https://github.com/catalystneuro/photon-flux-estimation
A Python library for estimating photon flux from multiphoton imaging data. This package provides tools to compute photon sensitivity and generate photon flux visualizations from imaging data.
Science Score: 13.0%
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Low similarity (9.5%) to scientific vocabulary
Repository
A Python library for estimating photon flux from multiphoton imaging data. This package provides tools to compute photon sensitivity and generate photon flux visualizations from imaging data.
Basic Info
- Host: GitHub
- Owner: catalystneuro
- License: mit
- Language: Python
- Default Branch: main
- Size: 58.4 MB
Statistics
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
Photon Flux Estimation
A Python library for estimating photon flux from multiphoton imaging data. This package provides tools to compute photon sensitivity and generate photon flux visualizations from imaging data.
Installation
bash
pip install photon-flux-estimation
Features
- Compute photon sensitivity from imaging data
- Generate photon transfer curve visualizations
- Calculate photon flux estimates
- Visualize coefficient of variation
- Demo notebook with DANDI dataset integration
Usage
```python from photonfluxestimation import PhotonFluxAnalyzer
Load your imaging data (height, width, time)
movie = yourdataloading_function()
Create estimator and compute sensitivity
estimator = PhotonFluxEstimator(movie) results = estimator.compute_sensitivity()
print(f"Sensitivity: {results['sensitivity']:.2f}") print(f"Zero level: {results['zero_level']:.2f}")
Get photon flux movie
photonflux = estimator.computephoton_flux()
Generate visualization
from photonfluxestimation import ( plotphotontransfercurve, plotaverageintensity, plotcoefficientvariation, plotphoton_flux, )
plotaverageintensity( movie=movie, title="Average Intensity", savepath=str(figurefilename) + "-A.png", ) plotphotontransfercurve( results=results, title="Photon Transfer Curve", savepath=str(figurefilename) + "-B.png", ) plotcoefficientvariation( movie=movie, results=results, title="Coefficient of Variation", savepath=str(figurefilename) + "-C.png", ) plotphotonflux( movie=movie, results=results, title="Average Photon Flux", savepath=str(figure_filename) + "-D.png", ) ```
Citation
This package is based on code from the compress-multiphoton repository. If you use this package in your research, please cite both this package and the original repository.
Documentation
For detailed documentation and examples, please see the demo notebook.
License
MIT License. See LICENSE for details.
Owner
- Name: CatalystNeuro
- Login: catalystneuro
- Kind: organization
- Email: hello@catalystneuro.com
- Website: catalystneuro.com
- Twitter: catalystneuro
- Repositories: 87
- Profile: https://github.com/catalystneuro
GitHub Events
Total
- Release event: 1
- Push event: 3
- Create event: 2
Last Year
- Release event: 1
- Push event: 3
- Create event: 2
Packages
- Total packages: 1
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Total downloads:
- pypi 15 last-month
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 2
- Total maintainers: 1
pypi.org: photon-flux-estimation
Library to compute estimated photon flux from multiphoton imaging data
- Homepage: https://github.com/catalystneuro/photon-flux-estimation
- Documentation: https://photon-flux-estimation.readthedocs.io/
- License: mit
-
Latest release: 0.1.1
published over 1 year ago
Rankings
Maintainers (1)
Dependencies
- actions/checkout v4 composite
- actions/download-artifact v4 composite
- actions/setup-python v5 composite
- actions/upload-artifact v4 composite
- pypa/gh-action-pypi-publish release/v1 composite
- colorcet *
- dandi *
- fsspec *
- h5py *
- matplotlib *
- numpy *
- pynwb *
- scikit-learn *