Running the pipeline on all of your time lapse should be as simple as loading in all of your images from all time points and running it.
how can I maintain same detected cells over time in order to plot individual traces?
In all of the cases below, you’ll want to make sure to set up your Groups module to lump all frames in a particular time lapse together- check the help for that module for good tips.
If the cells don’t really move at all over the course of your time lapse, you could try running one short pipeline first on all your T0s to identify cells, export the cell masks as images, then use the cell masks from T0 to measure the exact same cell outlines at all time points- this thread gives one example of doing this.
If the cells move some but not too much, you can use the TrackObjects module to maintain cell identity - in that case, you’ll want to look at the TrackObjects_Label, rather than ObjectNumber, to track which cell you’re looking at over time.
If the cells move a LOT, you can try TrackObjects but consider time sampling pretty densely so that your tracks are more likely to be accurate and complete.