BrightEyes-ISM’s documentation
BrightEyes-ISM is a Python package for analysing and simulating Image Scanning Microscopy (ISM) datasets.
Read about BrightEyes-ISM here:
Zunino, A., Slenders, E., Fersini, F. et al. Open-source tools enable accessible and advanced image scanning microscopy data analysis. Nat. Photon. (2023). https://doi.org/10.1038/s41566-023-01216-x
BrightEyes-ISM contains the following modules.
The analysis module contains libraries for:
Adaptive Pixel Reassignment (https://doi.org/10.1038/s41592-018-0291-9)
Focus-ISM (https://doi.org/10.1038/s41467-022-35333-y)
Image Deconvolution (https://doi.org/10.1088/1361-6420/accdc5)
Fourier Ring Correlation (https://doi.org/10.1038/s41467-019-11024-z)
The simulation module contains libraries for:
Generation of ISM point spread functions (https://doi.org/10.1016/j.cpc.2022.108315)
Generation of tubulin phantom samples
The dataio module contains libraries for
Reading the data and metadata from the MCS software (https://github.com/VicidominiLab/BrightEyes-MCS)
Note that all the image processing functions assume that the detector array has a squared geometry. Datasets acquired with a non-cartesian arrangement (e.g. AiryScan) might require additional pre-processing.