Hello science twips, in particular people interested in #tracking in Life-Sciences. Have you noticed this preprint?
Community Standards for Open Cell Migration Data https://www.biorxiv.org/content/10.1101/803064v1
Among other things, they propose a standard file format to store tracks. Even complex tracks like cell lineages with cell division, gaps in detection, complex points etc.
Check this repo:
They have a working implementation, and several import filters for files produced by some existing softwares. There is even one for #trackmate (I took this image from the TrackMate example folder)
And the file format is imho well designed. There are tables for locations, track segments (called links) and tracks (collection of links). This will make possible harnessing the very different outputs of SPT and CT softwares.
- Can we store extra object information in the shape of scalar real numbers? Like object mean intensity, estimated radius, etc.?
- Can we store 2D object contours? How?
- The same for 3D?
- Can we store settings information? By this I mean info that generated the tracks? link to the image file, parameters used for detection etc?
- What about performance in the main implementation? Do we have experience with large datasets, with e.g. 10^6 cells?
Because then it with this and interoperability it would be plain awesome.