jasontsmith2718 / unmix-me

UNMIX-ME (Unmix Multiple Emissions)

Deep Learning for Hyperspectral Fluorescence Lifetime Image (HFLI) Unmixing

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This GitHub contains relevant script, data and instructions for:

1. FLI data simulation workflow (MATLAB)

• HMFLI (Hyperspectral Macroscopic Fluorescence Lifetime Imaging)
• HMFLI-RET (HMFLI with Resonance Energy Transfer correction). Validated for AF700/AF750 FRET pair
• Other - for plotting hyperspectral TPSF information and ex. generation of emission spectral data.

2. Neural network training (python, [Tensorflow & Keras]).

• UNMIX-ME CNN model for HMFLI analysis

Authors: Jason T. Smith, Marien Ochoa

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Relevant Work:

Biomedical Optics Express Manuscript

• Smith JT, Ochoa M, Intes X. "UNMIX-ME: spectral and lifetime fluorescence unmixing via deep learning." Biomedical Optics Express. 2020 Jul 1;11(7):3857-74.

Original preprint

• Smith JT, Ochoa M, Intes X. "Spectral and lifetime fluorescence unmixing via deep learning." bioRxiv (2020): 745216.

OSA Biophotonics Congress Proceeding & Virtual Presentation

• Smith JT, Ochoa M, Intes X. "Hyperspectral Lifetime Unmixing via Deep Learning," in Biophotonics Congress: Biomedical Optics 2020 (Translational, Microscopy, OCT, OTS, BRAIN), OSA Technical Digest (Optical Society of America, 2020), paper SW1D.5

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Funding:

National Institutes of Health (R01 CA207725, R01 CA237267, R01 EB19443)

unmix-me's Issues

Unmixing tif stacks

Hi
I have a pretty simple use case i think. I have just 2 3d tif stacks (51251232, 32 is number of frames) belonging to different channel wavelengths. I want to unmix each of them as we think that each channel can contain some infra signals. Can you please tell me if i can use this tool to do this?

Broken links

Hello,
It seems that the links for train and test dataset given in the readme are broken. Would it be possible to update the links ?