What is the TGMM file format specification?

mamut
tgmm

#1

Does anybody know exactly what is the specification for the TGMM file format?

I received several conflicting bug reports for the TGMM import in MaMuT, the latest being this one: Importing TGMM Output to MaMuT.

It is caused by a bugfix suggested by Ko Sugawara that fixes his problem, as well as this one:

If I fix the bug reported in the post above, then I will probably break TGMM import for Ko and friends. So I reasoned that I am confused.

There is from my side a serious misunderstanding on how time frames are specified in the TGMM file format.

For instance, when I have GMEMfinalResult_frame0001.xml, does it mean that I should import spots from this file in the first time-point of the data (that is, the one with index 0)?

What happens when TGMM is ran skipping every other frames? For instance if it is ran on frame 0, 2, 4, 6, … of the data, does it generates
GMEMfinalResult_frame0001.xml
GMEMfinalResult_frame0002.xml
GMEMfinalResult_frame0003.xml
GMEMfinalResult_frame0004.xml

or
GMEMfinalResult_frame0001.xml
GMEMfinalResult_frame0003.xml
GMEMfinalResult_frame0005.xml
GMEMfinalResult_frame0007.xml

Also, what happens when we skip frames at the beginning? If TGMM is ran from frame 100, does the file index starts at 1 too?

The parent value for each spot, does it point to the previous XML file in the TGMM folder? Then what kind of “previous”? The one with the index just lower (GMEMfinalResult_frame0005.xml for target in GMEMfinalResult_frame0007.xml in the previous example)?

I am really looking for help on this, as I have to maintain an importer for a file format that I do not master… If you used TGMM before I would welcome your advices…


#2

Maybe this helps:

https://github.com/haohaibo/tgmm/blob/04a95d0cc4c38ecf263481e8c9a29ddc637ea70e/nmeth.3036-S2/README.txt#L104-L123


#3

Thanks.
I would still like to be 100% sure about timepoint specifications.