How can I run channel-wise acquisition programs on an AxioScan 7?

Software
1

Hi everyone,

It’s my first post for this forum so please direct me as needed.

I’ve run into some photoconversion issues with my slides that are marked for DAPI, AF488 an AF647 so I’m trying to acquire stitched slidescanner images using channel-wise acquisition starting from the AF647 wavelength, followed by AF488 and finally DAPI. However, this isn’t possible with the software and the vendor has indicated that macros won’t be able to perform this function either and that the software doesn’t come with a macro function.

The AxioScan 7 is the only slidescanner we have and being able to run channel-wise acquisitions would save me and our team a lot of time. Has anyone run into this issue before? What are some potential work-arounds I could try to get this function?

2

Your channels default filter cube may be a multi-band-pass cube, which can sometimes lead to unwanted crosstalk.

In the scan settings of the scan-profile (last tab) you should be able to select the filter cube (top → down is the acquisition order, remove and add in order you want to image) for each channel.

Select the channel you want to adjust, and in the graphical light path above it you can click on the cube to change it for that channel.

You may have to check a ‘show all’ check box in the top right of the channels-tab/widget
If it’s not there, you need to enable it in the options: tools > options > acquisitions > acquisitions tab > enable advanced imaging…

Selecting non-multi-bandpass filter cubes for each channel (if you have them in your filter turret) could resolve your issue.

Edit: I may have misread the problem, I have no idea how to image the whole selection one channel at a time.
But in principle you can change the channel order per tile which may already help.
Maybe 0% overlap (unsure where that option would be) could also do the trick.

3

Thanks for answering and the edit, imaging the whole section one channel at a time is what we’re going for.

Zeiss has told us anything other than 0% overlap isn’t possible with the current software. We also got a document that indicated a sequence of menus to find an “All tiles per channel” acquisition option (Tools > Options > Acquisition > Axioscan > Show Acquisition Order) but this option doesn’t show up for us.