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Jamie-Dean-Lab / Lineage-analysis

for private use only; work in progress
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Create converter for MaMuT files #6

Open K-Meech opened 1 week ago

K-Meech commented 1 week ago

Create a converter for MaMuT output files to the cell tracking challenge format.

Output files

MaMuT has the same output files as trackmate, with minor differences to the .xml. The .xml has some extra information relating to bigdataviewer files.

Existing converters

There doesn't seem to be an existing CTC converter integrated into MaMuT. As the output files are the same as Trackmate though, it should be possible to re-use most of the same code.

Also, it is possible to import MaMuT data into Mastodon, which does have a converter via a plugin. This is probably the best + easiest option to use!

K-Meech commented 1 day ago

Extracting other features (not directly in CTC file)

See the info for trackmate, as the file format is the same.

The only difference is that it is likely not possible to read the inter-frame time directly. MaMuT (unlike Trackmate) relies on opening images in BigDataViewer format. With this format, all metadata is stored in a .xml file but, unfortunately, this doesn't seem to include the time unit or the time each frame represents. As MaMuT opens these files directly it is likely it will always list the inter-frame interval as 1 frame rather than anything relating to a specific unit like seconds

Update: this was confirmed by one of the main maintainers on the image.sc forum