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Open Source Science

imio

Loading and saving of image data.

https://github.com/brainglobe/imio

Science Score: 10.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ○
    codemeta.json file
  • ○
    .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    2 of 9 committers (22.2%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (12.5%) to scientific vocabulary

Keywords

image-processing loading nifti saving tiff tiff-series

Keywords from Contributors

napari python-template particles mesh cellfinder brainreg neuroanatomy imaging image-analysis cell-detection
Last synced: 6 months ago · JSON representation

Repository

Loading and saving of image data.

Basic Info
  • Host: GitHub
  • Owner: brainglobe
  • License: mit
  • Language: Python
  • Default Branch: main
  • Homepage:
  • Size: 108 KB
Statistics
  • Stars: 10
  • Watchers: 4
  • Forks: 3
  • Open Issues: 0
  • Releases: 0
Archived
Topics
image-processing loading nifti saving tiff tiff-series
Created over 5 years ago · Last pushed about 2 years ago
Metadata Files
Readme License

README.md

This package has moved!

imio has been merged into brainglobe-utils and will no longer be provided standalone. If you want to continue using this package's functionality, we recommend you install brainglobe-utils and the corresponding submodule.

Python Version PyPI Downloads Wheel Development Status Tests codecov Code style: black Contributions

imio

Loading and saving of image data.

About

The aim of imio is to be a lightweight image loading library for the file types supported by cellfinder, and brainreg.

Supports loading of:

  • Tiff stack +
  • Tiff series (from a directory, a text file or a list of file paths). *+
  • nrrd
  • nifti (.nii & .nii.gz)

* Supports loading in parallel for speed

+ Suports scaling on loading. E.g. downsampling to load images bigger than the available RAM

Supports saving of:

  • Tiff stack
  • Tiff series
  • nifti

To install

bash pip install imio

Contributing

Contributions to imio are more than welcome. Please see the developers guide.

Owner

  • Name: BrainGlobe
  • Login: brainglobe
  • Kind: organization
  • Location: London/Munich

Open python tools for morphological analyses in systems neuroscience

GitHub Events

Total
Last Year

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 76
  • Total Committers: 9
  • Avg Commits per committer: 8.444
  • Development Distribution Score (DDS): 0.513
Past Year
  • Commits: 32
  • Committers: 5
  • Avg Commits per committer: 6.4
  • Development Distribution Score (DDS): 0.594
Top Committers
Name Email Commits
Adam Tyson c****e@a****m 37
pre-commit-ci[bot] 6****] 13
Adam Tyson a****n@u****k 12
David Stansby d****y@g****m 5
allcontributors[bot] 4****] 5
Jaime Rodríguez-Guerra j****p 1
crousseau c****u@u****k 1
Jules Scholler j****r@g****m 1
Will Graham 3****1 1
Committer Domains (Top 20 + Academic)
ucl.ac.uk: 2 adamltyson.com: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 8
  • Total pull requests: 46
  • Average time to close issues: 10 days
  • Average time to close pull requests: about 20 hours
  • Total issue authors: 1
  • Total pull request authors: 8
  • Average comments per issue: 1.13
  • Average comments per pull request: 1.13
  • Merged pull requests: 44
  • Bot issues: 0
  • Bot pull requests: 23
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
View more stats
Top Authors
Issue Authors
  • adamltyson (8)
Pull Request Authors
  • pre-commit-ci[bot] (18)
  • adamltyson (11)
  • dstansby (5)
  • allcontributors[bot] (5)
  • willGraham01 (3)
  • alessandrofelder (2)
  • jaimergp (1)
  • JulesScholler (1)
Top Labels
Issue Labels
enhancement (6) help wanted (2) good first issue (2) bug (1)
Pull Request Labels

Packages

  • Total packages: 2
  • Total downloads:
    • pypi 400 last-month
  • Total dependent packages: 11
    (may contain duplicates)
  • Total dependent repositories: 2
    (may contain duplicates)
  • Total versions: 27
  • Total maintainers: 1
pypi.org: imio

Loading and saving of image data.

  • Versions: 22
  • Dependent Packages: 9
  • Dependent Repositories: 2
  • Downloads: 400 Last month
Rankings
Dependent packages count: 1.2%
Downloads: 5.7%
Average: 10.6%
Dependent repos count: 11.6%
Forks count: 16.9%
Stargazers count: 17.8%
Maintainers (1)
adamltyson
Last synced: 6 months ago
conda-forge.org: imio
  • Versions: 5
  • Dependent Packages: 2
  • Dependent Repositories: 0
Rankings
Dependent packages count: 19.5%
Dependent repos count: 34.0%
Average: 41.2%
Forks count: 54.2%
Stargazers count: 57.0%
Last synced: 7 months ago

Dependencies

.github/workflows/test_and_deploy.yml actions
  • actions/checkout v2 composite
  • actions/setup-python v1 composite
  • neuroinformatics-unit/actions/lint v1 composite
  • neuroinformatics-unit/actions/test v1 composite
pyproject.toml pypi
  • brainglobe-utils [slurmio]
  • natsort *
  • nibabel *
  • nibabel >= 2.1.0
  • numpy *
  • psutil *
  • pynrrd *
  • scikit-image *
  • tifffile *
  • tqdm *