napari-roi
Select regions of interest (ROIs) using napari
Science Score: 44.0%
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
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (10.8%) to scientific vocabulary
Repository
Select regions of interest (ROIs) using napari
Basic Info
- Host: GitHub
- Owner: BodenmillerGroup
- License: mit
- Language: Python
- Default Branch: main
- Size: 50.8 KB
Statistics
- Stars: 5
- Watchers: 4
- Forks: 2
- Open Issues: 4
- Releases: 0
Metadata Files
README.md
napari-roi
Select regions of interest (ROIs) using napari
Installation
You can install napari-roi via pip:
pip install napari-roi
Alternatively, you can install napari-roi via conda:
conda install -c conda-forge napari-roi
Usage
The napari-roi plugin can be opened from within napari (napari -> napari-roi: regions of interest) and operates on napari Shapes layers.
ROIs can be added to any napari Shapes layer, either by drawing a standard napari shape (e.g. rectangle), or by adding a rectangular ROI of specified size using the Add ROI functionality in the napari-roi widget. Each ROI is associated with a name, a position (X/Y origin), and a size (width/height). The location of the X/Y origin of all ROIs can be chosen in the napari-roi widget. Note that any shape supported by napari (e.g. ellipse, rectangle, polygon, line, path) can serve as an ROI; for non-rectangular shapes, napari-roi computes rectangular bounding boxes aligned with the napari coordinate system to determine their positions and sizes. ROIs can be edited or deleted by modifying the corresponding shapes in napari, or by editing the corresponding row in the napari-roi widget.
All ROIs in the current Shapes layer can be saved to a comma-separated values (CSV) file using the Save functionality in the napari-roi widget. When the Autosave option is checked, the file is automatically updated on every ROI change. Note that the selected file is specific to the current Shapes layer; ROIs from different Shapes layers cannot be saved to the same file. ROIs can be loaded from a previously saved file and added to the current Shapes layer by opening the file in the napari-roi widget.
CSV files saved using napari-roi adhere to the following format:
| Columns | Description |
| --- | --- |
| Name | ROI name |
| X, Y | Position (X/Y origin) |
| W, H | Size (width/height) |
Authors
Created and maintained by Jonas Windhager until February 2023.
Maintained by Milad Adibi from February 2023.
Contributing
Changelog
License
Owner
- Name: BodenmillerGroup
- Login: BodenmillerGroup
- Kind: organization
- Repositories: 83
- Profile: https://github.com/BodenmillerGroup
Citation (CITATION.cff)
cff-version: 1.2.0 message: If you use this plugin, please cite it using these metadata title: 'napari-roi: Select regions of interest (ROIs) using napari' url: https://github.com/BodenmillerGroup/napari-roi authors: - given-names: Jonas family-names: Windhager
GitHub Events
Total
- Watch event: 1
- Push event: 11
- Fork event: 1
Last Year
- Watch event: 1
- Push event: 11
- Fork event: 1
Committers
Last synced: almost 3 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Jonas Windhager | j****r@u****h | 34 |
| Sean Martin | s****m@h****m | 3 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 9 months ago
All Time
- Total issues: 7
- Total pull requests: 6
- Average time to close issues: 1 day
- Average time to close pull requests: 3 months
- Total issue authors: 6
- Total pull request authors: 3
- Average comments per issue: 2.43
- Average comments per pull request: 0.0
- Merged pull requests: 5
- Bot issues: 0
- Bot pull requests: 3
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
Top Authors
Issue Authors
- jwindhager (2)
- HouPB (1)
- biswajitSM (1)
- haesleinhuepf (1)
- DennisDannecker (1)
- seankmartin (1)
Pull Request Authors
- pre-commit-ci[bot] (3)
- jwindhager (2)
- seankmartin (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 2
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Total downloads:
- pypi 124 last-month
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Total dependent packages: 2
(may contain duplicates) -
Total dependent repositories: 1
(may contain duplicates) - Total versions: 16
- Total maintainers: 3
pypi.org: napari-roi
Select regions of interest (ROIs) using napari
- Homepage: https://github.com/BodenmillerGroup/napari-roi
- Documentation: https://github.com/BodenmillerGroup/napari-roi#README.md
- License: MIT
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Latest release: 0.1.8
published about 3 years ago
Rankings
Maintainers (3)
conda-forge.org: napari-roi
- Homepage: https://github.com/BodenmillerGroup/napari-roi
- License: MIT
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Latest release: 0.1.7
published over 3 years ago
Rankings
Dependencies
- actions/checkout v2 composite
- actions/setup-python v2 composite