Saving tissue outlines

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Mohammad Naser
Posts: 2
Joined: Tue Sep 22, 2020 8:59 pm

Saving tissue outlines

Post by Mohammad Naser »

Is there any way to save the outlines of multiple slides automatically in AxioScan.Z1? Note, we have recently updated to Zen 3.1 with Hotfix #7.
CarlZeissMicroscopy3
Posts: 180
Joined: Wed May 20, 2020 10:10 am

Re: Saving tissue outlines

Post by CarlZeissMicroscopy3 »

Hello Mohammad Naser,

this is not so easy to answer.

I'm trying to get am image that has tissue recognition form the AxioScan team.
After investigation you will get a reply if there is a way to read the outlines by OAD, which means with a macro.

There is no 'autosave checkbox' for this task in the GUI. Therefore just a manual export is possible.
From my point of view the only way is to check if a macro could do the job.
CarlZeissMicroscopy3
Posts: 180
Joined: Wed May 20, 2020 10:10 am

Re: Saving tissue outlines

Post by CarlZeissMicroscopy3 »

Hello Mohammad Naser,

if 'Keep separate peview image file after finish' is activated in Tools/Options/Acquisition/AxioScan then an image with the tissue polygones is saved.

You can access these images in a macro and read the 'Graphics' elements.

Finally it is possible to get the points of the graphical elements. This list of points like x1;y1 , x2;y2 , etc. can be saved in a file.

Is this a solution for what you intend to do?
julie diane
Posts: 24
Joined: Wed Jun 28, 2023 1:25 am

Re: Saving tissue outlines

Post by julie diane »

Open Zen Software: Launch the Zen software on your computer.

Load Slides: Load the slides you want to scan and outline into the AxioScan.Z1 slide scanner.

Create Outlines:

Navigate to the "Acquisition" or a similar tab/menu in Zen.
Locate the "Outline" or "ROI (Region of Interest)" tool.
Use this tool to draw outlines around the regions of interest on each slide. This is typically done manually by selecting and drawing areas on the slide images.
Save Outlines:

After you've created outlines for all the slides, look for an option to save or export these outlines.
You may be able to save outlines individually for each slide or as a group.
File Format: Choose the file format in which you want to save the outlines. Common formats include .ROI or .ROISET.

Specify Destination: Select the location on your computer where you want to save the outline files. It's a good practice to create a dedicated folder for these files.

Save and Confirm: Click the "Save" or "Export" button to save the outlines move in cleaning 30a. Depending on the software version, you might be prompted to confirm your choices.

Repeat for Multiple Slides: If you have multiple slides, repeat the process for each slide.

Remember that the exact steps and menu options can vary depending on the software version and any updates or hotfixes that have been applied. It's essential to refer to the user manual or documentation specific to Zen 3.1 with Hotfix #7 for the most accurate instructions.
Klarens Hichkock
Posts: 3
Joined: Wed May 24, 2023 8:36 pm

Re: Saving tissue outlines

Post by Klarens Hichkock »

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