Myocam S with micro-manager

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Myocam S with micro-manager

Paul Hartley
Has anyone any experience with using Ionoptix Myocam S for high frame rate capture video microscopy (>150fps)?
many thanks
Psh

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Re: Myocam S with micro-manager

Mark Tsuchida-2
Hi Paul,

On Thu, Nov 21, 2013 at 10:53 AM, Paul Hartley <[hidden email]> wrote:
> Has anyone any experience with using Ionoptix Myocam S for high frame rate
> capture video microscopy (>150fps)?

Since the website (http://www.ionoptix.com/products/myocam_s) says
that it has a "Compatible driver for use with any standard Windows
video application", and the manual further says that the driver is
compatible with Windows DirectShow, it might work with the
OpenCVgrabber device adapter. It will be hard to tell how well it will
work without actually testing it.

Best,
Mark

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Re: Myocam S with micro-manager

Paul Hartley
Many thanks Mark, that's promising. Best, Paul.


On 27 November 2013 17:50, Mark Tsuchida <[hidden email]> wrote:
Hi Paul,

On Thu, Nov 21, 2013 at 10:53 AM, Paul Hartley <[hidden email]> wrote:
> Has anyone any experience with using Ionoptix Myocam S for high frame rate
> capture video microscopy (>150fps)?

Since the website (http://www.ionoptix.com/products/myocam_s) says
that it has a "Compatible driver for use with any standard Windows
video application", and the manual further says that the driver is
compatible with Windows DirectShow, it might work with the
OpenCVgrabber device adapter. It will be hard to tell how well it will
work without actually testing it.

Best,
Mark

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Re: Myocam S with micro-manager

Paul Hartley
In reply to this post by Mark Tsuchida-2
Hi Mark,
with reference to your earlier email; I connected the Ionoptix Myocam-S and used the OpenCVGrabber as you suggested. I get a nice live image (showing @30fps). I need to take relatively his speed footage of beating hearts. However frame capture rates are very slow, I'm needing to collect a 10second vimage sequence (1000 frames at 10ms exposure (i.e.100fps)), using 0ms interval, channels are off. Typically this is taking >30seconds when it should be close to 10seconds.

This slow capture rate occurs whether or not I save direct to disk or RAM; processor activity is only about 90% and Image resolution is not a problem; I also increased the buffer capacity to 400MB. I ran some 'diagnostics' using the demo camera, this can collect 500 20ms exposure images (0ms interval; i.e.50fps) but the live image is shown at 100fps.

I cannot tell if this is something I'm doing wrong, or whether this delay in frame capture is due to limitations in the OpenCVgrabber capabilities?

Any advice / help is very much appreciated.

Best wishes,
Paul Hartley.
University of Edinburgh.




On 28 November 2013 01:50, Mark Tsuchida <[hidden email]> wrote:
Hi Paul,

On Thu, Nov 21, 2013 at 10:53 AM, Paul Hartley <[hidden email]> wrote:
> Has anyone any experience with using Ionoptix Myocam S for high frame rate
> capture video microscopy (>150fps)?

Since the website (http://www.ionoptix.com/products/myocam_s) says
that it has a "Compatible driver for use with any standard Windows
video application", and the manual further says that the driver is
compatible with Windows DirectShow, it might work with the
OpenCVgrabber device adapter. It will be hard to tell how well it will
work without actually testing it.

Best,
Mark

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Re: Myocam S with micro-manager

EdESImaging
Hi Paul,

On 29/01/14 15:58, Paul Hartley wrote:

> Hi Mark,
> with reference to your earlier email; I connected the Ionoptix
> Myocam-S and used the OpenCVGrabber as you suggested. I get a nice
> live image (showing @30fps). I need to take relatively his speed
> footage of beating hearts. However frame capture rates are very slow,
> I'm needing to collect a 10second vimage sequence (1000 frames at 10ms
> exposure (i.e.100fps)), using 0ms interval, channels are off.
> Typically this is taking >30seconds when it should be close to 10seconds.
>
> This slow capture rate occurs whether or not I save direct to disk or
> RAM; processor activity is only about 90% and Image resolution is not
> a problem; I also increased the buffer capacity to 400MB. I ran some
> 'diagnostics' using the demo camera, this can collect 500 20ms
> exposure images (0ms interval; i.e.50fps) but the live image is shown
> at 100fps.
>
> I cannot tell if this is something I'm doing wrong, or whether this
> delay in frame capture is due to limitations in the OpenCVgrabber
> capabilities?
>
> Any advice / help is very much appreciated.
>
> Best wishes,
> Paul Hartley.
> University of Edinburgh.

I wrote OpenCVgrabber and I recall there being an issue with opencv that
caused this behaviour with some cameras.

If I recall correctly, some directshow devices accessed through opencv
return an old image on the first call to cvRetrieveFrame, thus needing
to call this twice. In the case of other cameras, this results in halved
frame rate.

Since this is a very odd 'feature', should we perhaps make this optional
by adding a property to enable or disable the extra call to cvRetrieveFrame?

Most directshow cameras don't respond to exposure settings via opencv,
thus opencvgrabber is a bit limited in this regard. In some cases, the
exposure can be set using a direct show application such as amcap first,
then quit this and run MM, the exposure set by amcap sometimes is still
set when loading OpenCVgrabber.

I can compile a dll for you to test with your camera, please could you
tell me whether you use 32 or 64 bit windows?

Thanks,
Ed

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Re: Myocam S with micro-manager

Mark Tsuchida-2
In reply to this post by Paul Hartley
Hi Paul,

On Wed, Jan 29, 2014 at 7:58 AM, Paul Hartley <[hidden email]> wrote:

> with reference to your earlier email; I connected the Ionoptix Myocam-S and
> used the OpenCVGrabber as you suggested. I get a nice live image (showing
> @30fps). I need to take relatively his speed footage of beating hearts.
> However frame capture rates are very slow, I'm needing to collect a 10second
> vimage sequence (1000 frames at 10ms exposure (i.e.100fps)), using 0ms
> interval, channels are off. Typically this is taking >30seconds when it
> should be close to 10seconds.
>
> This slow capture rate occurs whether or not I save direct to disk or RAM;
> processor activity is only about 90% and Image resolution is not a problem;
> I also increased the buffer capacity to 400MB. I ran some 'diagnostics'
> using the demo camera, this can collect 500 20ms exposure images (0ms
> interval; i.e.50fps) but the live image is shown at 100fps.
>
> I cannot tell if this is something I'm doing wrong, or whether this delay in
> frame capture is due to limitations in the OpenCVgrabber capabilities?

In addition to what Ed wrote about OpenCV, it looks like there are
other possibilities to consider.

Which version of Micro-Manager are you using? I would recommend trying
a recent nightly build, and to make sure to turn on "Fast Image
Storage" in Tools > Options (even if acquiring to RAM).

With the DemoCamera, are you able to produce 100 fps images if you set
the exposure to 10 ms? You can test this with the same image size as
your real camera by setting the "CCD size" and pixel type in the
Device Property Browser. If not, does turning on "Fast Images" (in the
Device Property Browser) make a difference?

It would also be useful to know
- What is the size of the images you are acquiring (width, height, and
bit depth)
- What are the specs of your computer (CPU, number of cores, RAM
capacity and type (such as DDR3 1333 MHz))
- What is your OS version?

Best,
Mark

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Re: Myocam S with micro-manager

Paul Hartley
In reply to this post by EdESImaging
Hi Mark,
thanks for the reply,
I will certainly give it a try; I'm using a 32-bit system (windows XP).
best wishes,
Paul.


On 29 January 2014 16:41, Ed Simmons <[hidden email]> wrote:
Hi Paul,

On 29/01/14 15:58, Paul Hartley wrote:
> Hi Mark,
> with reference to your earlier email; I connected the Ionoptix
> Myocam-S and used the OpenCVGrabber as you suggested. I get a nice
> live image (showing @30fps). I need to take relatively his speed
> footage of beating hearts. However frame capture rates are very slow,
> I'm needing to collect a 10second vimage sequence (1000 frames at 10ms
> exposure (i.e.100fps)), using 0ms interval, channels are off.
> Typically this is taking >30seconds when it should be close to 10seconds.
>
> This slow capture rate occurs whether or not I save direct to disk or
> RAM; processor activity is only about 90% and Image resolution is not
> a problem; I also increased the buffer capacity to 400MB. I ran some
> 'diagnostics' using the demo camera, this can collect 500 20ms
> exposure images (0ms interval; i.e.50fps) but the live image is shown
> at 100fps.
>
> I cannot tell if this is something I'm doing wrong, or whether this
> delay in frame capture is due to limitations in the OpenCVgrabber
> capabilities?
>
> Any advice / help is very much appreciated.
>
> Best wishes,
> Paul Hartley.
> University of Edinburgh.

I wrote OpenCVgrabber and I recall there being an issue with opencv that
caused this behaviour with some cameras.

If I recall correctly, some directshow devices accessed through opencv
return an old image on the first call to cvRetrieveFrame, thus needing
to call this twice. In the case of other cameras, this results in halved
frame rate.

Since this is a very odd 'feature', should we perhaps make this optional
by adding a property to enable or disable the extra call to cvRetrieveFrame?

Most directshow cameras don't respond to exposure settings via opencv,
thus opencvgrabber is a bit limited in this regard. In some cases, the
exposure can be set using a direct show application such as amcap first,
then quit this and run MM, the exposure set by amcap sometimes is still
set when loading OpenCVgrabber.

I can compile a dll for you to test with your camera, please could you
tell me whether you use 32 or 64 bit windows?

Thanks,
Ed

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Re: Myocam S with micro-manager

Paul Hartley
In reply to this post by EdESImaging
Hi Ed,
(not sure you just got my 1st reply - which may have only gone to Mark)
many thanks, I will give the dll a try; I'm using a 32-bit system (windows XP),
bets wishes,
Paul.


On 29 January 2014 16:41, Ed Simmons <[hidden email]> wrote:
Hi Paul,

On 29/01/14 15:58, Paul Hartley wrote:
> Hi Mark,
> with reference to your earlier email; I connected the Ionoptix
> Myocam-S and used the OpenCVGrabber as you suggested. I get a nice
> live image (showing @30fps). I need to take relatively his speed
> footage of beating hearts. However frame capture rates are very slow,
> I'm needing to collect a 10second vimage sequence (1000 frames at 10ms
> exposure (i.e.100fps)), using 0ms interval, channels are off.
> Typically this is taking >30seconds when it should be close to 10seconds.
>
> This slow capture rate occurs whether or not I save direct to disk or
> RAM; processor activity is only about 90% and Image resolution is not
> a problem; I also increased the buffer capacity to 400MB. I ran some
> 'diagnostics' using the demo camera, this can collect 500 20ms
> exposure images (0ms interval; i.e.50fps) but the live image is shown
> at 100fps.
>
> I cannot tell if this is something I'm doing wrong, or whether this
> delay in frame capture is due to limitations in the OpenCVgrabber
> capabilities?
>
> Any advice / help is very much appreciated.
>
> Best wishes,
> Paul Hartley.
> University of Edinburgh.

I wrote OpenCVgrabber and I recall there being an issue with opencv that
caused this behaviour with some cameras.

If I recall correctly, some directshow devices accessed through opencv
return an old image on the first call to cvRetrieveFrame, thus needing
to call this twice. In the case of other cameras, this results in halved
frame rate.

Since this is a very odd 'feature', should we perhaps make this optional
by adding a property to enable or disable the extra call to cvRetrieveFrame?

Most directshow cameras don't respond to exposure settings via opencv,
thus opencvgrabber is a bit limited in this regard. In some cases, the
exposure can be set using a direct show application such as amcap first,
then quit this and run MM, the exposure set by amcap sometimes is still
set when loading OpenCVgrabber.

I can compile a dll for you to test with your camera, please could you
tell me whether you use 32 or 64 bit windows?

Thanks,
Ed

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Re: Myocam S with micro-manager

Paul Hartley
In reply to this post by Paul Hartley
Hi Mark,
I did some testing with the democam using a SONY Vaio (64bit; Windows7; 2.4GHz) and an old DELL Dimension 9200 (32-bit; Windows XP; 2.1GHz). Using a 10second, 100fps image acquisition target, the sony could handle 1000, 512x256px images; with 10ms exposure, 10ms interval - really well, recording this in 10.4seconds consistently. The DELL was a little slower, taking 14.5 seconds to record this number of images. The Myocam-S is capable of high speeds, but recording with openCV is sluggish at >30 seconds on the DELL using the same criteria as mentioned above. I used Fast Storage option and the 1.4.15 version of Micro Manager.

hope this is enough info,
best wishes and thanks for the help,
Paul.



On 29 January 2014 18:05, Paul Hartley <[hidden email]> wrote:
Hi Mark,
thanks for the reply,
I will certainly give it a try; I'm using a 32-bit system (windows XP).
best wishes,
Paul.


On 29 January 2014 16:41, Ed Simmons <[hidden email]> wrote:
Hi Paul,

On 29/01/14 15:58, Paul Hartley wrote:
> Hi Mark,
> with reference to your earlier email; I connected the Ionoptix
> Myocam-S and used the OpenCVGrabber as you suggested. I get a nice
> live image (showing @30fps). I need to take relatively his speed
> footage of beating hearts. However frame capture rates are very slow,
> I'm needing to collect a 10second vimage sequence (1000 frames at 10ms
> exposure (i.e.100fps)), using 0ms interval, channels are off.
> Typically this is taking >30seconds when it should be close to 10seconds.
>
> This slow capture rate occurs whether or not I save direct to disk or
> RAM; processor activity is only about 90% and Image resolution is not
> a problem; I also increased the buffer capacity to 400MB. I ran some
> 'diagnostics' using the demo camera, this can collect 500 20ms
> exposure images (0ms interval; i.e.50fps) but the live image is shown
> at 100fps.
>
> I cannot tell if this is something I'm doing wrong, or whether this
> delay in frame capture is due to limitations in the OpenCVgrabber
> capabilities?
>
> Any advice / help is very much appreciated.
>
> Best wishes,
> Paul Hartley.
> University of Edinburgh.

I wrote OpenCVgrabber and I recall there being an issue with opencv that
caused this behaviour with some cameras.

If I recall correctly, some directshow devices accessed through opencv
return an old image on the first call to cvRetrieveFrame, thus needing
to call this twice. In the case of other cameras, this results in halved
frame rate.

Since this is a very odd 'feature', should we perhaps make this optional
by adding a property to enable or disable the extra call to cvRetrieveFrame?

Most directshow cameras don't respond to exposure settings via opencv,
thus opencvgrabber is a bit limited in this regard. In some cases, the
exposure can be set using a direct show application such as amcap first,
then quit this and run MM, the exposure set by amcap sometimes is still
set when loading OpenCVgrabber.

I can compile a dll for you to test with your camera, please could you
tell me whether you use 32 or 64 bit windows?

Thanks,
Ed

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Re: Myocam S with micro-manager

Mark Tsuchida-2
Hi Paul,

On Wed, Jan 29, 2014 at 10:22 AM, Paul Hartley <[hidden email]> wrote:
> I did some testing with the democam using a SONY Vaio (64bit; Windows7;
> 2.4GHz) and an old DELL Dimension 9200 (32-bit; Windows XP; 2.1GHz). Using a
> 10second, 100fps image acquisition target, the sony could handle 1000,
> 512x256px images; with 10ms exposure, 10ms interval - really well, recording
> this in 10.4seconds consistently. The DELL was a little slower, taking 14.5
> seconds to record this number of images. The Myocam-S is capable of high
> speeds, but recording with openCV is sluggish at >30 seconds on the DELL
> using the same criteria as mentioned above. I used Fast Storage option and
> the 1.4.15 version of Micro Manager.

>From the results with the DemoCamera, it looks like your Dell is
unable to record images fast enough with Micro-Manager (assuming you
set "FastImage" to "1" - otherwise, there is some overhead from
computing the sine-wave demo images). There is some overhead from
things like metadata recording, so capturing in Micro-Manager at high
frame rate can require some more resources than some simpler video
capturing software.

It may well still be worth trying Ed's solution (these things often
don't behave linearly), but it will certainly help if you are able to
test this on a faster computer. Recent desktops with Core i7 can do >
3000 fps, 512x512, 16-bit, from the DemoCamera (FastImage = 1), so I
don't think you need anything extreme (as your laptop results also
suggest).

Best,
Mark

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Re: Myocam S with micro-manager

Paul Hartley
thanks Mark,
I'll hunt down a faster computer,

best wishes,
Paul.


On 29 January 2014 18:57, Mark Tsuchida <[hidden email]> wrote:
Hi Paul,

On Wed, Jan 29, 2014 at 10:22 AM, Paul Hartley <[hidden email]> wrote:
> I did some testing with the democam using a SONY Vaio (64bit; Windows7;
> 2.4GHz) and an old DELL Dimension 9200 (32-bit; Windows XP; 2.1GHz). Using a
> 10second, 100fps image acquisition target, the sony could handle 1000,
> 512x256px images; with 10ms exposure, 10ms interval - really well, recording
> this in 10.4seconds consistently. The DELL was a little slower, taking 14.5
> seconds to record this number of images. The Myocam-S is capable of high
> speeds, but recording with openCV is sluggish at >30 seconds on the DELL
> using the same criteria as mentioned above. I used Fast Storage option and
> the 1.4.15 version of Micro Manager.

>From the results with the DemoCamera, it looks like your Dell is
unable to record images fast enough with Micro-Manager (assuming you
set "FastImage" to "1" - otherwise, there is some overhead from
computing the sine-wave demo images). There is some overhead from
things like metadata recording, so capturing in Micro-Manager at high
frame rate can require some more resources than some simpler video
capturing software.

It may well still be worth trying Ed's solution (these things often
don't behave linearly), but it will certainly help if you are able to
test this on a faster computer. Recent desktops with Core i7 can do >
3000 fps, 512x512, 16-bit, from the DemoCamera (FastImage = 1), so I
don't think you need anything extreme (as your laptop results also
suggest).

Best,
Mark

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Re: Myocam S with micro-manager

NLeblanc
In reply to this post by Paul Hartley
I am trying to use Micro-Manager with the Ion Optix MyoCam-S camera. I read
all 11 posts that suggest to use the OpenCVGrabber. I have installed several
versions of that package but Micro-Manager can't recognize the camera. I was
able to download a driver for the camera from Ion Optix and was able to test
it using a free software. I just need help to find out how to use the camera
with Micro-Manager.

Thanks.

Normand Leblanc, Ph.D.
University of Nevada, Reno




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Re: Myocam S with micro-manager

Nico Stuurman-2

On 3/24/2018 7:30 AM, NLeblanc wrote:
> I am trying to use Micro-Manager with the Ion Optix MyoCam-S camera. I read
> all 11 posts that suggest to use the OpenCVGrabber. I have installed several
> versions of that package but Micro-Manager can't recognize the camera. I was
> able to download a driver for the camera from Ion Optix and was able to test
> it using a free software. I just need help to find out how to use the camera
> with Micro-Manager.

The OpenCVGrabber code has been unmaintained for quite some time. If I
am not mistaken, even the documentation page has disappeared. Unless
someone takes over maintenance and documentation, I am afraid that it
will be hit or miss with the OpenCVGrabber (and once it nolonger works
for anyone, we will need to remove the code).  In the mean time, it may
help if you at least state which OS you use, and version of Micro-Manager.

Best,

Nico



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Re: Myocam S with micro-manager

NLeblanc
I am using 64-bit Windows 7. I have also tried a 32-bit computer with Windows
XP, both without success. I have tried Micro-Manager 1.4 and the newly
released Beta version 2. Unless there is something incompatible with the
OpenCVGrabber driver, I am thinking it has to do with the OpenCV
installation. I’ve tried version 3.3.1 and more recently the earlier version
2.4, with several versions of Visual Studio including 15, 17 and an earlier
version I don’t remember. I am not a programmer. Is there an easy way to
find out whether OpenCV is properly installed? Thanks.

Norm



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