OME-XML / Precisions on Image / AcquisitionDate

bio-formats
ome-xml
Tags: #<Tag:0x00007fa307710168> #<Tag:0x00007fa307710b18>

#1

Hello!

I’m currently writing a plugin to synchronize the display of several images (and 1D plots) based on their real date and time of acquisition (imagine one camera is acquiring at 1fps, a second at 30fps, and a patch clamp signal at 2kHz). Also the acquisition starting date can be different between devices.

I’d like to make this plugin a bit general: I want to get the timing information of images based on standardized metadata. If I understand correctly, what I can do is retrieve the timing information from:

  1. the Element Image / AcquisitionDate of the OME-XML schemas.
  2. +the DeltaT “parameter” (with its associated time unit)

Is that correct ? Is there a better way to do this ? Will I run into troubles ?

My second question is regarding the acquisition date of OME-XML. Is this supposed to be the start of the acquisition or the end ? I didn’t see anything specified here (http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#Image_AcquisitionDate).

Thanks for your insights!

N.B. For Slidebook data, the specified AcquisitionDate is the end of the acquisition, not the beginning as I would have assumed.


#2

Hi @NicoKiaru,

thanks for raising this important question. In addition to the OME schema, we have reviewed the various documentation and notes about the Image.AcquisitionDate element and its predecessor Image.AcquiredDate.

As you said, the schema currently does not specify whether this corresponds to the beginning or the end of the acquisition. Tightening this specification e.g. to enforce AcquisitionDate to be the start of the acquisition would be a possibility but would constitute a breaking change of the OME model.

At the moment, the exact interpretation of this date is format-specific and reflects the implied interpretation of the file format.

Best,
Sebastien


#3

Ok, thanks for taking the time to answer.