Updating the Live.czi file in the temp folder

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Stefan Maurer
Posts: 5
Joined: Wed Apr 06, 2022 8:09 pm

Updating the Live.czi file in the temp folder

Post by Stefan Maurer »

I would like to access the Live.czi file in the temp folder for further evaluation in another script. It seems like this Live.czi file is only updated when I stop the Live mode in ZEN and then restart it again, which takes about 700ms. Is there another, faster way to trigger updating the Live.czi file from inside a macro?

Best
CarlZeissMicroscopy3
Posts: 180
Joined: Wed May 20, 2020 10:10 am

Re: Updating the Live.czi file in the temp folder

Post by CarlZeissMicroscopy3 »

to access the Live.czi
Hello Stefan Maurer,

for a better understanding I would like to point out, that the Live-View is a high-performance part of the Zen software. From the look and feel it seems that this is an image like all the others that can be opened etc. but internally it is a ‘different world’ that enables a reasonable Live-View with an image rate between 10 to 20 images per second.

From our experience it is possible to save an average of 2 (simple) czi files per second, and that is in accordance with the 700ms you mentioned.

Taking these two statements together it is clear that a fluent Live-View cannot be combined with writing czi files that represent the Live-View. And consequently, the question ‘Is there another, faster way to trigger updating the Live.czi file from inside a macro?’ must be denied.

To further help you it would be necessary for us to know what you intend to do. E.g., if you want to analyze the image during acquisition the ‘Experiment Feedback’ scripting might be something to look at.
Stefan Maurer
Posts: 5
Joined: Wed Apr 06, 2022 8:09 pm

Re: Updating the Live.czi file in the temp folder

Post by Stefan Maurer »

Hi,

thank you for the fast reply. I was afraid that would be the case. For now, I am taking snapshot (600-700ms), which are saved to the temp folder, then immediately load and analyze them into an external script, that sends back instructions the ZEN software on where the stage of the microscope should move (150ms) and repeat. So most of the time is used for just taking a snapshot and I was hoping there was a way to speed up that process or somehow access the live view of the microscope to immediately get an image (I don't need any high resolution) that can be analyzed externally.

Are the current pixel values of the live image maybe accessible in the macro environment? Or could you guide me to a document with further information on the experimental feedback scripting you are referring to?
CarlZeissMicroscopy3
Posts: 180
Joined: Wed May 20, 2020 10:10 am

Re: Updating the Live.czi file in the temp folder

Post by CarlZeissMicroscopy3 »

Hello Stefan Maurer,

your description reminded me very much of 'Experiment Feedback' & 'Guided Acquisition'

for a quick Introducktion please have a look in the SoftwareManual at Chapter 12.1 Advanced Processing containing
12.1.1 Experiment Feedback and 12.1.2 Workflow Experiment Feedback
as well as
12.10 Guided Acquisition

E.g.: http://czisamples.blob.core.windows.net ... Manual.pdf

As mentioned, there is more information in .../Manuals/ZEN(blue edition)/OAD Content/Experiment Feedback etc. on your DVD.

Your Question:
Are the current pixel values of the live image maybe accessible in the macro environment?
No, sorry, the Live-Image is not accessible from OAD macro language.
But Experiment Feedback has a Scripting language that runs within the experiment, and not in a separate macro. This allows you to get hold of the last image taken etc. by design.
Stefan Maurer
Posts: 5
Joined: Wed Apr 06, 2022 8:09 pm

Re: Updating the Live.czi file in the temp folder

Post by Stefan Maurer »

Excellent! Thank you very much, I'll see what I can do
CarlZeissMicroscopy3
Posts: 180
Joined: Wed May 20, 2020 10:10 am

Re: Updating the Live.czi file in the temp folder

Post by CarlZeissMicroscopy3 »

You also may find useful documentation
(not only) for 'Experiment Feedback' & 'Guided Acquisition' on
https://github.com/zeiss-microscopy/OAD
Ali Koyuncuer
Posts: 2
Joined: Thu Oct 13, 2022 9:22 pm

Re: Updating the Live.czi file in the temp folder

Post by Ali Koyuncuer »

I have a primostar 3 microscope, axiocam 208 color camera, but it gives an error that it could not find the live.czi file and I cannot open the live camera, I cannot use the microscope and camera integrated at the moment, can you help me, thanks.
CarlZeissMicroscopy3
Posts: 180
Joined: Wed May 20, 2020 10:10 am

Re: Updating the Live.czi file in the temp folder

Post by CarlZeissMicroscopy3 »

Hello Ali Koyuncuer,

please note that this is a forum for Open Application Development (OAD) and not for Zen or Microscope specific themes.

Maybe this contribution helps to clarify the situation:
viewtopic.php?t=3018

It seems to me that this forum
viewforum.php?f=34
may be better suited for your question.

You can also look for 'primostar' contributions in all forums using the Search... on the top of the right hand side of the page!

For further information please contact your local ZEISS sales team.
ahsan khan
Posts: 1
Joined: Tue Sep 26, 2023 8:07 am

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Post by ahsan khan »

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Posts: 3
Joined: Thu Oct 19, 2023 11:47 am

Re: Updating the Live.czi file in the temp folder

Post by fnaf breach »

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