This code is associated with the paper from Volkov et al., "Multivalency of NDC80 in the outer kinetochore is essential to track shortening microtubules and generate forces". eLife, 2018. http://dx.doi.org/10.7554/eLife.36764
matlab script to trace fluorescent particles in kymograph
- load a kymograph in tiff format
- select your region of interest by clicking on its top left and bottom right corners in your image
- select the background region with two clicks
- select the start region of your trace with two clicks (determines the initial values for position and height of the peak). the script fits a gaussian to each line of a kymograph, then displays intensity (area under the gaussian) and position (peak of the gaussian) as a function of time (line number * frame rate).
- check if your fitting is adequte, if yes press "save" to store the results.
run the script specifying the path - 'path', filename (no extension) - 'file', fluorescent channel of your particle of choice for multichannel kymos (for single channel leave '1') - 'dim', timestep of your acquisition (seconds per frame, or seconds per line of the kymograph - 'timestep', pixel dimensions in micrometers - 'pix'
kymo('path','example',2,1,0.16);
works only on single particles.