I am trying to track bacteria using Ilastik and correcting them with Mamut. From the original tracking I have a huge dataset, around 3000 detected tracks, which include a lot of scattered pieces that Ilastik could not properly reconnect. Therefore I cannot just take less tracks, or I may loose relevant pieces. At the end, I would like to have, let’s say 200 full tracks, than verify if the statistics is enough and, if not, add some more tracks. The problem is that Mamut is constantly renaming and reordering the tracks after I modify them. When I link two pieces from different tracks, or even if I just add some points, sometimes (not always) the number of the new track I get changes into something which is neither of the two original ones and the neighbouring tracks change their number too. The criterium by which he does it is quite obscure to me, as the numeration skips numbers, some tracks end up at the end (in the Track Scheme), some other remain the same, some tracks change the previous name in a non-consecutive number etc. I tried to change the names myself every time I modify a track. Unfortunately, he would still rename it aftwerwards if something else change. If I try to enforce the name I want after he renames it, he also does not let me do it: he would change the name of the neighbour tracks instead or do nothing at all…no error message even. The problem is that, in this way, it is impossible for me to distinguish the tracks that I already checked from the others, as they end up in a way that looks randomly mixed to me. Any suggestion would be highly appreciated.
Travelling on holidays
Brief answers sorry
You can rename a track by double clicking on its name
Thanks for your fast answer! I have tried exactly that system. Two cases:
- If the ‘new’ track got the same name (from Mamut), that it had before my resorting, it works fine and I can rename it
- If the ‘new’ track got a different name, it does not let me rename it when I double click on its name. In some cases, it tries to rename one of the neighbouring tracks. In some cases it doesn’t do anything (the typing interface does not appear). To me it looks like a possible bug.
Further problem: if I manage to rename my track (case 1), this does not mean that the newly named track will retain the name I gave. If I go on with my sorting and in the next track Mamut does the shuffling of numeration, I have seen it shuffling also the tracks I already renamed: under the name I gave, it appears a different track.
Refreshing the view does not change the situation in neither of those cases, unfortunately.
Noticed last week
Click redo layout
Then MOVE THE WINDOW ELSE THE TRACK NAMES ARE NOT REFRESHED
Sorry for the bug and the phone keyboard