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Metamorph .nd file timestamps

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Please note:
Historical discussions about the Bio-Formats library. Please look for and ask new questions at https://forum.image.sc/tags/bio-formats

If you are having trouble with image files, there is information about reporting bugs in the Bio-Formats documentation. Please send us the data and let us know what version of Bio-Formats you are using. For issues with your code, please provide a link to a public repository, ideally GitHub.

Metamorph .nd file timestamps

Postby ajost » Fri Jul 21, 2017 6:31 pm

Hi all,

I've been writing an ImageJ macro to pull timestamps from multichannel z-stack timelapse data acquired using Metamorph's multi-dimensional acquisition tool, and I've discovered a discrepancy between the timestamps in images I acquire in Metamorph when viewed in Metamorph vs. when viewed in Fiji with BioFormats.

In Metamorph, every image is timestamped individually when it is acquired, even when two or more channels are acquired at every timepoint. If I view the metadata in Metamorph, the timestamp for slice 1, timepoint 1, channel 1 is different from the timestamp for slice 1, timepoint 1, channel 2 - as it should be. However, when I open either a .tif from the time series or the .nd file in Fiji using BioFormats, the timestamps that show up in the OME-XML metadata are identical for both channels. At each z position, the timestamp of channel 1 is duplicated for channel 2.

I'm working on a set of macros that I'll be using to monitor microscope performance and diagnose problems, so it's important for me to be able to access accurate timestamps for each channel that reflect when each image was acquired. Is there any way I can configure BioFormats to do this? I've started to explore other options for extracting the timestamp, and of course I can access the timestamps in Metamorph, but it would be great to be able to continue to use BioFormats.

Best,
Anna
ajost
 
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Re: Metamorph .nd file timestamps

Postby dgault » Mon Jul 31, 2017 10:10 am

Hi Anna,

This is not an issue which we have seen before so thank you for bringing it to our attention. I have opened a Trello card on the Bio-Formats inbox to further investigate the issue (https://trello.com/c/Ws8V7CyG/164-metam ... timestamps).

If it is possible would you be able to upload a sample file showing this to the link below in order to help us put a fix in place?

https://www.openmicroscopy.org/qa2/qa/upload/

David Gault
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dgault
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Re: Metamorph .nd file timestamps

Postby ajost » Thu Aug 03, 2017 6:50 pm

Thanks David! I uploaded a sample data set including the TIF files per wavelength and timepoint and the .ND file. Let me know if there's anything else that would be helpful for me to provide.

Best,
Anna
ajost
 
Posts: 2
Joined: Thu Jul 20, 2017 5:08 pm

Re: Metamorph .nd file timestamps

Postby dgault » Tue Aug 08, 2017 9:02 am

Hi Anna,

Thanks you for submitting the files, I was able to test them and reproduce the issue as you described.
I believe I was able to debug the root cause of the issue and I have opened a PR with a potential solution that we will begin testing: https://github.com/openmicroscopy/bioformats/pull/2922

David Gault
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