Zen metadata for registration

Dear all,

is there a possibility to automatically extract metadata of the slide coordinates from Zen images for registration purposes?
We have 10x microscopy data from an AxioScan Slide scanner that we register onto other imaging modalities (CT, MRI, Atlas,…) using Fiji. Now we want to look at specific subregions of these 10x images at a higher resolution, by partly reimaging the samples either with the AxioScan or another Zeiss microscope (AxioImagerM1/Z2).
Our registration pipeline needs the outlines of the 10x images. So the logical step for implementing e.g. 40x images would be to register them onto the 10x images in order to locate them in the other imaging modalities. This would be easier and faster if we knew the coordinates of the imaged regions relative to the glass slide.
Any help is appreciated!

Best wishes,

Hi Theresa,

I used to do this using BioFormats 5.1.10 and a bunch of scripts. Have a look here: test_planeXYZ.py

Or you try it directly in ZEN using: ExtractPlaneTable.py

Let me know what worked for you.

1 Like