Matlab code for tracking edge of cell and extracting kymographs. Github repository here: https://github.com/mullinslabUCSF/edge-kymograph
From:
Initiation and disassembly of filopodia tip complexes containing VASP and lamellipodin
Karen W. Cheng, R. Dyche Mullins
MBoC 2020
https://doi.org/10.1091/mbc.E20-04-0270
Here is a tutorial / guide on how to use ChimeraX with 5D light microscopy:https://www.rbvi.ucsf.edu/chimera/data/light-apr2017/light4d.html
It is on the ChimeraX web site under the Tutorials section, and also there is a link on the left side of the main ChimeraX web page called Presentations:https://www.rbvi.ucsf.edu/chimerax/
Here’s another tutorial about how to place markers on time series in Chimera (this can also be done in ChimeraX but user interface is slightly different) using Lil’s collagen filament time series as an example:https://www.cgl.ucsf.edu/chimera/data/markers-may2017/markers.html
Also there are details about how we handled Lil’s data in Chimera and ChimeraX
These are simple scripts to control the TIRF angle with the keyboard. In Micro-Manager, you load the scripts (under Tools->Shortcuts), then direct a keyboard shortcut (“Hotkey”) to run the script. The scripts add or subtract 50 and 1000 (coarse and fine), so I set each to be a different keyboard shortcut and marked those keys with tape and sharpie. After you optimize the TIRF angle, you open Tools->Device/Property Browser in uM and copy the new value then paste it into the relevant configuration.
Zip file here: NikonTiTRIFscripts