Bioformats and OMERO not recognising time data

Usage & Issues
#1

I am having an issue with OMERO not recognising the time data for my TIFF file (each tiff has 2 channles, 7 z-slices, and 21 frames/time points). When I open the files in Fiji, I can see the times (hh mm ss), but not in OMERO/OMERO.figure. I then realised I cannot see the times in Fiji when opening the file using he Bioformas Importer (see attached screenshot, left image opened without Bioformats, right, with Bioformats).

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I don’t know whether this has to do with the fact the file, which comes from Metamorph, assigns a time to each channel in each frame. You can access the original file in this link.

Any help on this issue will be much appreciated!

Thanks in advance!

Fede

1 Like
#2

Hi @fpelisch, I suspect the timestamp has been added from elsewhere, when you are opening the files are you using a macro? If so do you have the code for it?

#3

Hi @dgault, thanks for replying. This is the macro I use to create the movie files from Metamorph (this is not my creation): 012_Metamorph_Movies(Nicolas).txt (26.1 KB). This is the file I then save in my folders and in OMERO and has the issue I stated in my initial message.

Thanks

#4

just to give full credit: the macro is from Nicolas Loyer, from Jens Januschke’s lab.

#5

Part of the issue here seems to be that in processing the file with the macro and saving the result the file is no longer recognised as a MetaMorph file and is simply read as a basic TIFF. Do you have the original unedited files that were used to create the movie?

#6

Hi. Thanks. Here’s a link to the files I get from MetaMorph.

#7

Thanks, what I would probably recommend would be importing the original data using a pattern file and if you wanted it as a single file then converting to OME-TIFF to retain all of the original metadata.

To import the original files you can use the Bio-Formats Importer with the group files option selected and check the box to use a pattern with the below pattern name:
JDU38_ctl_02_<w1491 with 594 ,w2594 with 491>_t00<01-45>.TIF

That should group all of the timepoints, channels and Z stacks as a single import. If you wanted you could then use the Bio-Formats Exporter to save that as a single OME-TIFF.

Doing so will retain all of the original metadata (in the Show Info view) but wont rename the labels to include the timestamps as with the original macro. If you need the timestamps displayed in the label then you could likely reuse parts of that macro to provide them as before.