Image Pyramid downsampling values

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user-5723
Posts: 2
Joined: Thu Jan 01, 1970 1:00 am

Image Pyramid downsampling values

Post by user-5723 »

Hello,

I have been working with Zen on two different microscopes. First, a microscope that we have in our lab locally, which handles automated single slide acquisition. Second, we are looking at getting a scanner than fully automates scanning around 100 slides in a single acquisition run.

We had Zeiss scan some sample slides for us using their fully automated scanner and received CZI output files. These files contained pyramids with 2x downsampling. We tried to reproduce these using our local microscope, but for some reason it created 3x downsampled pyramids.

Unfortunately, our pyramid viewer requires 2x downsampled images.

How can we ensure that Zen is going to produce 2x downsampled images for both our local microscope and the fully automated scanner.

Thanks,
Tim
user-4
Posts: 398
Joined: Thu Jan 01, 1970 1:00 am

Post by user-4 »

Hello Tim,

Yes, there are two Pyramid Factors (2 and 3) in czi files.

The pyramid factor does not directly depend on the microscope but more on the way the image was taken. The pyramid factor 2 is used when the acquisition machine of ZEN (Zen Service) generates the image during ‘pure’ acquisition. The pyramid factor 3 is generated when any processing by ZEN (the application itself) is done. So if you get an image with factor 3 after ‘acquisition’ usually two steps, acquisition via ZEN Service (factor 2) and post processing by ZEN (factor 3), have been done.
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