ome / bioformats

Bio-Formats is a Java library for reading and writing data in life sciences image file formats. It is developed by the Open Microscopy Environment. Bio-Formats is released under the GNU General Public License (GPL); commercial licenses are available from Glencoe Software.
https://www.openmicroscopy.org/bio-formats
GNU General Public License v2.0
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Metamorph ND time-lapse no longer recognised #4226

Open dominikl opened 1 month ago

dominikl commented 1 month ago

See https://forum.image.sc/t/metamorph-time-lapse-no-longer-recognised-during-bio-formats-import/101193/1

imagesc-bot commented 1 month ago

This issue has been mentioned on Image.sc Forum. There might be relevant details there:

https://forum.image.sc/t/metamorph-time-lapse-no-longer-recognised-during-bio-formats-import/101193/4

melissalinkert commented 1 month ago

I suspect #4093 is related, as a work-around for this problem is to modify the stage names in the .nd file, so that the modified file looks like this:

$ cat test_timelapse_20240816.nd
"NDInfoFile", Version 2.0
"Description", 
"StartTime1", 20240816 09:49:28
"DoTimelapse", TRUE
"NTimePoints", 13
"DoStage", TRUE
"NStagePositions", 6
"Stage1", "1"
"Stage2", "2"
"Stage3", "3"
"Stage4", "4"
"Stage5", "5"
"Stage6", "6"
"DoWave", FALSE
"NWavelengths", 0
"DoZSeries", FALSE
"WaveInFileName", FALSE
"NEvents", 0
"EndFile"

and the diff is:

$ diff test_timelapse_20240816.nd test_timelapse_20240816.nd.bak 
8,13c8,13
< "Stage1", "1"
< "Stage2", "2"
< "Stage3", "3"
< "Stage4", "4"
< "Stage5", "5"
< "Stage6", "6"
---
> "Stage1", "B2"
> "Stage2", "B3"
> "Stage3", "B4"
> "Stage4", "C4"
> "Stage5", "C3"
> "Stage6", "C2"

Data has now been copied to inbox/gh-4226 for further evaluation.