leica DM6B; XY stage calibration

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leica DM6B; XY stage calibration

Stanislav Vitha-2

Hello,

I am running Micro-manager 2 beta  (Windows  10, 64-bit)  to control a Leica DM6B upright microscope and the Photometrics Prime sCMOS camera.

The Pixel Calibrator  produces incorrect pixel size (almost double what it should be), it appears the stage calibration is not read properly (or is set wrong).

The motorized stage is # 11501260 (Leica DM 100 x 100 scanning stage); Leica LasX hardware setup reports pitch 1.999995  (not sure what units it is; revolutions per mm?)

 

Is there a way to input or change the pitch in MicroManager settings? Device Property Browser does not show this item.

 

Thanks in advance!

 

Stan Vitha

Microscopy and Imaging Center 
Texas A&M University

301 Old Main Dr

College Station, TX 77843-2257

http://microscopy.tamu.edu

 



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Re: leica DM6B; XY stage calibration

m.losen

Hi Stan,

 

Some thoughts regarding this issue:

>“The Pixel Calibrator  produces incorrect pixel size (almost double what it should be), it appears the stage calibration is not read properly (or is set wrong).

I had the same issue with stages from Ludl and from Marzhauser. In MM, both calibrations were off by a factor 2 exactly.

For the Ludl stage, the pitch (or gear factor) could be adjusted in MM directly, while the Marzhauser Tango stage settings had to be changed by using Marzhauser Switchboard software (free download or their website).

 

>“The motorized stage is # 11501260 (Leica DM 100 x 100 scanning stage); Leica LasX hardware setup reports pitch 1.999995  (not sure what units it is; revolutions per mm?)

Is this maybe a stage that is made originally by Marzhauser? [with M/W logo on the (usually yellow) wheels of the stepper motors)?

Is there a way to input or change the pitch in MicroManager settings? Device Property Browser does not show this item.

If your stage has a Marzhauser controller, then the Switchboard software could be used to change the setting.

Or can the setting be changed in the Leica software?

Hope this helps,

Mario

 

 

 

 



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Re: leica DM6B; XY stage calibration

Stanislav Vitha-2

Hi Mario,

Thanks for the suggestions.

It does not look like a Marzhauser stage  (we have that one on our inverted Leica confocal, I believe),  but I will  take a closer look.

I discovered that I am able to change the pitch in the Leica software (LasX Hardware setup) but this is something that the software calculates during stage calibration, which I performed.  

So I believe the stage is properly calibrated.

Perhaps the current number (1.999995) is an inverse of what Micromanager expects – instead of millimeters per revolutuion it could be revolutions per millimeter (or vice versa),
I am using both the Leica software (for color camera imaging) and Micromanager (for monochrome camera imaging), so I am hesitant to change the pitch in the Leica SW. It may solve the problem in MicroManager but cause errors when running the Leica lasX.

If I could confirm what MM reads from the stage calibration during the Pixel Calibrator routine, perhaps it would reveal something.

For now I just have to remember to manually change XY pixel size for the acquired datasets.

 

Stan

 

 

From: Losen, M (NP) [[hidden email]]
Sent: Thursday, March 28, 2019 6:41 AM
To: 'Micro-Manager General'
Subject: Re: [micro-manager-general] leica DM6B; XY stage calibration

 

Hi Stan,

 

Some thoughts regarding this issue:

>“The Pixel Calibrator  produces incorrect pixel size (almost double what it should be), it appears the stage calibration is not read properly (or is set wrong).

I had the same issue with stages from Ludl and from Marzhauser. In MM, both calibrations were off by a factor 2 exactly.

For the Ludl stage, the pitch (or gear factor) could be adjusted in MM directly, while the Marzhauser Tango stage settings had to be changed by using Marzhauser Switchboard software (free download or their website).

 

>“The motorized stage is # 11501260 (Leica DM 100 x 100 scanning stage); Leica LasX hardware setup reports pitch 1.999995  (not sure what units it is; revolutions per mm?)

Is this maybe a stage that is made originally by Marzhauser? [with M/W logo on the (usually yellow) wheels of the stepper motors)?

Is there a way to input or change the pitch in MicroManager settings? Device Property Browser does not show this item.

If your stage has a Marzhauser controller, then the Switchboard software could be used to change the setting.

Or can the setting be changed in the Leica software?

Hope this helps,

Mario

 

 

 

 



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Re: leica DM6B; XY stage calibration

m.losen

Hi Stan,

 

>“For now I just have to remember to manually change XY pixel size for the acquired datasets.”

That’s perfectly ok of course.

 

But if you’re keen to correct the issue:

According to this document…

https://www.scribd.com/document/357009591/LAS-4-9-0-System-Requirements

…your stage is from Marzhauser (“11501260 Märzhäuser Scanning stage 100x100 mot., for DM4000-6000, S 2mm”)

 

You could have a look if the documentation on this website matches the stage you have:

https://www.marzhauser.com/en/products/microscope-stages/motorized-microscope-stages/scan-series/scan.html

(There are 3 versions of Marzhauser SCAN 100 x 100 stages, with ball screw pitches of 1 mm, 2 mm and 4 mm)

 

If so, the next step could be to test if the Marzhauser “SwitchBoard” software can access the stage controller.

The pitch can be changed (and stored) there (at least for the stage we have).

 

Alternatively, you could:

-See if the Windows Device control, within Ports (Com & LPT) a Tango USB port is listed.

-Try in MM if this device adapter…

https://micro-manager.org/wiki/Marzhauser

…can control your stage with the same serial port settings you already use.

 

greetings,

Mario

 

 

 

 



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Re: leica DM6B; XY stage calibration

Stanislav Vitha-2

Hi Mario,

Thanks a million. I will give this a try and report back.

 

Stan

 

 

From: Losen, M (NP) [mailto:[hidden email]]
Sent: Thursday, April 04, 2019 7:23 AM
To: 'Micro-Manager General'
Subject: Re: [micro-manager-general] leica DM6B; XY stage calibration

 

Hi Stan,

 

>“For now I just have to remember to manually change XY pixel size for the acquired datasets.”

That’s perfectly ok of course.

 

But if you’re keen to correct the issue:

According to this document…

https://www.scribd.com/document/357009591/LAS-4-9-0-System-Requirements

…your stage is from Marzhauser (“11501260 Märzhäuser Scanning stage 100x100 mot., for DM4000-6000, S 2mm”)

 

You could have a look if the documentation on this website matches the stage you have:

https://www.marzhauser.com/en/products/microscope-stages/motorized-microscope-stages/scan-series/scan.html

(There are 3 versions of Marzhauser SCAN 100 x 100 stages, with ball screw pitches of 1 mm, 2 mm and 4 mm)

 

If so, the next step could be to test if the Marzhauser “SwitchBoard” software can access the stage controller.

The pitch can be changed (and stored) there (at least for the stage we have).

 

Alternatively, you could:

-See if the Windows Device control, within Ports (Com & LPT) a Tango USB port is listed.

-Try in MM if this device adapter…

https://micro-manager.org/wiki/Marzhauser

…can control your stage with the same serial port settings you already use.

 

greetings,

Mario

 

 

 

 



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Re: leica DM6B; XY stage calibration

Stanislav Vitha-2
In reply to this post by m.losen

Hi Mario,

I was unable to connect to the Leica/Marzhauser stage using the SwitchBoard software.

The stage is connected to the Leica microscope control box (which is connected via USB to the computer) but the Switchboard software does not see the XY stage.

The list of ports does not list the Tango USB port.

 

So at least for now it  looks like I will be doing a post-acquisition XY calibration unless I can change the settings elsewhere.

 

After I used the Pixel Calibrator plugin, I ended up with Pixel Calibration (pixel XY size) settings listed for each objective. I am able to edit these values.  But if I do, will it cause problems when doing tiling and image stitching, or are these settings applied after the acquisition?  

 

Stan

 

     

 

From: Losen, M (NP) [mailto:[hidden email]]
Sent: Thursday, April 04, 2019 7:23 AM
To: 'Micro-Manager General'
Subject: Re: [micro-manager-general] leica DM6B; XY stage calibration

 

Hi Stan,

 

>“For now I just have to remember to manually change XY pixel size for the acquired datasets.”

That’s perfectly ok of course.

 

But if you’re keen to correct the issue:

According to this document…

https://www.scribd.com/document/357009591/LAS-4-9-0-System-Requirements

…your stage is from Marzhauser (“11501260 Märzhäuser Scanning stage 100x100 mot., for DM4000-6000, S 2mm”)

 

You could have a look if the documentation on this website matches the stage you have:

https://www.marzhauser.com/en/products/microscope-stages/motorized-microscope-stages/scan-series/scan.html

(There are 3 versions of Marzhauser SCAN 100 x 100 stages, with ball screw pitches of 1 mm, 2 mm and 4 mm)

 

If so, the next step could be to test if the Marzhauser “SwitchBoard” software can access the stage controller.

The pitch can be changed (and stored) there (at least for the stage we have).

 

Alternatively, you could:

-See if the Windows Device control, within Ports (Com & LPT) a Tango USB port is listed.

-Try in MM if this device adapter…

https://micro-manager.org/wiki/Marzhauser

…can control your stage with the same serial port settings you already use.

 

greetings,

Mario

 

 

 

 



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Re: leica DM6B; XY stage calibration

m.losen

Hi Stan,

“The stage is connected to the Leica microscope control box (which is connected via USB to the computer) but the Switchboard software does not see the XY stage.”

I understand; if the stage controller is not directly connected to your PC, the stage software can’t find it of course.

 

“So at least for now it  looks like I will be doing a post-acquisition XY calibration unless I can change the settings elsewhere.”

I think so too. The best then would be if the device adapter could be modified to match the function of your stage.

“After I used the Pixel Calibrator plugin, I ended up with Pixel Calibration (pixel XY size) settings listed for each objective. I am able to edit these values.  But if I do, will it cause problems when doing tiling and image stitching, or are these settings applied after the acquisition? “

there’s a big chance that that changing these settings would cause problems with stitching; either with the slide explorer or with the tile creator, or both. For the function of the pixel calibrator there’s some interesting info here:

http://micro-manager.3463995.n2.nabble.com/Slide-Explorer-and-Pixel-Calibrator-plugins-td7584496.html

“Not only the pixel size, but a complete affine transform that maps the stage to the camera is stored using Java Preferences (i.e., the rest of Micro-Manager has no knowledge of these data).  In other words, the Pixel Calibrator keeps its own copy of pixel size, rotation, translation operations needed to map the stage to the camera, and the Pixel Calibrator is nice enough to offer you to copy the pixel size to the Micro-Manager preferences.  “

 

Instead of editing all pixel calibration values, you could simply use the “Doptovar” device adapter within the Demo Camera Hub:

It’s normally used to let MM know if an extra magnification lens (typically 1.6x) is placed manually into the light path or not. In the hardware configuration wizard, add the DHub, and within its ‘Peripherals’ tick the box of the Doptovar. In the next step you can set the “high magnification position” to 2. In theory that should allow you to let MM use a 1x or 2x changed pixel calibration for all objectives. You can also switch between the two values quickly.

 

Greetings,

Mario

 



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Re: leica DM6B; XY stage calibration

Stanislav Vitha-2

Dear Mario,

Thanks for the suggestions!

I will test the DOptovar, and may play with the Pixel Calibration values on a separate  copy of the config file, just to see what happens when stitching tiled images together.

 

Best regards,

 

Stan

 

From: Losen, M (NP) [mailto:[hidden email]]
Sent: Friday, April 12, 2019 9:22 AM
To: 'Micro-Manager General'
Subject: Re: [micro-manager-general] leica DM6B; XY stage calibration

 

Hi Stan,

“The stage is connected to the Leica microscope control box (which is connected via USB to the computer) but the Switchboard software does not see the XY stage.”

I understand; if the stage controller is not directly connected to your PC, the stage software can’t find it of course.

 

“So at least for now it  looks like I will be doing a post-acquisition XY calibration unless I can change the settings elsewhere.”

I think so too. The best then would be if the device adapter could be modified to match the function of your stage.

 

“After I used the Pixel Calibrator plugin, I ended up with Pixel Calibration (pixel XY size) settings listed for each objective. I am able to edit these values.  But if I do, will it cause problems when doing tiling and image stitching, or are these settings applied after the acquisition? “

there’s a big chance that that changing these settings would cause problems with stitching; either with the slide explorer or with the tile creator, or both. For the function of the pixel calibrator there’s some interesting info here:

http://micro-manager.3463995.n2.nabble.com/Slide-Explorer-and-Pixel-Calibrator-plugins-td7584496.html

“Not only the pixel size, but a complete affine transform that maps the stage to the camera is stored using Java Preferences (i.e., the rest of Micro-Manager has no knowledge of these data).  In other words, the Pixel Calibrator keeps its own copy of pixel size, rotation, translation operations needed to map the stage to the camera, and the Pixel Calibrator is nice enough to offer you to copy the pixel size to the Micro-Manager preferences.  “

 

Instead of editing all pixel calibration values, you could simply use the “Doptovar” device adapter within the Demo Camera Hub:

It’s normally used to let MM know if an extra magnification lens (typically 1.6x) is placed manually into the light path or not. In the hardware configuration wizard, add the DHub, and within its ‘Peripherals’ tick the box of the Doptovar. In the next step you can set the “high magnification position” to 2. In theory that should allow you to let MM use a 1x or 2x changed pixel calibration for all objectives. You can also switch between the two values quickly.

 

Greetings,

Mario

 



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