I’ve been working with lightsheet microscopy data for a project, and we have successfully ran the most recent version of TGMM cell tracking from the Keller Lab. We were hoping to visually inspect and manually filter/correct some of our tracks using MaMuT on Fiji. However, I have been having some issues with opening the TGMM output files on MaMuT.
For background on the data: we have about 1082 time points of 960x960x599px images, all single channel and all converted to the keller lab blocktype (klb) format. I’ve successfully generated an XML for these KLBs using BigDataViewer. On the TGMM output side, we have 817,323 objects detected across the movie in 9,166 lineages.
When I attempt to import this data onto MaMuT via “Plugins>MaMuT>Import TGMM results in MaMuT”, and enter the xml directory for the image file, the “XML_finalResult_lht” folder for the TGMM output files, Fiji will start a progress bar with the title “Loading TGMM outputs”. However, even after running this overnight, there is no progress on the bar. This holds true also when I click and unclick the “crop data” option in MaMuT (as suggested in the TGMM manual). Does anybody have any idea what might be the issue in loading the data? The lack of an error message has made it tricky for us to debug it.
Thanks ahead of time for all answers!