Quantify dynamics of protein accumulation at adhesion clusters
Cas-integrin-paper-2023-Cooper-lab contains MATLAB scripts used to quantify the time shift between red (CasmSc) and green (YFP-VCL, b1-EctopH, ITGB1GFP or CrkmGL) cluster formation from TIRF microscopy datasets described in Kumar et al:
Cas phosphorylation regulates focal adhesion assembly.
Kumar S, Stainer A, Dubrulle J, Simpkins C, Cooper JA.
Elife. 2023 Jul 25;12:e90234. doi: 10.7554/eLife.90234. PMID: 37489578
The pipeline involves the following steps: drift correction, image preprocessing and denoising, cluster segmentation and tracking, intensities extraction and normalization, and signal analysis.
adhesiondynamicstirf.m measures the time shift in the accumulation of two different proteins at the same adhesion cluster. It relies on bfmatlab, the bio-format package for MATLAB that can be freely downloaded at:
https://www.openmicroscopy.org/bio-formats/downloads/
ImregStack.m corrects the image stack for stage-drifting using translation transformation.
progressText.m is a helper function developed by the Danuser lab to show progress of a loop as text on the screen. It is employed by both adhesiondynamicstirf() and ImRegStack().
DemoFATIRF.tif is an example of TIRF dataset that can be used for demo purposes.