I have a sequence of 2 channel tif images taken of live cells. My goal is to use a stable nuclear reporter from the TxRed channel to identify and track nuclei masks and then measure the intensity of a GFP reporter within each nuclei. I run a pixel classifier on the TxRed nuclei and create a hdf5 file of the probabilities. I then run a tracking project that takes the TxRed images as the raw data and the hdf5 file of the probabilities and outputs a CSV_Table using the Plugin export. I then run the same tracking project giving it the same hdf5 file of the probabilities but in this run give it the GFP images as the raw data. I get a second CSV_Table file from this run.
While my results look reasonable, are the tracks and lineages in the TxRed and the GFP CSV files referring to the same cells? I’d like to know if this is a valid approach and if there are optimizations I can create.