LEADS publication - Githubissues

As discussed, I'll write down here more or less what we discussed to make LEADS publishable. Not exhaustive, but more as a starting point.

selling points:

interactive (GUI), yet reproducible since parameters are saved
growing community using such an assay
flexible (loop extrusion, condensation, roadblock studies, plectonemes (+SMC), multi-video alignment and comparison)
extensible

To do:

[ ] ~done: finish bug-free version of cropping routing
[ ] useful feature for visualization: export kymo with tracks overlaid (multiple colors side-by-side?)
[x] combine cropping and kymograph routines, maybe by making kymograph/cropping tabs of the LEADS application
[ ] make two versions on github: one 'plug-and-play' exe version and one developer source-code available version
[ ] Possible extensions: 2D tracking, bleaching curve extraction+step finding algo, MSD fits and saving of resulting fit parameters in hdf5

Examples to show:

[ ] #15
[ ] roadblock
[ ] plectonemes
[ ] up to 3 colors
[ ] MSD of diffusing/translocating SMCs (w/ fit and parameter extraction)
[ ] Optical Tweezer data (where from?)
[ ] saving publication-quality videos and kymo's
[ ] Filtering (median, n2v?, others?) and background subtraction (tophat, ...?) options
[ ] bleaching curves + step finding
[ ] 1D/2D tracking
[ ] Force calculation based on MT data (maybe provided for a few SxO concentrations?)

Next steps:

biswajitSM / LEADS