Description
BrightEyes-ISM is a Python package for analysing and simulating Image Scanning Microscopy (ISM) datasets.
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.
Installation
The source code can be found at https://github.com/VicidominiLab/BrightEyes-ISM. The latest version of the package can be installed directly from GitHub:
pip install git+https://github.com/VicidominiLab/BrightEyes-ISM
Or the most recent stable version can be installed using pip:
pip install brighteyes-ism
We also provide most of the package’s functionalities via a Napari plugin, which can be used as a graphical user interface. The plugin is called Napari-ISM and can be found at https://github.com/VicidominiLab/napari-ISM. It can be installed using pip:
pip install napari-ism
Dependencies
BrightEyes-ISM requires Python >= 3.7 and the following packages:
numpy
scipy
matplotlib
scikit-image
scikit-learn
poppy
PyCustomFocus
h5py
tqdm
statsmodels
Importing
The modules can be imported as in the following example
import brighteyes_ism.analysis.APR_lib as apr
import brighteyes_ism.simulation.PSF_sim as psf
import brighteyes_ism.dataio.mcs as mcs
Note that the installation requires an hyphen symbol (brighteyes-ism), but the import requires an underscore symbol (brighteyes_ism).
Example
Some examples of usage of BrightEyes-ISM can be found in the following notebooks:
Citing
BrightEyes-ISM and Napari-ISM can be cited as
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