Z-stack z drive-image capture calibration?

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Z-stack z drive-image capture calibration?

Jake Winiski
Hello,
I'm operating a Zeiss Axioplan 2 with an AmScope MU1400 camera. The scope and z-drive are being operated with the ZeissCAN adapter, and the camera is being operated with the AmScope Camera adapter. During multi-z acquisition it appears that the z-drive is operating consistently, but image acquisition is out-of-sync with the z-drive adjustment leading to images being captured out of sequence (for instance, several images may be captured at a single position, or only the top and bottom positions are captured). I am curious if anybody else has experienced this and may have some insight? 

Best,
Jake




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Re: Z-stack z drive-image capture calibration?

Stuurman, Nico
Hi Jake,
> I'm operating a Zeiss Axioplan 2 with an AmScope MU1400 camera. The
> scope and z-drive are being operated with the ZeissCAN adapter, and
> the camera is being operated with the AmScope Camera adapter. During
> multi-z acquisition it appears that the z-drive is operating
> consistently, but image acquisition is out-of-sync with the z-drive
> adjustment leading to images being captured out of sequence (for
> instance, several images may be captured at a single position, or only
> the top and bottom positions are captured). I am curious if anybody
> else has experienced this and may have some insight?

My guess is that there is a problem with the DeviceAdapter for the
AmScope camera.  The "contract" for a Micro-Manager camera adapter is
that when the "SnapImage" code is called, exposure should start
immediately, and the function should return immediately after exposure
is finished.  Synchronization with external devices (such as the
Z-dtrve, but also shutters) depends on correct implementation.  It is
often difficult to do this correctly, especially with the more
affordable cameras, where manufacturers have not given much thought to
synchronization.

I find this more likely than a problem with the Zeiss scope, since many
(including our own lab) have successfully used the ZeissCAN adapter for
device synchronization.

Looking at the source code (in DeviceAdapters/Amscope), it indeed looks
as if the camera runs in streaming (video) mode, and the device adapter
just grabs the latest image when SnapImage is called, not trying to
synchronize.

Best,

Nico



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Re: Z-stack z drive-image capture calibration?

Jake Winiski
That makes a lot of sense, thank you very much Nico. I'm planning on setting up a canon dSLR with this microscope, would you be able to speak to whether synchronization will function with the canon driver? Or perhaps recommend a good camera/driver combination for getting good synchronization during z capture? 
Thank you very much for your help, 
Jake

On Fri, Jan 4, 2019 at 8:37 PM Stuurman, Nico <[hidden email]> wrote:
Hi Jake,
> I'm operating a Zeiss Axioplan 2 with an AmScope MU1400 camera. The
> scope and z-drive are being operated with the ZeissCAN adapter, and
> the camera is being operated with the AmScope Camera adapter. During
> multi-z acquisition it appears that the z-drive is operating
> consistently, but image acquisition is out-of-sync with the z-drive
> adjustment leading to images being captured out of sequence (for
> instance, several images may be captured at a single position, or only
> the top and bottom positions are captured). I am curious if anybody
> else has experienced this and may have some insight?

My guess is that there is a problem with the DeviceAdapter for the
AmScope camera.  The "contract" for a Micro-Manager camera adapter is
that when the "SnapImage" code is called, exposure should start
immediately, and the function should return immediately after exposure
is finished.  Synchronization with external devices (such as the
Z-dtrve, but also shutters) depends on correct implementation.  It is
often difficult to do this correctly, especially with the more
affordable cameras, where manufacturers have not given much thought to
synchronization.

I find this more likely than a problem with the Zeiss scope, since many
(including our own lab) have successfully used the ZeissCAN adapter for
device synchronization.

Looking at the source code (in DeviceAdapters/Amscope), it indeed looks
as if the camera runs in streaming (video) mode, and the device adapter
just grabs the latest image when SnapImage is called, not trying to
synchronize.

Best,

Nico



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--
Jake Winiski
Research Scientist
Ecovative Design, LLC
70 Cohoes Ave
Green Island, NY 12183
(518) 273-3753



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Re: Z-stack z drive-image capture calibration?

Stuurman, Nico
Hi Jake,

> That makes a lot of sense, thank you very much Nico. I'm planning on
> setting up a canon dSLR with this microscope, would you be able to
> speak to whether synchronization will function with the canon driver?
> Or perhaps recommend a good camera/driver combination for getting good
> synchronization during z capture?

SLRs are not very well supported in Micro-Manager.  The DSLRRemoteCamera
device adapter is no longer supported (it may, or may not work, and
there is no maintainer of the code).  I once worked on a Canon SDK
adapter, but never got that to work satisfactorily.  I would use a
machine vision camera from either FLIR (Point Grey), Ximea, Matrix
Vision, or Thorlabs.  We have a couple of FLIR cameras ourselves, and
they synchronize well.  For FLIR, make sure that the camera supports the
Flycap2 interface (i.e., there is still no support for the Spinnaker
interface).

Best,

Nico




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Re: Z-stack z drive-image capture calibration?

Jake Winiski
Thank you very much for your input Nico, I appreciate it. I will look into the cameras you suggested. 
Best,
Jake

On Tue, Jan 8, 2019 at 12:59 PM Stuurman, Nico <[hidden email]> wrote:
Hi Jake,

> That makes a lot of sense, thank you very much Nico. I'm planning on
> setting up a canon dSLR with this microscope, would you be able to
> speak to whether synchronization will function with the canon driver?
> Or perhaps recommend a good camera/driver combination for getting good
> synchronization during z capture?

SLRs are not very well supported in Micro-Manager.  The DSLRRemoteCamera
device adapter is no longer supported (it may, or may not work, and
there is no maintainer of the code).  I once worked on a Canon SDK
adapter, but never got that to work satisfactorily.  I would use a
machine vision camera from either FLIR (Point Grey), Ximea, Matrix
Vision, or Thorlabs.  We have a couple of FLIR cameras ourselves, and
they synchronize well.  For FLIR, make sure that the camera supports the
Flycap2 interface (i.e., there is still no support for the Spinnaker
interface).

Best,

Nico




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--
Jake Winiski
Research Scientist
Ecovative Design, LLC
70 Cohoes Ave
Green Island, NY 12183
(518) 273-3753



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Re: Z-stack z drive-image capture calibration?

Jake Winiski
In reply to this post by Stuurman, Nico
Hi Nico,
Per our last conversation I purchased a ThorLabs camera (CS505CU) for synchronization with our Zeiss Axioplan 2. After following the installation instructions per the TSI adapter, when attempting to add the TSICam in the hardware configuration wizard I'm receiving the error "Error in device TSICam: Couldn't detect any TSI cameras. Make sure cameras are attached and the power is ON. (10012)." The camera is attached and working correctly in the Thorlabs software. Could you provide any advice on how to remedy this error? 

Best,
Jake

On Tue, Jan 8, 2019 at 12:59 PM Stuurman, Nico <[hidden email]> wrote:
Hi Jake,

> That makes a lot of sense, thank you very much Nico. I'm planning on
> setting up a canon dSLR with this microscope, would you be able to
> speak to whether synchronization will function with the canon driver?
> Or perhaps recommend a good camera/driver combination for getting good
> synchronization during z capture?

SLRs are not very well supported in Micro-Manager.  The DSLRRemoteCamera
device adapter is no longer supported (it may, or may not work, and
there is no maintainer of the code).  I once worked on a Canon SDK
adapter, but never got that to work satisfactorily.  I would use a
machine vision camera from either FLIR (Point Grey), Ximea, Matrix
Vision, or Thorlabs.  We have a couple of FLIR cameras ourselves, and
they synchronize well.  For FLIR, make sure that the camera supports the
Flycap2 interface (i.e., there is still no support for the Spinnaker
interface).

Best,

Nico




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--
Jake Winiski
Research Scientist
Ecovative Design, LLC
70 Cohoes Ave
Green Island, NY 12183
(518) 273-3753



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Re: Z-stack z drive-image capture calibration?

Stuurman, Nico
On 1/30/19 12:48 PM, Jake Winiski wrote:
> Hi Nico,
> Per our last conversation I purchased a ThorLabs camera (CS505CU) for
> synchronization with our Zeiss Axioplan 2. After following the
> installation instructions per the TSI adapter, when attempting to add
> the TSICam in the hardware configuration wizard I'm receiving the
> error "Error in device TSICam: Couldn't detect any TSI cameras. Make
> sure cameras are attached and the power is ON. (10012)." The camera is
> attached and working correctly in the Thorlabs software. Could you
> provide any advice on how to remedy this error?


Best to ask Thorlabs for help.


Nico



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