discard cells touching the exit

[julou]

because cells about to leave a growth lane will always be problematic (partly cut, blurred, etc) and hence discarded from the data analysis, it would be very useful to discard them in MoMA already. This probably means giving a special status to segments that touch the exit (at least pruning them, even better would be to exclude them from the optimization).

At the moment, I give myself a visual threshold and don't fix issues closer to the exit (sometimes pruning the corresponding lineage to be sure that the error cannot be propagated). However, this has 2 limitations:

• in some datasets, a large fraction of the errors occur on cells touching the exit (or the one below), I guess the optimisation would work best if all segments touching the exit would be discarded
• the visual curation would be easier if segments and assignments of the cell touching the exit (and hence shrinking with time) would not be displayed.

I hope this request makes sense. Curious to read whether you've considered (and hence discarded something similar during the development)…

Best, Thomas

[erikvannimwegen]

Explanation: I discussed this with Thomas and I am not 100% sure that this is an easy issue. It is easy enough to let the user set a vertical position that cells are not allowed to go above (i.e. pixel coordinate going UNDER some critical value), but I am worried that you might get cells that move up and down across this critical value and that one might get problems with the tracking (i.e. cells would appear from nowhere when they come back from above the threshold). So maybe this is something to discuss.

[fjug]

Simple thing one could do: provide a function in MoMA that (after an optimization run) automatically prunes the lineages as soon as a cell touches the top of the GC. A discussion about benefits for the optimization itself might be interesting, but I do not expect this to be very helpful (as you said as well).

[erikvannimwegen]

This sounds like a good solution to me but let me check with Thomas.

[julou]

It sounds very good! not sure though how it will behave after optimising again… what do you think? or you think of running it automatically after each optimisation?