Replies: 4 comments
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Hi Peter, It looks like things are working. For example, if I look at cell 45 - it divides into 175 and 176, and correctly builds the tree (I can see the white branching point in your movie above). Most likely, some parameters need tuning, to maximise the number of mitotic detections. I would also say that if you can add any extra state information, like pre-mitotic labels, that really helps. If you use arboretum do you see a lineage tree for cell 45, for example? |
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Hi Alan, Thanks for the suggestions. 45 seems to divide/be picked up correctly, but then the daughter cells mis-track later in the timeseries and then mess up the lineage tracing. Here's an arboretum screenshot: Thanks for your help! PS--I'm pinging 2 of my colleagues who are also looking into this: @emmanuel-contreras and @rupsadatta |
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Ah - I see, OK. Well this can happen during the optimisation step for a couple of reasons:
What we've found best is if you can use the object Finally, there is also a new (developmental) option in #143 - It adds in extra |
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I'm going to convert this to a discussion so that others can use this |
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Hi Alan/team:
We've been working with B-Track on a few projects, and overall it appears to be working super well for tracking cells; however, we can't usually get daughter cells to be properly detected. I've attached my config file cell_config.txt as well as a sample
of what I'm referring to where a cell clearly divides, but no parents/generations are detected.
If I understand correctly, if a cell divides and it's accepted, we should be seeing 2 new id's right? Also, there are no divided fates being accepted in the log either that I can see.
Happy to attach additional data/examples if that would be helpful. I'm also not sure if my configuration file is properly set up for this--can you shed some light on what adjusting each of the parameters in the configuration under the motion model and hypothesis do?
Thanks for all of your work on this!
Peter
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