Cortex-wide transcranial localization microscopy with fluorescently labeled red blood cells

To demonstrate how to obtain the structural/velocity/flow direction maps using the localization data, a small script (i.e., MainFunc_static_TNTutrack.m) along with a sample dataset which was generated using the open-source TrackNTrace toolbox, which was originally developed for single-molecule localization microscopy (Stein, S. C. & Thiart, J. TrackNTrace: A simple and extendable open-source framework for developing single-molecule localization and tracking algorithms. Scientific reports 6, 1-7 (2016)). 

The current script was test with MATLAB R2020b in Windows 10 system. The localization and tracking of stained RBCs in the raw image stack were performed using the TrackNTrace toolbox GUI and the results were saved in the sample data. The sample script calculates the functional maps. Depending how many localized and tracked points, it takes 5 - 10 min to render the functional maps. The output results will be saved in another .mat file.

If you have questions on the use of the sample code or request further information, please contact Dr. Zhenyue Chen at the following email adress zhenchen@ethz.ch.