https://github.com/bodenmillergroup/napari-imc

Imaging Mass Cytometry (IMC) file type support for napari

Science Score: 49.0%

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
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.zenodo.json file
Found .zenodo.json file
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DOI references
Found 3 DOI reference(s) in README
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Academic publication links
Links to: biorxiv.org
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Committers with academic emails
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Institutional organization owner
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JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (12.7%) to scientific vocabulary

Last synced: 7 months ago · JSON representation

Repository

Imaging Mass Cytometry (IMC) file type support for napari

Basic Info

Host: GitHub
Owner: BodenmillerGroup
License: mit
Language: Python
Default Branch: main
Size: 87.9 KB

Statistics

Stars: 12
Watchers: 3
Forks: 4
Open Issues: 11
Releases: 0

Created about 5 years ago · Last pushed over 2 years ago

Metadata Files

Readme Changelog Contributing License

README.md

napari-imc

Imaging Mass Cytometry (IMC) file type support for napari

Load panoramas and multi-channel acquisitions co-registered within the machine's coordinate system from Fluidigm TXT/MCD files

Installation

You can install napari-imc via pip:

pip install napari-imc

Alternatively, you can install napari-imc via conda:

conda install -c conda-forge napari-imc

For example, to install napari and napari-imc in a fresh conda environment using pip:

conda create -n napari-imc python=3.9
conda activate napari-imc
pip install "napari[all]" napari-imc

Usage

Simply open your Fluidigm TXT/MCD file using napari.

Authors

Created and maintained by Jonas Windhager jonas.windhager@uzh.ch

Citation

Please cite the following paper when using napari-imc in your work:

Windhager J, Bodenmiller B, Eling N (2021). An end-to-end workflow for multiplexed image processing and analysis. bioRxiv. doi: https://doi.org/10.1101/2021.11.12.468357.

@article{Windhager2021,
  author = {Windhager, Jonas and Bodenmiller, Bernd and Eling, Nils},
  title = {An end-to-end workflow for multiplexed image processing and analysis},
  year = {2021},
  doi = {10.1101/2021.11.12.468357},
  URL = {https://www.biorxiv.org/content/early/2021/11/13/2021.11.12.468357},
  journal = {bioRxiv}
}

Contributing

Changelog

License

MIT

Owner

Name: BodenmillerGroup
Login: BodenmillerGroup
Kind: organization

Repositories: 83
Profile: https://github.com/BodenmillerGroup

GitHub Events

Total

Issues event: 1
Watch event: 3
Issue comment event: 1
Pull request event: 2
Fork event: 2

Last Year

Issues event: 1
Watch event: 3
Issue comment event: 1
Pull request event: 2
Fork event: 2

Committers

Last synced: almost 3 years ago

All Time

Total Commits: 62
Total Committers: 3
Avg Commits per committer: 20.667
Development Distribution Score (DDS): 0.145

Past Year

Commits: 2
Committers: 1
Avg Commits per committer: 2.0
Development Distribution Score (DDS): 0.0

Top Committers

Name	Email	Commits
Jonas Windhager	j**r@u**h	53
Jonas Windhager	j**r@u**m	6
Justin Kiggins	j**s@g**m	3

Committer Domains (Top 20 + Academic)

uzh.ch: 1

Issues and Pull Requests

Last synced: 7 months ago

All Time

Total issues: 28
Total pull requests: 5
Average time to close issues: 4 days
Average time to close pull requests: 13 days
Total issue authors: 9
Total pull request authors: 4
Average comments per issue: 1.18
Average comments per pull request: 2.0
Merged pull requests: 2
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 1
Pull requests: 2
Average time to close issues: N/A
Average time to close pull requests: 7 minutes
Issue authors: 1
Pull request authors: 1
Average comments per issue: 2.0
Average comments per pull request: 0.0
Merged pull requests: 0
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

jwindhager (17)
nilseling (4)
DarioS (1)
StefanosVoglis (1)
pdimitron (1)
wflynny (1)
kvetab (1)
cocofreefarm (1)
lassedochreden (1)

Pull Request Authors

albert180 (2)
neuromusic (1)
jwindhager (1)
nilseling (1)

Top Labels

Issue Labels

enhancement (11) bug (8) wontfix (3) documentation (1)

Pull Request Labels

enhancement (1)

Packages

Total packages: 2
Total downloads:
- pypi 317 last-month

Total dependent packages: 0
(may contain duplicates)
Total dependent repositories: 1
(may contain duplicates)
Total versions: 27
Total maintainers: 1

pypi.org: napari-imc

Imaging Mass Cytometry (IMC) file type support for napari

Homepage: https://github.com/BodenmillerGroup/napari-imc
Documentation: https://github.com/BodenmillerGroup/napari-imc#README.md
License: MIT
Latest release: 0.6.5
published almost 4 years ago

Versions: 24
Dependent Packages: 0
Dependent Repositories: 1
Downloads: 317 Last month

Rankings

Dependent packages count: 10.1%

Forks count: 16.9%

Average: 16.9%

Stargazers count: 17.7%

Downloads: 18.2%

Dependent repos count: 21.6%

Maintainers (1)

jwindhager

Last synced: 7 months ago

conda-forge.org: napari-imc

Homepage: https://github.com/BodenmillerGroup/napari-imc
License: MIT
Latest release: 0.6.5
published almost 4 years ago

Versions: 3
Dependent Packages: 0
Dependent Repositories: 0

Rankings

Dependent repos count: 34.0%

Average: 48.2%

Dependent packages count: 51.2%

Stargazers count: 53.5%

Forks count: 54.2%

Last synced: 7 months ago