I use two pipelines to track 87 image sets (time points) * 3 channels. The 1st identifies, manually corrects and saves the nuclei objects. The 2nd loads and tracks the objects. When the tracking comes to the 36th image set, the following errors start to occur.
If I ignore them (from 36 to 87 except 37) all, the following error occurs before post-processing.
If I remove the object manual correction module from the 1st pipeline, the 2nd pipeline can run successfully without errors.
Does anyone know what is wrong in here?
I really am not sure what’s happening here, but I wonder if he manual editing leaves objects with ‘gaps’ in their numbering which then confuses TrackObjects in some way.
You might be able to check this by examining spreadsheet output of object data from the 1st pipeline - do the object numbers have gaps?
One quick thing to try is ReassignObjectNumbers after the manual editing step. It’s a bit of a hack but I wonder whether the Split option will have the effect of numbering your objects sequentially - I am really not sure. A more certain way to do the renumbering would be to re-identify the nuclei using IdentifyPrimary after the manual step, but that involves a bit more finagling to get the object identification right.
Another very quick thing to try is an alternate tracking method in your second pipeline, to see if you get the same problems.
If these ideas do not help, someone else will need to help brainstorm and troubleshoot!
Possibly related to this known error- are you using the “Distance” method of tracking, and if so can you try the “Overlap” method instead to see if that works?
Gaps do exist as I check the pixel values of ‘objects’ images in matlab with ‘unique’ function. Nearly every manually edited image has gaps (difference > 1), but when the gap becomes large (difference > 2, perhaps), the bug appears. I will try ReassignObjectNumbers and will not try to re-identify the objects. The alternative tracking method works, but I still hopes to be able to use ‘distance’.
Thank you for the help!
Yes, they are exactly the same problem. The “overlap” method can track without bugs. Thanks for the help!