ZEN multiple Z stack acquisitions

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J Seeler
Posts: 1
Joined: Mon Sep 27, 2021 9:34 am

ZEN multiple Z stack acquisitions

Post by J Seeler »

Hi,
I am trying to acquire multiple Z-stacks from the same slide. Thus, for each I’d like to define a ‘first’ Z stack position and fix the interval and number of images per stack (say, a 10-image stack upwards from the fixed first position, with slices 0.4 um apart). It would therefore be ideal to define multiple points on the slide (perhaps as ‘tile regions’ where each is a 1-image - i.e. 1x1 - tile), with the only difference between each region/tile being a predetermined (absolute) Z position of the first (bottom) slice in each stack.

To me, this seems impossible because the Z-stack dialog box requires a ‘last’ Z position for each stack and therefore insists on recalculating the interval for each 'first-last' choice (The ‘Center’ option is not much help either because it is far easier to define a first, i.e. bottom position, in the sample). The fact that the last, top-most acquired image(s) in each stack using this strategy might be out of focus is not important, if necessary it/they can be edited out before, for example, collapsing the Z stack into a multi-image projection or other (3D) processing.

Many thanks for your help,
Best,
j
CarlZeissMicroscopy3
Posts: 180
Joined: Wed May 20, 2020 10:10 am

Re: ZEN multiple Z stack acquisitions

Post by CarlZeissMicroscopy3 »

Hello J Seeler,

from my understanding you want to fix your z-Stack with the first (bottom) slice.

Did you try the Offset in the Center tab. This can shift the ‘center’ to the ‘first’ slice.
Something like Offset 15 and Interval 3, Slices 11 (Range 30)

Maybe the ‘Show all’ on the right-hand side of the Z-Stack-Window gives you additional possibilities like the ‘Keep’-Feature.

If this is not enough the last option via OAD is to save a Z-Stack Experiment as a template and then do the following steps, maybe multiple times:
1) modify the template via macro code
2) load it and finally
3) execute it

I hope this helps.
julie diane
Posts: 24
Joined: Wed Jun 28, 2023 1:25 am

Re: ZEN multiple Z stack acquisitions

Post by julie diane »

J Seeler wrote: Mon Sep 27, 2021 9:52 am Hi,
I am trying to acquire multiple Z-stacks from the same slide. Thus, for each I’d like to define a ‘first’ Z stack position and fix the interval and number of images per stack (say, a 10-image stack upwards from the fixed first position, with slices 0.4 um apart). It would therefore be ideal to define multiple points on the slide website(perhaps as ‘tile regions’ where each is a 1-image - i.e. 1x1 - tile), with the only difference between each region/tile being a predetermined (absolute) Z position of the first (bottom) slice in each stack.

To me, this seems impossible because the Z-stack dialog box requires a ‘last’ Z position for each stack and therefore insists on recalculating the interval for each 'first-last' choice (The ‘Center’ option is not much help either because it is far easier to define a first, i.e. bottom position, in the sample). The fact that the last, top-most acquired image(s) in each stack using this strategy might be out of focus is not important, if necessary it/they can be edited out before, for example, collapsing the Z stack into a multi-image projection or other (3D) processing.

Many thanks for your help,
Best,
j
Define Tile Regions: Create separate tile regions on your slide for each Z-stack you want to acquire. Each tile region represents the area you want to capture with one Z-stack.

Configure Z-Stack Settings: When configuring the Z-stack settings, set the "first" Z position for the bottom slice of your stack in the dialog box. You can set the "last" Z position to a value that is significantly higher than the actual range you need.

Acquire Z-Stack: Start the acquisition process for the first Z-stack with the defined settings. The software will acquire images starting from the "first" Z position and continue until the "last" Z position is reached. It's okay if some of the top-most acquired images are out of focus.

Edit Out-of-Focus Images: After acquiring the Z-stack, review the images. If some of the top-most images are out of focus and not needed, you can edit or discard them as necessary.

Repeat for Each Stack: Repeat the process for each Z-stack you want to acquire, adjusting the "first" Z position for each region according to your requirements. Each Z-stack will have its starting Z position, fixed interval, and number of images per stack.

Post-Processing: If you need to create multi-image projections or perform other 3D processing, you can do so after acquiring all the Z-stacks. The edited and focused images can be used in your post-processing steps.

By creating separate tile regions and adjusting the "first" Z position for each Z-stack, you can effectively acquire multiple Z-stacks with the desired parameters. While the software may require both "first" and "last" Z positions, you can manipulate the settings as needed to achieve your specific goals.
cccvb fdfdg
Posts: 4
Joined: Wed Oct 18, 2023 7:45 am

Re: ZEN multiple Z stack acquisitions

Post by cccvb fdfdg »

It seems like you're referring to "ZEN," which is a microscopy software suite provided by Carl Zeiss Microscopy for controlling and analyzing microscope systems. When dealing with multiple Z-stack acquisitions clicks per minute, it usually means capturing a series of images at different focal planes along the z-axis to create a 3D representation of a specimen.
fnaf breach
Posts: 5
Joined: Thu Oct 19, 2023 11:47 am

Re: ZEN multiple Z stack acquisitions

Post by fnaf breach »

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julie diane
Posts: 24
Joined: Wed Jun 28, 2023 1:25 am

Re: ZEN multiple Z stack acquisitions

Post by julie diane »

It seems like you're referring to "ZEN," which is a microscopy software suite provided by Carl Zeiss Microscopy for controlling and analyzing microscope systems. When dealing with multiple Z-stack acquisition insulting names for friends, it usually means capturing a series of images at different focal planes along the z-axis to create a 3D representation of a specimen.
Tommy Hellson
Posts: 1
Joined: Sat Nov 25, 2023 2:14 pm
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Re: ZEN multiple Z stack acquisitions

Post by Tommy Hellson »

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