pybasic-illumination-correction
Python implementation of the BaSiC shading correction method
Science Score: 67.0%
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✓CITATION.cff file
Found CITATION.cff file -
✓codemeta.json file
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✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 3 DOI reference(s) in README -
✓Academic publication links
Links to: springer.com, zenodo.org -
○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 (12.4%) to scientific vocabulary
Keywords
Repository
Python implementation of the BaSiC shading correction method
Basic Info
- Host: GitHub
- Owner: linum-uqam
- Language: Python
- Default Branch: master
- Size: 36.1 KB
Statistics
- Stars: 9
- Watchers: 4
- Forks: 1
- Open Issues: 2
- Releases: 1
Topics
Metadata Files
README.md
PyBaSiC
Python implementation of the BaSiC shading correction method.
- Original paper: T. Peng et al., “A BaSiC tool for background and shading correction of optical microscopy images,” Nat. Commun., vol. 8, p. 14836, Jun. 2017. DOI:10.1038/ncomms14836
- Nature Supplementary Materials: PDF
- Matlab implementation: https://github.com/QSCD/BaSiC
- Fiji plugin: URL
- Demo data examples: Dropbox
Installation
Option 1: pip
pip install pybasic-illumination-correction
Option 2: poetry
- You need Poetry.
- Install with
poetry install
This will create a virtual environment and install all the dependencies. To execute the basic_shading_correction.py script,
activate the virtual environment with poetry shell, then execute the script with python <path/to/script.py>
Usage
The main script to perform the retrospective shading estimation and correction is basic_shading_correction.
Here is a description of its arguments. Note: You must first activate the pybasic environment to run this script.
```bash
basicshadingcorrection --help usage: Shading correction algorithm based on the BaSiC method [-h] [--extension EXTENSION] [--estimatedarkfield] [--applycorrection] [--useflatfield USEFLATFIELD] [--usedarkfield USEDARKFIELD] [--epsilon EPSILON] [--ls LS] [--ld LD] [--outputflatfieldfilename OUTPUTFLATFIELDFILENAME] [--outputdarkfieldfilename OUTPUTDARKFIELD_FILENAME] directory outputdirectory
positional arguments: directory Full path a directory containing the tiles to process output_directory Full path to a directory where the output will be saved
optional arguments: -h, --help show this help message and exit --extension EXTENSION Image tile extension (default=.tif) --estimatedarkfield Estimate the darkfield in addition to the flatfield. --applycorrection Apply the shading correction with the estimated or loaded profiles. --useflatfield USEFLATFIELD Use existing flatfield (skip estimation) --usedarkfield USEDARKFIELD Use existing darkfield (skip estimation) --epsilon EPSILON Stability coefficient to use for the shading correction. (default=1e-06) --ls LS Flat-field regularization parameter (set automatically if None) --ld LD Dark-field regularization parameter (set automatically if None) --outputflatfieldfilename OUTPUTFLATFIELDFILENAME Optional output flatfield filename (if none, flatfield.tif will be saved in the output directory). --outputdarkfieldfilename OUTPUTDARKFIELDFILENAME Optional output flatfield filename (if none, darkfield.tif will be saved in the output directory). --verbose ```
Owner
- Name: LINUM @ UQAM
- Login: linum-uqam
- Kind: organization
- Location: Canada
- Website: https://linum.info.uqam.ca
- Repositories: 6
- Profile: https://github.com/linum-uqam
Laboratoire d'imagerie numérique, neurophotonique et microscopie
Citation (CITATION.cff)
cff-version: 1.1.0
message: "If you use this software, please cite it as below."
authors:
- family-names: "Lefebvre"
given-names: "Joël"
orcid: "https://orcid.org/0000-0002-6652-2130"
title: "linum-uqam/PyBaSiC: v1.0.0"
version: v1.0.0
doi: 10.5281/zenodo.7305570
date-released: 2022-11-08
url: "https://github.com/linum-uqam/PyBaSiC"
GitHub Events
Total
Last Year
Committers
Last synced: almost 3 years ago
All Time
- Total Commits: 16
- Total Committers: 2
- Avg Commits per committer: 8.0
- Development Distribution Score (DDS): 0.438
Top Committers
| Name | Commits | |
|---|---|---|
| joe-from-mtl | j****e@g****m | 9 |
| Joël Lefebvre | l****l@u****a | 7 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 1
- Total pull requests: 2
- Average time to close issues: N/A
- Average time to close pull requests: less than a minute
- Total issue authors: 1
- Total pull request authors: 2
- Average comments per issue: 0.0
- Average comments per pull request: 0.0
- Merged pull requests: 1
- Bot issues: 0
- Bot pull requests: 1
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
- sleepingcat4 (1)
Pull Request Authors
- dependabot[bot] (1)
- joe-from-mtl (1)
Top Labels
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Packages
- Total packages: 1
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Total downloads:
- pypi 56 last-month
- Total dependent packages: 0
- Total dependent repositories: 1
- Total versions: 2
- Total maintainers: 1
pypi.org: pybasic-illumination-correction
Python Implementation of the BaSiC shading correction algorithm
- Homepage: https://github.com/linum-uqam/PyBaSiC
- Documentation: https://pybasic-illumination-correction.readthedocs.io/
-
Latest release: 0.1.1
published over 3 years ago
Rankings
Maintainers (1)
Dependencies
- colorama 0.4.5
- numpy 1.23.2
- opencv-python 4.6.0.66
- scipy 1.9.0
- tqdm 4.64.0
- numpy ^1.23.2
- opencv-python ^4.6.0
- python >=3.10,<3.12
- scipy ^1.9.0
- tqdm ^4.64.0