https://github.com/bbquercus/deepblink
Threshold independent detection and localization of diffraction-limited spots.
Science Score: 23.0%
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
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○.zenodo.json file
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✓DOI references
Found 10 DOI reference(s) in README -
✓Academic publication links
Links to: zenodo.org -
○Academic email domains
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (17.1%) to scientific vocabulary
Keywords
Repository
Threshold independent detection and localization of diffraction-limited spots.
Basic Info
- Host: GitHub
- Owner: BBQuercus
- License: other
- Language: Python
- Default Branch: master
- Homepage: https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkab546/6312733
- Size: 329 MB
Statistics
- Stars: 32
- Watchers: 4
- Forks: 8
- Open Issues: 1
- Releases: 0
Topics
Metadata Files
README.md
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deepBlink 
Threshold independent detection and localization of diffraction-limited spots.
Contents
Overview
In biomedical microscopy data, a common task involves the detection of diffraction-limited spots that visualize single proteins, domains, mRNAs, and many more. These spots were traditionally detected with mathematical operators such as Laplacian of Gaussian. These operators, however, rely on human input ranging from image-intensity thresholds, approximative spot sizes, etc. This process is tedious and not always reliable. DeepBlink relies on neural networks to automatically find spots without the need for human intervention. DeepBlink is available as a ready-to-use command-line interface.
| Usage | Example |
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Documentation
More documentation about deepBlink including how to train, create a dataset, contribute etc. is available at https://github.com/BBQuercus/deepBlink/wiki.
Installation
This package is built for Python versions newer than 3.6 and can easily be installed with pip:
bash
pip install deepblink
Or using conda:
bash
conda install -c bbquercus deepblink
Additionally for GPU support, install tensorflow-gpu through pip and with the
appropriate CUDA and cuDNN verions matching your GPU setup. Lastly, you can also use our KNIME node for inference. Please follow the installation instructions on KNIME hub.
Usage
A video overview can be found here. Inferencing on deepBlink is performed at the command line as follows:
bash
deepblink predict -m MODEL -i INPUT [-o OUTPUT] [-r RADIUS] [-s SHAPE]
With MODEL being a pre-trained or custom model and INPUT being the path to a input image or folder containing images.
Citation
deepBlink is currently available on Nucleic Acid Research here. If you find deepBlink useful, consider citing us:
bibtex
@article{10.1093/nar/gkab546,
author = {Eichenberger, Bastian Th and Zhan, YinXiu and Rempfler, Markus and Giorgetti, Luca and Chao, Jeffrey A},
title = "{deepBlink: threshold-independent detection and localization of diffraction-limited spots}",
journal = {Nucleic Acids Research},
year = {2021},
month = {07},
issn = {0305-1048},
doi = {10.1093/nar/gkab546},
url = {https://doi.org/10.1093/nar/gkab546},
note = {gkab546},
eprint = {https://academic.oup.com/nar/advance-article-pdf/doi/10.1093/nar/gkab546/38848972/gkab546.pdf},
}
Owner
- Name: Bastian Eichenberger
- Login: BBQuercus
- Kind: user
- Location: Basel, Switzerland
- Company: FMI
- Website: bastianeichenberger.ch
- Repositories: 6
- Profile: https://github.com/BBQuercus
A coding molecular biologist.
GitHub Events
Total
- Watch event: 2
- Fork event: 1
Last Year
- Watch event: 2
- Fork event: 1
Issues and Pull Requests
Last synced: over 1 year ago
All Time
- Total issues: 20
- Total pull requests: 82
- Average time to close issues: 26 days
- Average time to close pull requests: 2 days
- Total issue authors: 11
- Total pull request authors: 6
- Average comments per issue: 3.35
- Average comments per pull request: 0.57
- Merged pull requests: 72
- Bot issues: 0
- Bot pull requests: 1
Past Year
- Issues: 2
- Pull requests: 0
- Average time to close issues: 16 days
- Average time to close pull requests: N/A
- Issue authors: 2
- Pull request authors: 0
- Average comments per issue: 1.5
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- BBQuercus (7)
- mimuelle (2)
- wikk-chy (2)
- imzhangyd (2)
- SosUts (1)
- BioinfoTongLI (1)
- Boehmin (1)
- resace3 (1)
- nickeener (1)
- alcrevenna (1)
- tamasbalassa (1)
Pull Request Authors
- BBQuercus (55)
- zhanyinx (16)
- pyup-bot (8)
- BioinfoTongLI (1)
- fossabot (1)
- dependabot[bot] (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- pypi 30 last-month
- Total dependent packages: 1
- Total dependent repositories: 1
- Total versions: 13
- Total maintainers: 2
pypi.org: deepblink
Threshold independent detection and localization of diffraction-limited spots.
- Homepage: https://github.com/bbquercus/deepblink/
- Documentation: https://github.com/BBQuercus/deepBlink/wiki
- License: MIT
-
Latest release: 0.1.4
published over 3 years ago
Rankings
Dependencies
- sphinx >=1.3
- sphinx-rtd-theme ==0.5.0
- matplotlib *
- numpy *
- pandas *
- pyyaml *
- requests *
- scikit-image *
- scipy *
- tensorflow >=2.0.0