saibr 0.1.6

Python implementation of SAIBR: a tool for performing spectral autofluorescence correction on biological images

SAIBR (python implementation)

Python implementation of SAIBR: a simple, platform independent protocol for spectral autofluorescence correction

Paper

FIJI plugin

Tutorial notebook

As a first step, I would recommend checking out the tutorial notebook. This can be run in the cloud using Binder (please note that it may take several minutes to open the notebook):

To run locally, download the code and install the relevant requirements (requirements.txt) in a virtual environment.

Install instructions

To explore further and incorporate into your own analysis pipelines, you can install the package from PyPI using pip:

pip install saibr

If you want to make changes to the code you can download/clone this folder, navigate to it, and run:

pip install -e .[dev]

Citation

If you use this method as part of a publication, please cite the following reference:

Nelio T. L. Rodrigues, Tom Bland, Joana Borrego-Pinto, KangBo Ng, Nisha Hirani, Ying Gu, Sherman Foo, Nathan W. Goehring; SAIBR: a simple, platform-independent method for spectral autofluorescence correction. Development 15 July 2022; 149 (14): dev200545. doi: https://doi.org/10.1242/dev.200545

License

This work is licensed under a Creative Commons Attribution 4.0 International License.