| Sam K | s****n@u****u | 7 |
| Eric Perlman | p****n@g****m | 2 |
| Martin Schorb | m****b@e****e | 2 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 11 months ago
All Time
- Total issues: 29
- Total pull requests: 91
- Average time to close issues: 10 months
- Average time to close pull requests: 4 days
- Total issue authors: 7
- Total pull request authors: 7
- Average comments per issue: 1.41
- Average comments per pull request: 1.11
- Merged pull requests: 79
- Bot issues: 0
- Bot pull requests: 2
Past Year
- Issues: 7
- Pull requests: 8
- Average time to close issues: N/A
- Average time to close pull requests: 23 days
- Issue authors: 1
- Pull request authors: 3
- Average comments per issue: 0.0
- Average comments per pull request: 0.25
- Merged pull requests: 5
- Bot issues: 0
- Bot pull requests: 2
Top Authors
Issue Authors
- RussTorres (17)
- fcollman (8)
- zuwenqiang (2)
- martinschorb (1)
- mahaling (1)
- tfliss (1)
- zikai1 (1)
Pull Request Authors
- fcollman (47)
- RussTorres (29)
- mahaling (13)
- sharmishtaa (4)
- rathsidd (3)
- samrkinn (2)
- dependabot[bot] (2)
Top Labels
Issue Labels
Pull Request Labels
Dependencies
- argschema >=1.15.17
- bokeh *
- jinja2 *
- marshmallow *
- matplotlib *
- myst_parser *
- networkx *
- numpy >=1.11.1
- opencv-python *
- pathlib *
- pillow *
- render-python >=1.9.1
- rtree *
- scikit-image *
- scipy *
- sphinxcontrib-napoleon *
- tifffile *
- argschema <2.0
- bigfeta *
- bokeh <=1.4.0
- descartes *
- em_stitch *
- imageio *
- jinja2 <3.1
- lxml *
- marshmallow <3.0
- matplotlib *
- mpld3 *
- networkx *
- numpy *
- opencv-contrib-python *
- pathlib2 *
- pillow *
- render-python >=2.2.2
- rtree *
- scikit-image *
- scipy *
- seaborn *
- shapely *
- six *
- tifffile *
- triangle *
- uri_handler *
- for *
- if *
- codecov * test
- coverage >=4.1 test
- flake8 >=3.0.4 test
- jinja2 * test
- mock >=2.0.0 test
- pep8 >=1.7.0 test
- pylint >=1.5.4 test
- pytest >=3.0.5 test
- pytest-cov >=2.2.1 test
- pytest-pep8 >=1.0.6 test
- pytest-xdist >=1.14 test
- fcollman/render-python-client master build