I’m using MaMut for tracking cells in a 3D time-lapse. I have already annotated all single cells and manually linked them across time, and I currently have a quite complex lineage with some tracks including splitting events (cell divisions). Up to now I was using the spot names given by default (ID##), but now I’d like to edit all of them so I can provide some consistency and biological meaning classifying them by lineage (for instance, same prefix to all linked spots of every track). I don’t find how can I do it easily. My question is: is there any way to set the names of each linked spot at once? The idea afterwards would be to export the trackScheme info-pane with the numerical feature values of all the spots, so I assume each spot must have a different and unique name even if they belong to the same branch. At the end, I would like to get something like: tracking 01 containing spots 01-01, 01-02, 01-03 (for the 3 first frames) and when the cell divides (for example in frame 03), the daughter cells will be: 01-03-01, 01-03-02. (so I will force each branch to be displayed left or right after a division. I would really appreciate any suggestion to be able to do this kind of name editing that will help me to export the numerical data in a coherent manner.
At the current time, there is no automate naming of cells in MaMuT.
Not that I know actually, if someone wrote a plugin to do so please come forward.
The only thing that exists is batch renaming. Do you know how to do that?
Thanks for your reply @tinevez
Actually I don’t know how to do this batch renaming, how can I proceed?
It’s all done in TrackScheme.
First go to the
full display mode and select a bunch of cells:
Right click on the background to bring the popup menu:
Select the action that says
Edit X spot names. A text box should appear on one of the cell.
Edit the name then press
Et voilà !
Thanks again @tinevez,
I already tried that (following the guidelines at the website https://imagej.net/Getting_started_with_MaMuT
but then all the selected spots will have exactly the same name (the one edited in the text box), and consequently I think that the trackScheme info pane is only able to detect one of the spots, right?
That’s why I understood each spot must have a different and unique name, so was trying to include some kind of suffix like on each one (for instance NAME-01,NAME-02, NAME-03…)
Do you know any alternative to export the numerical data (xyz coordinates, R…) of each spot?
Normally MaMuT is made to be extended so if you can know a bit of Java, you should be able to create a renamer.
Hi again @tinevez
We’ll try to create that renamer to help me giving a different code to each cell. I thing that modifying the java code is not a problem, but I don’t know where is exactly the part corresponding to this batch renaming in the Mamut code (in https://github.com/fiji/MaMuT/tree/master/src/main/java/fiji/plugin/mamut)
Could you please indicate me how can I find the code line so I could try editing? And afterwards, how can I proceed to install it as a plugin? Thanks!
It does not exist. You will have to create it from scratch.
I meant to say the option you indicated before, selecting a bunch of cells in the track Scheme and editing the names. Could be possible to edit this parte of the Mamut code?