I need to scan quicker . Zeiss Axio Scan Z1

I use Axio Scan Z1. I scan at 40x, but it is very slow i think. With default options, 2x2 cm tissue takes minimum 15 minutes. And usually 10% of image is blur. I don’t think that is normal. @sebi06

  • I clean slide before loading.
  • I use default adaptive focus strategy settings.

Anyone can help about that?

Hello Mehmet,

Are you using a brightfield or a fluorescence scan profile? (some tips to speed up acquisition only apply to fluorescence profiles)

Do you know what proportion of your scan is spent at the coarse focus, fine focus, and scanning steps? (I only know how to do this by observing the scan status text, but perhaps there is a smarter way that I am unaware of) That will provide an idea of what step should be optimized (or if it can be optimized further).

Also consider if the 40X objective is needed for your experiment. If the 20X is sufficient, then you can complete the imaging step with 1/4 of the images. You may or may not save time during the coarse/fine focus steps, depending on how they are configured.

Can you describe the location of the 10% of the image that is blurred?
If the tissue has folds or areas with different thickness throughout the tissue, then those areas will be very hard to image without imaging at multiple z positions as well, due to the way that the focus map is generated. If you find that the blurred areas are due to gradual changes in tissue height across the sample (either because the edges are at a different height than the center or because opposing edges are at different heights), then modifying your focus strategy should be able to compensate for the height change. Additionally, if your coarse or fine focus steps do not have enough range (or fine enough focus steps) to focus on your tissue, then that could explain the blur.


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I use brightfield.

Coarse focus 5x, fine focus 40x range 60 micrometer, scanning 40x.

I talked with team and offered again I can scan with 20x quicker, they want 40x.

I cannot discribe location of 10% of image, because it is variable. Z positions also takes time.

Team compares with other devices like leica, hammamatsu etc. and they say “this takes too long”. Even one of them said “even the oldest devices we could scan it in 10 minutes”. I’m trying to figure it out.

There is also a series of videos by Zeiss on the Axioscan here that might be useful: https://www.zeiss.com/microscopy/us/local/zen-knowledge-base/axio-scan.html

Unfortunately, I am not experienced with other dedicated slide scanning instruments, so I cannot address those comparisons. My perspective is from operating the Axioscan as a drop-off service for bulk slide imaging, so the time that the instrument takes to finish is usually not critical to researchers, except those scanning slides that require further processing after the scan. The 15 minute scan time doesn’t sound unreasonable for tissue of that size, but it might be a bit slower than necessary.

In the tissue detection step, make sure that you are minimizing the amount of empty/unneeded space that is being scanned. This will save time during the coarse focus, fine focus, and scanning. It will also improve the accuracy of the focus maps. The empty space is probably already being minimized, but I’ll mention this for the sake of completion.

In the Axioscan, brightfield scanning has far fewer variables than fluorescence scanning. Perhaps confirm that your coarse/fine focus range and interval are following the Zeiss recommendations in the video/manual. The default adaptive focus point strategy should be relatively fast as it uses no more than 24 reference points in either coarse or fine focus (fewer for small samples). Changing the focus point strategy could save you some time during the focus steps, but will likely require more sample-by-sample fine-tuning. In the exposure section of the coarse/fine/scan steps, flash duration should only be a few microseconds per image with good illumination intensity (on our setup, your equipment may be different). If you optimize speed for a specific sample, the scan profile may be less robust or even fail for other samples, so please be careful and ask your Zeiss rep about any change that you are unsure of.