Zeiss Axio Scan Z1 scan with two objectives

Hi everyone,

I am wondering whether it’s possible to scan with two objectives in bright field and store the images of both images inside one CZI file (or separately). Does anybody knows whether this is possible? For image analysis I need low resolution preview for pre-screening and a high resolution image, to extract detailed information of the regions of interest.

Any ides would be very much appreciated

To scan the same sample with two objectives, I would scan with one profile, and then run the same slides manually with a second profile. One profile would use a lower NA imaging lens, and the other would use a higher NA imaging lens. ROI selection could be identical between both profiles, but there will likely be slight changes in the area covered when using two different imaging lenses.

However, it’s not clear to me why two scans would be needed (unless you want to pre-screen low-resolution images taken quickly and then only image selected samples at high-resolution).

The Axioscan should store images in an image pyramid, where down-sampled image data (low-resolution) is loaded when viewing all stitched tiles at low digital zoom. When you digitally zoom in, higher resolution images will be loaded (up to the highest-resolution raw image tile) . With this, you should be able to look across the entire scan for pre-screening. Then, you should be able to analyze using the raw, highest-resolution image data that is already stored in the same file.

If you are reviewing data with Fiji, then you will be prompted to load one level of the image pyramid, which is not nearly as useful as what QuPath can offer. QuPath (Welcome to QuPath! — QuPath 0.3.0 documentation) will be much more useful when working with Axioscan images as you can seamlessly move from low resolution to high resolution viewing. Additionally, it can handle quite a few common analysis pipelines (and some more exotic ones if you dig deeply into examples posted at Topics tagged qupath)