Spectral Imaging Toolbox

Segmentation, hyperstack reconstruction, and batch processing of spectral images

Spectral imaging with polarity-sensitive fluorescent probes enables the quantification of cell and model membrane lipid packing and membrane fluidity, usually characterized by the generalized polarization (GP) parameter. The Spectral Imaging Toolbox provides a powerful way to process large spectral imaging data sets with no programming experience required.
For more details please see our publication here:
https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-017-1656-2
DOI: 10.1186/s12859-017-1656-2
If you publish work inspired by or using this code, please cite us.

Features:
- GUI - no programming experience required
- In-depth user manual pdf
- Calculates distributions of GP values
- Plots GP histograms with Gaussian or 2-peak Gaussian fit
- Generates pseudo-colored GP maps
- Plots spectra
- Segments cells/vesicles and their membranes by watershed, lasso, or circle-detection methods
- Handles 4D hyperstacks
- Can reconstruct GP in 3D for spectral z-stacks
- Determines particle size distributions in circular-object mode
- ROI processing enabled
- Batch processing enabled
- Outputs all data to excel files
- Outputs publication-quality figures for spectra, GP histograms, pseudo-colored GP maps, and 3D reconstruction
- Outputs .mat files with data for further processing if desired
- Output organized for each level of segmentation (ie: full image, segmented objects, segmented membranes)

IMPORTANT: bfmatlab which reads bio-format images was too large (~20 MB) to be included on the file exchange. It is necessary for use of the Spectral Imaging Toolbox. Please include it in your MATLAB path: https://www.openmicroscopy.org/site/support/bio-formats5.4/users/matlab/index.html

Also, there is a copy of bfmatlab and a fully-featured demo of the Spectral Imaging Toolbox available at https://ora.ox.ac.uk/objects/uuid:4375842f-3598-418d-8aa3-9b31f5023401. The demo includes large image files from actual spectral imaging experiments using a variety of popular spectral imaging probes such as Laurdan and Di-4-ANEPPDHQ. The images were too large to include here. Please note that this is the official repository for the Spectral Imaging Toolbox. The demo link will not be updated but will always be available.

Lastly, this code will be actively maintained and updated. Please do not hesitate to comment or contact me directly with questions, feature requests, pull requests etc. I am happy to help.