Optimizing the speed of aquiring images in large scans

Discuss macros to control the hardware functions of your ZEISS microscope
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Fredrik Olsson
Posts: 16
Joined: Mon May 25, 2020 9:53 am

Optimizing the speed of aquiring images in large scans

Post by Fredrik Olsson »

Hi,

I just would like to know if there might be any good optimisations one could make in order to speed up the time per image for stage movement and subsequent image aquisition in large scans?

We have an AxioImager M2m system with Axiocam 506 color camera and stage controller Stage Controller XY STEP SMC 2009. As it is know the time per image is about 1.3 - 1.6s with about 0.6-0.9s for image aquisition (images are kept in RAM so there is no time penalty for image saving) and 0.7s for stage movement.

I know that reducing the image quality has impact on the acquisition time, such as changing the binning from 1x1 to 2x2 or reducing the bits from 16 to 8. Is there anything therewhich could lower the time without reducing the image quality?

I have not found any way to have a simultaneous movement of both z-direction and xy-direction. Could that be done? I try to minimize the z-movement by having a verification step to see if the z-position still is in the acceptable focus interval for the selected objective and only move if not. Stage movements are z-shaped to minimize each step in xy-plane. I try to set the stage movement for the selected objective to its maximum speed (manually) can settings such as acceleration and speed of the stage be set even higher? My thinking is that the speed for x5 objective normally is higher than for x10, which is good when manully using it but for automatic run one would like to move it as fast as possible but with condition that the sample is not moving and that all movements are done when image aquisition takes place.


Thank you.

Kind regards
Fredrik Olsson
CarlZeissMicroscopy3
Posts: 180
Joined: Wed May 20, 2020 10:10 am

Re: Optimizing the speed of aquiring images in large scans

Post by CarlZeissMicroscopy3 »

Hello Fredrik Olsson,

You are right, a MoveTo(X,Y,Z) is indeed missing.
I will put this on the OAD-ToDo-List!

The stage speed and acceleration is carefully set and tested for each stage. It is optimized for manual operation and cannot be changed. I will come back to you if I have any further information.
CarlZeissMicroscopy3
Posts: 180
Joined: Wed May 20, 2020 10:10 am

Re: Optimizing the speed of aquiring images in large scans

Post by CarlZeissMicroscopy3 »

Hello Fredrik Olsson,

There is a nice alternative to 'a future'
MoveTo(X,Y,Z)

In Zen blue there is the possibility to generate a hardware setting.
Select Tools - Settings Editor in the menu bar.
In the dialog Stage and Focus can be set 'together'.
Finally save the hardware setting to the file system located at
C:\Users\...\Documents\Carl Zeiss\ZEN\Documents\Hardware Settings

In my case the hardware looks like:

Code: Select all

<?xml version="1.0" encoding="utf-8"?>
<HardwareSetting Name="Untitled2">
  <ParameterCollection Id="MTBStageAxisX">
    <Position Status="Valid" IsActivated="true" Unit="µm">20</Position>
  </ParameterCollection>
  <ParameterCollection Id="MTBStageAxisY">
    <Position Status="Valid" IsActivated="true" Unit="µm">30</Position>
  </ParameterCollection>
  <ParameterCollection Id="MTBFocus">
    <Position Status="Valid" IsActivated="true" Unit="µm">0.7</Position>
  </ParameterCollection>
</HardwareSetting>
Now you can load the hardware setting, modify it in the macro and finally apply it.

I hope this idea helps.
Andrew Nicholson
Posts: 2
Joined: Tue Jan 31, 2023 10:41 am

Re: Optimizing the speed of aquiring images in large scans

Post by Andrew Nicholson »

CarlZeissMicroscopy3 wrote: Fri Aug 21, 2020 2:09 pm Hello Fredrik Olsson,

There is a nice alternative to 'a future'
MoveTo(X,Y,Z)

In Zen blue there is the possibility to generate a hardware setting.
Select Tools - Settings Editor in the menu bar.
In the dialog Stage and Focus can be set 'together'.
Finally save the hardware setting to the file system located at
C:\Users\...\Documents\Carl Zeiss\ZEN\Documents\Hardware Settings

In my case the hardware looks like:

Code: Select all

<?xml version="1.0" encoding="utf-8"?>
<HardwareSetting Name="Untitled2">
  <ParameterCollection Id="MTBStageAxisX">
    <Position Status="Valid" IsActivated="true" Unit="µm">20</Position>
  </ParameterCollection>
  <ParameterCollection Id="MTBStageAxisY">
    <Position Status="Valid" IsActivated="true" Unit="µm">30</Position>
  </ParameterCollection>
  <ParameterCollection Id="MTBFocus">
    <Position Status="Valid" IsActivated="true" Unit="µm">0.7</Position>
  </ParameterCollection>
</HardwareSetting>
Now you can load the hardware setting, modify it in the macro and finally apply it.

I hope this idea helps.
Many thanks, very clearly. It's worked.
Lily Smith
Posts: 1
Joined: Mon Apr 17, 2023 6:30 am

Re: Optimizing the speed of aquiring images in large scans

Post by Lily Smith »

Thanks. It works well. phoodle
Sidnie Sin
Posts: 1
Joined: Wed Jul 19, 2023 2:23 pm

Re: Optimizing the speed of aquiring images in large scans

Post by Sidnie Sin »

CarlZeissMicroscopy3 wrote: Fri Aug 21, 2020 2:09 pm Hello Fredrik Olsson,

There is a nice alternative to 'a future'
MoveTo(X,Y,Z)

In Zen blue there is the possibility to generate a hardware setting.
Select Tools - Settings Editor in the menu bar.
In the dialog Stage and Focus can be set 'together'.
Finally save the hardware setting to the file system located at
C:\Users\...\Documents\Carl Zeiss\ZEN\Documents\Hardware Settings

In my case the hardware looks like:

Code: Select all

<?xml version="1.0" encoding="utf-8"?>
<HardwareSetting Name="Untitled2">
  <ParameterCollection Id="MTBStageAxisX">
    <Position Status="Valid" IsActivated="true" Unit="µm">20</Position>
  </ParameterCollection>
  <ParameterCollection Id="MTBStageAxisY">
    <Position Status="Valid" IsActivated="true" Unit="µm">30</Position>
  </ParameterCollection>
  <ParameterCollection Id="MTBFocus">
    <Position Status="Valid" IsActivated="true" Unit="µm">0.7</Position>
  </ParameterCollection>
</HardwareSetting>
Now you can load the hardware setting, modify it in the macro and finally apply it.

I hope this idea helps.
Finally! thanks
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