Science Score: 65.0%
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
Found 4 DOI reference(s) in README -
○Academic publication links
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○Academic email domains
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✓Institutional organization owner
Organization bmcv has institutional domain (www.bioquant.uni-heidelberg.de) -
○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (6.2%) to scientific vocabulary
Keywords
usegalaxy
usegalaxy-eu
Last synced: 9 months ago
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JSON representation
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Repository
Galaxy tools for image analysis
Basic Info
- Host: GitHub
- Owner: BMCV
- License: mit
- Language: Python
- Default Branch: master
- Size: 34.2 MB
Statistics
- Stars: 18
- Watchers: 7
- Forks: 18
- Open Issues: 4
- Releases: 0
Topics
usegalaxy
usegalaxy-eu
Created almost 10 years ago
· Last pushed 11 months ago
Metadata Files
Readme
Contributing
License
Code of conduct
Citation
README.md
Galaxy Image Analysis
Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. If you would like to contribute, please see our contribution instructions.
Galaxy Image Analysis is part of the Image Community in Galaxy.
If Galaxy Image Analysis helped with the analysis of your data, please do not forget to cite: https://doi.org/10.1016/j.jbiotec.2017.07.019
List of Tools on Galaxy Europe
Image processing
- Apply anisotropic diffusion with MedPy
- Apply a morphological operation with SciPy
- Concatenate images or channels
- Crop image with giatools
- Filter 2D image with scikit-image
- Perform histogram equalization with scikit-image
- Permutate image axes
- Process images using arithmetic expressions with NumPy
- Remove image background with scikit-image
- Scale image with scikit-image
- Show image info with Bioformats
- Slice image into patches
- Split image along axes with NumPy
- Switch axis coordinates
Image conversion
- Convert binary image to label map
- Convert binary image to points (center of masses)
- Convert binary image to points (point coordinates)
- Convert image format with Bioformats
- Convert label map to binary image with NumPy
- Convert label map to points (center of masses)
- Convert point coordinates to label map
- Convert single-channel to multi-channel image with NumPy
- Convert to OME-Zarr with Bioformats
- Perform color deconvolution or transformation
Segmentation, partitioning, and detection
- Compute Voronoi tessellation with scikit-image
- Count objects in label map
- Extract 2D features with scikit-image
- Filter label map by rules
- Merge neighbors in label map
- Perform 2D spot detection
- Perform segmentation in densely packed 3-D volumetric images with PlantSeg
- Perform segmentation using region-based fitting of overlapping ellipses with RFOVE
- Perform segmentation using deformable shape models with SuperDSM
- Split label map using morphological operators
- Threshold image with scikit-image
Registration
- Compute image orientation with OrientationPy
- Perform affine image registration (intensity-based)
- Perform affine image registration (landmark-based)
- Performs projective transformation with/without labels
- Performs projective transformation
Tracking
Visualization and validation
- Colorize labels with NetworkX
- Compute image segmentation and object detection performance measures with SegMetrics
- Evaluate segmentation with EvaluateSegmentation
- Overlay images
- Visualize detections
Miscellaneous
- Compute image features with Mahotas
- Extract top view with OpenSlide
- Perform curve fitting
- Unzip
Acknowledgment
This work has been supported by the BMBF-funded Heidelberg Center for Human Bioinformatics (HD-HuB) within the German Network for Bioinformatics Infrastructure (de.NBI) #031A537C.
Owner
- Name: BMCV
- Login: BMCV
- Kind: organization
- Location: Heidelberg, Germany
- Website: http://www.bioquant.uni-heidelberg.de/no_cache/research/groups/biomedical-computer-vision
- Repositories: 14
- Profile: https://github.com/BMCV
Biomedical Computer Vision Group
Citation (CITATION.cff)
cff-version: 1.2.0
message: "If you use this software, please cite it as below."
preferred-citation:
type: article
journal: "Journal of Biotechnology"
month: 7
start: 70 # First page number
end: 75 # Last page number
title: "Workflows for microscopy image analysis and cellular phenotyping"
doi: 10.1016/j.jbiotec.2017.07.019
volume: 261
year: 2017
authors:
- family-names: "Wollmann"
given-names: "Thomas"
orcid: "https://orcid.org/0000-0002-4741-3844"
- family-names: "Erfle"
given-names: "Holger"
- family-names: "Eils"
given-names: "Roland"
- family-names: "Rohr"
given-names: "Karl"
- family-names: "Gunkel"
given-names: "Manuel"
orcid: "https://orcid.org/0000-0002-5363-8943"
GitHub Events
Total
- Watch event: 4
- Delete event: 1
- Issue comment event: 34
- Push event: 11
- Pull request review event: 25
- Pull request review comment event: 23
- Pull request event: 27
- Fork event: 2
- Create event: 1
Last Year
- Watch event: 4
- Delete event: 1
- Issue comment event: 34
- Push event: 11
- Pull request review event: 25
- Pull request review comment event: 23
- Pull request event: 27
- Fork event: 2
- Create event: 1
Issues and Pull Requests
Last synced: 10 months ago
All Time
- Total issues: 0
- Total pull requests: 16
- Average time to close issues: N/A
- Average time to close pull requests: 4 days
- Total issue authors: 0
- Total pull request authors: 2
- Average comments per issue: 0
- Average comments per pull request: 0.88
- Merged pull requests: 9
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 16
- Average time to close issues: N/A
- Average time to close pull requests: 4 days
- Issue authors: 0
- Pull request authors: 2
- Average comments per issue: 0
- Average comments per pull request: 0.88
- Merged pull requests: 9
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- kostrykin (3)
- bernt-matthias (1)
- thawn (1)
- cgirardot (1)
- rmassei (1)
Pull Request Authors
- kostrykin (46)
- bernt-matthias (1)
- pavanvidem (1)
- rmassei (1)
Top Labels
Issue Labels
todo (3)