I am looking for a particle tracking algorithm implemented in R. Something that would work at the level of data from image segmentation and that would use XYZT coordinates to link objects over T. For example, something similar to the LAP algorithm implemented in Jaqaman’s u-track. So far, I’ve only come across the flowcatchR package from BioConductor.
Is there a specific reason why it needs to be implemented in R? Otherwise I’d suggest the LAP tracker in TrackMate that comes with Fiji.
If it’s just about XYZT coordinates, it should be fairly easy to import/export as csv files and use whatever framework is providing a suitable implementation. Moreover, there are tools like #knime that let you seamlessly integrate a lot of tools in a single workflow. For example, I regularly use the ImageJ integration in KNIME for segmentation and tracking (making use of the LAP tracker implementation of #trackmate), followed by visualization using
ggplot2 in KNIME’s R View nodes.
Thank you, but indeed I’d prefer to have it in R as it’d be part of a bigger R project where XYZT coordinates are not directly coming from images.