Python package for modeling spectral propagation through fluorescence microscopy systems, including fluorophores, filters, dichroics, illumination spectra and detector sensitivity.
Requirements: numpy, matplotlib, tqdm
Installation: Download or clone (git clone https://github.com/CoulonLab/SpectraPy.git) this repository.
Usage: A notebook SpectraPy_examples.ipynb is available, illustrating use cases ranging from simple examples to advanced optimization of filter selection (the latter requiring additional third-party spectra files – see below).
The SpectraPy source code is distributed under the GPL v3 license. See the LICENSE file for details.
Third-party spectra files included in the spectra/ folder are not covered by the repository license.
SpectraPy is currently unpublished work. If you use this software in research work, please check this repository before publishing to see whether a publication describing SpectraPy is available and can be cited. Otherwise, please reference this GitHub repository.
Only a small number of spectra files are included in the spectra/ folder for demo and testing purposes.
If you want to obtain additional spectra files, useful resources include:
- the SearchLight™ Spectral Modeling & Analysis Tool, which provides downloadable spectra for many fluorophores, light sources, and detectors, as well as the full catalog of Semrock (IDEX Health & Science) filters and dichroics.
- the Spectra Database of the University of Arizona.
- the FPbase database.
More generally, many commercial websites selling fluorophores, filters/dichroics, light sources or detectors provide spectra files that can be downloaded individually.
Please check and respect the corresponding terms of use and licenses of these external resources.
Note: When obtaining fluorophore spectra from the resources above (or any other source), make sure to also obtain the corresponding extinction coefficient (EC) and quantum yield (QY) values. These quantities should be provided when loading fluorophores with Fluorophore(), as they are essential for meaningful fluorophore comparisons and accurate cross-channel contamination estimates.
Antoine Coulon, CNRS, Institut Curie. antoine.coulon@curie.fr
This software is provided without warranty. Users are responsible for validating the accuracy and suitability of the results for their specific applications.