SCOS data processing

Communications Biology 2023 - Measuring human cerebral blood flow and brain function with fiber-based speckle contrast optical spectroscopy system

We created a data analysis pipeline for SCOS under photon starved conditions. This repository contains:

1. Sample speckle images and dark camera image from Hamamatsu ORCA-Fusion camera (./sample data)
2. Camera parameters such as gain and mask (./camera calibration)
3. Functions and script to run the noise correction pipeline

To run the code:

1. Download all the files and subfolders in one folder
2. Run HamamatsuPipeline.m

The HamamatsuPipeline.m outputs:

1. Processed data files (img_file_mean_img.mat, analyzed_K2_img_file_YYYY_MM_DD_HH_mm.mat) in ./sample data.

2. Raw standard deviation and mean intensity time course
   

3. Linear estimation of window I(t) in the contrast measurement

4. Contribution of noise sources to the measured speckle contrast

5. Fundamental speckle contrast after noise correction and the corresponding blood flow index

   

For any issue reporting or suggestions, please contact Byungchan Kim, kennykim@bu.edu