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
Found CITATION.cff file -
✓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
1 of 2 committers (50.0%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (10.8%) to scientific vocabulary
Last synced: 7 months ago
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JSON representation
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Repository
Basic Info
- Host: GitHub
- Owner: NMontanaBrown
- License: other
- Language: Python
- Default Branch: main
- Size: 12.2 MB
Statistics
- Stars: 27
- Watchers: 1
- Forks: 2
- Open Issues: 5
- Releases: 0
Created almost 3 years ago
· Last pushed over 1 year ago
Metadata Files
Readme
Contributing
License
Citation
README.rst
SARAMIS: Simulation Assets for Robotic-Assisted and Minimally Invasive Surgery
===============================
.. image:: /docs/static/main_fig.png
Author: Nina Montana Brown
SARAMIS is developed at the `Wellcome EPSRC Centre for Interventional and Surgical Sciences`_, part of `University College London (UCL)`_.
Downloading the Data
----------
SARAMIS data may be downloaded at the following links:
* https://huggingface.co/datasets/NMontanaBrown/saramis_abdomen/tree/main
* https://huggingface.co/datasets/NMontanaBrown/saramis_amos/tree/main
* https://huggingface.co/datasets/NMontanaBrown/saramis_total/tree/main
* https://huggingface.co/datasets/NMontanaBrown/saramis_metadata/tree/main
* https://huggingface.co/datasets/NMontanaBrown/saramis_rl_expt/tree/main
Installing
----------
Using SARAMIS and it's functionalities will require the compilation of some libraries locally, installation of open-source software, or the use of a Docker image.
For more information, see the `Install`_ folder.
You can pip install the code from the repository as follows:
::
pip install git+https://github.com/NMontanaBrown/saramis
Usage Of SARAMIS
----------
* `Labelling`_: full instructions to run the labelling, meshing, tetrahedralisation, and texturing of the SARAMIS dataset are included at the `Labelling`_ portion of the docs.
* `RL Experiment`_: full instructions to run the training of a navigation agent are included in the `RL experiment`_ section of the docs.
Developing
----------
Cloning
^^^^^^^
You can clone the repository using the following command:
::
git clone https://github.com/NMontanaBrown/saramis
Contributing
^^^^^^^^^^^^
Please see the `contributing guidelines`_.
Licensing and copyright
-----------------------
Copyright 2023 University College London.
SARAMIS code is released under the BSD-3 license. Please see the `license file`_ for details.
SARAMIS data is released under CC-BY-NC-SA license. Please see the paper and Supplementary Materials for full details.
Acknowledgements
----------------
Supported by `Wellcome`_ and `EPSRC`_.
.. _`Wellcome EPSRC Centre for Interventional and Surgical Sciences`: http://www.ucl.ac.uk/weiss
.. _`source code repository`: https://github.com/NMontanaBrown/saramis
.. _`RL Experiment`: https://github.com/NMontanaBrown/saramis/blob/main/docs/RL/README.md
.. _`Labelling`: https://github.com/NMontanaBrown/saramis/blob/main/docs/labelling/README.md
.. _`Install`: https://github.com/NMontanaBrown/saramis/blob/main/docs/install/SARAMIS.md
.. _`University College London (UCL)`: http://www.ucl.ac.uk/
.. _`Wellcome`: https://wellcome.ac.uk/
.. _`EPSRC`: https://www.epsrc.ac.uk/
.. _`contributing guidelines`: https://github.com/NMontanaBrown/saramis/blob/master/CONTRIBUTING.rst
.. _`license file`: https://github.com/NMontanaBrown/saramis/blob/master/LICENSE
Owner
- Name: Nina Montana-Brown
- Login: NMontanaBrown
- Kind: user
- Location: London
- Website: nina.brown.15@ucl.ac.uk
- Twitter: public_enembe
- Repositories: 26
- Profile: https://github.com/NMontanaBrown
PhD Student Medical Imaging @ UCL WEISS + CMIC || ML Engineer @ Verdure Imaging Inc. || she/they ||
Citation (CITATION.cff)
cff-version: 1.2.0
message: "If you use any of this package in your research, please cite it as below."
authors:
- family-names: "Montana-Brown"
given-names: "Nina"
orcid: ""
title: "SARAMIS"
url: "https://github.com/NMontanaBrown/saramis"
preferred-citation:
type: article
authors:
- family-names: "Montana Brown"
given-names: "Nina"
orcid: "https://orcid.org/0000-0001-7286-1326"
doi: TBC
journal: TBC
start: TBC
end: TBC
title: TBC
volume: TBC
issue: TBC
year: TBC
GitHub Events
Total
- Issues event: 1
- Watch event: 2
- Issue comment event: 2
Last Year
- Issues event: 1
- Watch event: 2
- Issue comment event: 2
Committers
Last synced: 8 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| NMontanaBrown | n****5@u****k | 49 |
| Shaheer U. Saeed | 4****d | 3 |
Committer Domains (Top 20 + Academic)
ucl.ac.uk: 1
Issues and Pull Requests
Last synced: 8 months ago
All Time
- Total issues: 7
- Total pull requests: 0
- Average time to close issues: 2 months
- Average time to close pull requests: N/A
- Total issue authors: 4
- Total pull request authors: 0
- Average comments per issue: 1.29
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 2
- Pull requests: 0
- Average time to close issues: 5 days
- Average time to close pull requests: N/A
- Issue authors: 2
- Pull request authors: 0
- Average comments per issue: 3.0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- NMontanaBrown (4)
- Khoa-NT (1)
- jywu511 (1)
- haowang020110 (1)
Pull Request Authors
Top Labels
Issue Labels
Pull Request Labels
Dependencies
.github/workflows/ci.yml
actions
- actions/checkout v2 composite
- actions/checkout v3 composite
- actions/checkout master composite
- actions/setup-python v1 composite
- actions/setup-python v4 composite
- pypa/gh-action-pypi-publish master composite
requirements-dev.txt
pypi
- coverage * development
- ipykernel * development
- mock * development
- nbsphinx * development
- parameterized * development
- pyfakefs * development
- pyinstaller * development
- pylint * development
- pytest * development
- sphinx * development
- sphinx_rtd_theme * development
- tox * development
requirements.txt
pypi
- SimpleITK *
- meshio *
- nrrd *
- numpy *
- pymeshlab *
- scikit-image *
- scikit-surgerycore *
- scikit-surgeryvtk *
- slicerio *
- tdqm *
- vtk *
setup.py
pypi