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OME-XML Z Scan Direction

General user discussion about using and improving the OME Data Model.

OME-XML Z Scan Direction

Postby rosscarter3 » Tue Nov 22, 2016 2:13 pm

Hello,
I've been scouring the OME-XML schema to no avail.

I need to know in which z-direction the confocal images I'm looking at were acquired in, either 'top to bottom' or 'bottom to top'. Is there anything in the OME-XML that would tell me this?

Link to OME-XML file
https://gist.github.com/rosscarter3/9f6 ... 7e7bc491ba

Thanks in advance,
Ross
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Re: OME-XML Z Scan Direction

Postby rleigh » Wed Nov 23, 2016 3:03 pm

Dear Ross,

The x,y,z origin is defined as being the (top,left,bottom) corner of the volume. However, the Z origin isn't clearly defined in the formal specification. Note that the plane order does not need to match the acquisition order. If you do acquire top-to-bottom that's totally fine.

Regards,
Roger
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