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sainsc

Segmentation-free Analysis of In Situ Capture data

https://github.com/hidihlabs/sainsc

Science Score: 57.0%

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
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 3 DOI reference(s) in README
  • ○
    Academic publication links
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    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (11.1%) to scientific vocabulary
Last synced: 10 months ago · JSON representation ·

Repository

Segmentation-free Analysis of In Situ Capture data

Basic Info
Statistics
  • Stars: 10
  • Watchers: 5
  • Forks: 0
  • Open Issues: 1
  • Releases: 7
Created almost 2 years ago · Last pushed 12 months ago
Metadata Files
Readme License Citation

README.md

sainsc

License: MIT Code style: Ruff Checked with mypy pre-commit

/ˈsaiəns/

"Segmentation-free Analysis of In Situ Capture data" or alternatively "Stupid Acronyms In Science"

sainsc is a segmentation-free analysis tool for spatial transcriptomics from in situ capture technologies (but also works for imaging-based technologies). It is easily integratable with the scverse (i.e. scanpy and squidpy) by exporting data in AnnData or SpatialData format.

Installation

sainsc is available on PyPI and bioconda.

```sh

PyPI

pip install sainsc ```

```sh

or conda

conda install bioconda::sainsc ```

For detailed installation instructions please refer to the documentation.

Documentation

For an extensive documentation of the package please refer to the ReadTheDocs page

Versioning

This project follows the SemVer guidelines for versioning.

Citations

If you are using sainsc for your research please cite

N. Müller-Bötticher, S. Tiesmeyer, R. Eils, N. Ishaque, "Sainsc: A Computational Tool for Segmentation-Free Analysis of In Situ Capture Data" Small Methods (2025) https://doi.org/10.1002/smtd.202401123

@article{sainsc2025, author = {Müller-Bötticher, Niklas and Tiesmeyer, Sebastian and Eils, Roland and Ishaque, Naveed}, title = {Sainsc: A Computational Tool for Segmentation-Free Analysis of In Situ Capture Data}, journal = {Small Methods}, year = {2025}, volume = {9}, number = {5}, pages = {2401123}, doi = {10.1002/smtd.202401123}, }

License

This project is licensed under the MIT License - for details please refer to the LICENSE file.

Owner

  • Name: HiDiH - Hub for Innovations in Digital Health
  • Login: HiDiHlabs
  • Kind: organization
  • Email: info@hidih.org
  • Location: Berlin, Germany

Citation (CITATION.cff) 

cff-version: 1.2.0
message: "If you use this software, please cite the article from preferred-citation."
authors:
  - family-names: "Müller-Bötticher"
    given-names: Niklas
    orcid: "https://orcid.org/0000-0001-5103-7282"
title: sainsc
date-released: "2024-07-10"
url: "https://github.com/HiDiHlabs/sainsc"
preferred-citation:
  type: article
  authors:
    - family-names: "Müller-Bötticher"
      given-names: Niklas
      orcid: "https://orcid.org/0000-0001-5103-7282"
    - family-names: Tiesmeyer
      given-names: Sebastian
      orcid: "https://orcid.org/0000-0002-0492-1523"
    - family-names: Eils
      given-names: Roland
      orcid: "https://orcid.org/0000-0002-0034-4036"
    - family-names: Ishaque
      given-names: Naveed
      orcid: "https://orcid.org/0000-0002-8426-901X"
  title: "Sainsc: A Computational Tool for Segmentation-Free Analysis of In Situ Capture Data"
  doi: 10.1002/smtd.202401123
  journal: "Small Methods"
  pages: 2401123
  year: 2025
  volume: 9
  number: 5
  publisher: "Wiley Online Library"

GitHub Events

Total
  • Create event: 15
  • Issues event: 7
  • Release event: 3
  • Watch event: 9
  • Delete event: 14
  • Issue comment event: 9
  • Push event: 56
  • Pull request event: 36
Last Year
  • Create event: 15
  • Issues event: 7
  • Release event: 3
  • Watch event: 9
  • Delete event: 14
  • Issue comment event: 9
  • Push event: 56
  • Pull request event: 36

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 1
  • Total pull requests: 9
  • Average time to close issues: 4 days
  • Average time to close pull requests: 29 days
  • Total issue authors: 1
  • Total pull request authors: 3
  • Average comments per issue: 0.0
  • Average comments per pull request: 0.78
  • Merged pull requests: 6
  • Bot issues: 0
  • Bot pull requests: 2
Past Year
  • Issues: 1
  • Pull requests: 9
  • Average time to close issues: 4 days
  • Average time to close pull requests: 29 days
  • Issue authors: 1
  • Pull request authors: 3
  • Average comments per issue: 0.0
  • Average comments per pull request: 0.78
  • Merged pull requests: 6
  • Bot issues: 0
  • Bot pull requests: 2
View more stats
Top Authors
Issue Authors
  • pakiessling (2)
  • bradgigax (1)
  • niklasmueboe (1)
  • rasools (1)
Pull Request Authors
  • niklasmueboe (21)
  • pre-commit-ci[bot] (3)
  • joaolsf (1)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 297 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 6
  • Total maintainers: 1
pypi.org: sainsc

Segmentation-free Analysis of In Situ Capture data

  • Homepage: https://github.com/HiDiHlabs/sainsc
  • Documentation: https://sainsc.readthedocs.io
  • License: MIT License Copyright (c) 2024 Niklas Müller-Bötticher, Naveed Ishaque, Roland Eils, Berlin Institute of Health @ Charité Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
  • Latest release: 0.3.1
    published over 1 year ago
  • Versions: 6
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 297 Last month
Rankings
Dependent packages count: 10.5%
Average: 34.9%
Dependent repos count: 59.3%
Maintainers (1)
niklasmueboe
Last synced: 10 months ago

Dependencies

.github/workflows/CI.yml actions
  • actions-rust-lang/rustfmt v1 composite
  • actions-rust-lang/setup-rust-toolchain v1 composite
  • actions/checkout v4 composite
.github/workflows/cibuildwheel.yml actions
  • actions-rust-lang/setup-rust-toolchain v1 composite
  • actions/checkout v4 composite
  • actions/download-artifact v4 composite
  • actions/setup-python v5 composite
  • actions/upload-artifact v4 composite
  • pypa/cibuildwheel v2.19.2 composite
  • pypa/gh-action-pypi-publish release/v1 composite
Cargo.toml cargo
pyproject.toml pypi
  • anndata >=0.9
  • matplotlib *
  • matplotlib-scalebar *
  • numba >=0.44
  • numpy >=1.21
  • pandas *
  • polars [pandas]>=1
  • scikit-image >=0.18
  • scipy >=1.9
  • seaborn >=0.11