Frame rate limits

classic Classic list List threaded Threaded
8 messages Options
Reply | Threaded
Open this post in threaded view
|

Frame rate limits

otills
Hi, I am currently trialling a Basler 5 MP camera with an Optiscan stage and trying to use MicroManager to control both. Although I've managed to get the two controlled through MM (not without fairly frequent error messages, however I'm hoping these can be ironed out) I'm currently unable to acheive the fps rate I require. I don't know if this is due to the computer I'm using (which isn't particularly high spec; if the trial is successful I will be buying a high spec machine to control the system) or the limitations of MM/Image J. Is MM/Image J capable of capturing 5 MB frames at 10 fps, does anyone have experience of this kind of application? If so, what machine do you use to acheive this? When I use burst capture mode or try multidimensional acquisition I end up with a metadata file but no images so I just wanted confirmation that what I'm trying to acheive is acheivable!

Many thanks,

Oli Tills
________________________________
From: Oliver Tills [[hidden email]]
Sent: 14 January 2010 16:32
To: [hidden email]
Subject: [micro-manager-general] (no subject)

Hi,

When I try to add a TWAIN camera in hardware configurator I get the error message “string index is out of range: 0”.

Does anyone know what this message means and how to overcome it?

Oliver Tills
[hidden email]<mailto:[hidden email]>



------------------------------------------------------------------------------
Throughout its 18-year history, RSA Conference consistently attracts the
world's best and brightest in the field, creating opportunities for Conference
attendees to learn about information security's most important issues through
interactions with peers, luminaries and emerging and established companies.
http://p.sf.net/sfu/rsaconf-dev2dev
_______________________________________________
micro-manager-general mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/micro-manager-general
Reply | Threaded
Open this post in threaded view
|

Re: Frame rate limits

E Chalaron
Hi Oliver
Have you tried Coriander / libdc1394-2 ?
Its only limitation (that I know of) is that it cant display 16 bits/
pixels frames.
Since we are here : has anyone tried to use MM as a control display
getting frames from stdin or through Vloopback ?
Thanks a lot
E
Wellington NZ



On 17/01/10 01:36, Oliver Tills wrote:

> Hi, I am currently trialling a Basler 5 MP camera with an Optiscan stage and trying to use MicroManager to control both. Although I've managed to get the two controlled through MM (not without fairly frequent error messages, however I'm hoping these can be ironed out) I'm currently unable to acheive the fps rate I require. I don't know if this is due to the computer I'm using (which isn't particularly high spec; if the trial is successful I will be buying a high spec machine to control the system) or the limitations of MM/Image J. Is MM/Image J capable of capturing 5 MB frames at 10 fps, does anyone have experience of this kind of application? If so, what machine do you use to acheive this? When I use burst capture mode or try multidimensional acquisition I end up with a metadata file but no images so I just wanted confirmation that what I'm trying to acheive is acheivable!
>
> Many thanks,
>
> Oli Tills
> ________________________________
> From: Oliver Tills [[hidden email]]
> Sent: 14 January 2010 16:32
> To: [hidden email]
> Subject: [micro-manager-general] (no subject)
>
> Hi,
>
> When I try to add a TWAIN camera in hardware configurator I get the error message “string index is out of range: 0”.
>
> Does anyone know what this message means and how to overcome it?
>
> Oliver Tills
> [hidden email]<mailto:[hidden email]>
>
>
>
> ------------------------------------------------------------------------------
> Throughout its 18-year history, RSA Conference consistently attracts the
> world's best and brightest in the field, creating opportunities for Conference
> attendees to learn about information security's most important issues through
> interactions with peers, luminaries and emerging and established companies.
> http://p.sf.net/sfu/rsaconf-dev2dev
> _______________________________________________
> micro-manager-general mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/micro-manager-general
>
>  

------------------------------------------------------------------------------
Throughout its 18-year history, RSA Conference consistently attracts the
world's best and brightest in the field, creating opportunities for Conference
attendees to learn about information security's most important issues through
interactions with peers, luminaries and emerging and established companies.
http://p.sf.net/sfu/rsaconf-dev2dev
_______________________________________________
micro-manager-general mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/micro-manager-general
Reply | Threaded
Open this post in threaded view
|

Re: Frame rate limits

Nico Stuurman-4
In reply to this post by otills
> Hi, I am currently trialling a Basler 5 MP camera with an Optiscan  
> stage and trying to use MicroManager to control both. Although I've  
> managed to get the two controlled through MM I'm currently unable to  
> acheive the fps rate I require.  Is MM/Image J capable of capturing  
> 5 MB frames at 10 fps, does anyone have experience of this kind of  
> application?

Frame rate in Micro-Manager is limited by what the camera/driver/
adapter can deliver.  In the case of Hamamatsu, Andor, Roper EM  
cameras, we routinely acquire 512x512x2 bytes at 30 fps (i.e. 15MB per  
second).  50MB per second will likely push the limits (USB 2.0 maxes  
out at 60 MB per second). If you are using the TWAIN adapter, then you  
are certainly out of luck as that does not make efficient use of the  
capabilities of your hardware.

> Have you tried Coriander / libdc1394-2 ?
> Its only limitation (that I know of) is that it cant display 16 bits/
> pixels frames.

Micro-Manager has a libdc1394-2 adapter that should be able to acquire  
images at the speeds libdc1394 can deliver them.

Best,

Nico


------------------------------------------------------------------------------
Throughout its 18-year history, RSA Conference consistently attracts the
world's best and brightest in the field, creating opportunities for Conference
attendees to learn about information security's most important issues through
interactions with peers, luminaries and emerging and established companies.
http://p.sf.net/sfu/rsaconf-dev2dev
_______________________________________________
micro-manager-general mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/micro-manager-general
Reply | Threaded
Open this post in threaded view
|

Re: Frame rate limits

otills
Hi, the camera is connected by GigE so should be capable of the framerates I require (and is within the Basler demo software). What is the reason for the TWAIN driver being unable to deliver similar frame rates.. is this really a limitation of the driver or just the hardware (or some setting of the driver I've yet to fathom)?

________________________________________
From: Nico Stuurman [[hidden email]]
Sent: 16 January 2010 21:52
To: Micro-Manager General
Subject: Re: [micro-manager-general] Frame rate limits

> Hi, I am currently trialling a Basler 5 MP camera with an Optiscan
> stage and trying to use MicroManager to control both. Although I've
> managed to get the two controlled through MM I'm currently unable to
> acheive the fps rate I require.  Is MM/Image J capable of capturing
> 5 MB frames at 10 fps, does anyone have experience of this kind of
> application?

Frame rate in Micro-Manager is limited by what the camera/driver/
adapter can deliver.  In the case of Hamamatsu, Andor, Roper EM
cameras, we routinely acquire 512x512x2 bytes at 30 fps (i.e. 15MB per
second).  50MB per second will likely push the limits (USB 2.0 maxes
out at 60 MB per second). If you are using the TWAIN adapter, then you
are certainly out of luck as that does not make efficient use of the
capabilities of your hardware.

> Have you tried Coriander / libdc1394-2 ?
> Its only limitation (that I know of) is that it cant display 16 bits/
> pixels frames.

Micro-Manager has a libdc1394-2 adapter that should be able to acquire
images at the speeds libdc1394 can deliver them.

Best,

Nico


------------------------------------------------------------------------------
Throughout its 18-year history, RSA Conference consistently attracts the
world's best and brightest in the field, creating opportunities for Conference
attendees to learn about information security's most important issues through
interactions with peers, luminaries and emerging and established companies.
http://p.sf.net/sfu/rsaconf-dev2dev
_______________________________________________
micro-manager-general mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/micro-manager-general
------------------------------------------------------------------------------
Throughout its 18-year history, RSA Conference consistently attracts the
world's best and brightest in the field, creating opportunities for Conference
attendees to learn about information security's most important issues through
interactions with peers, luminaries and emerging and established companies.
http://p.sf.net/sfu/rsaconf-dev2dev
_______________________________________________
micro-manager-general mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/micro-manager-general
Reply | Threaded
Open this post in threaded view
|

Re: Frame rate limits

Nico Stuurman-4
> Hi, the camera is connected by GigE so should be capable of the  
> framerates I require (and is within the Basler demo software). What  
> is the reason for the TWAIN driver being unable to deliver similar  
> frame rates.. is this really a limitation of the driver or just the  
> hardware (or some setting of the driver I've yet to fathom)?

TWAIN is an old, generic protocol designed for scanners and not very  
applicable for what you try to accomplish.  Ask Basler to write a  
Micro-Manager adapter for their cameras.

Best,

Nico

------------------------------------------------------------------------------
Throughout its 18-year history, RSA Conference consistently attracts the
world's best and brightest in the field, creating opportunities for Conference
attendees to learn about information security's most important issues through
interactions with peers, luminaries and emerging and established companies.
http://p.sf.net/sfu/rsaconf-dev2dev
_______________________________________________
micro-manager-general mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/micro-manager-general
Reply | Threaded
Open this post in threaded view
|

Re: Help on how to use groups and presets...

S. Pagakis
Hello

I was looking for a manual/short document which could explain to me how to use the features of GROUPS and PRESETS.
Is there such a document?

If not, could someone please explain briefly?

For example could a group be the dichroic filter wheel of the microscope and each preset could be a specific filter position?  Or a group could be something more comprehensive such as a specific filter, a stage position and a camera exposure time as well?

Some info on the optimum usage of these features would be appreciated.


Thanks in advance


S. Pagakis



*********************************

Stamatis Pagakis Ph.D.

Biological Imaging Unit

Biomedical Research Foundation, Academy of Athens

Soranou Efessiou 4, Athens 115 27 - Greece

M:     +306946644955                 

W:     +302106597481

FAX: +302106597545

http://www.bioacademy.gr/Faculty/core.php?cr=17



------------------------------------------------------------------------------
Throughout its 18-year history, RSA Conference consistently attracts the
world's best and brightest in the field, creating opportunities for Conference
attendees to learn about information security's most important issues through
interactions with peers, luminaries and emerging and established companies.
http://p.sf.net/sfu/rsaconf-dev2dev
_______________________________________________
micro-manager-general mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/micro-manager-general
Reply | Threaded
Open this post in threaded view
|

Re: Help on how to use groups and presets...

Shalin Mehta
Hi Pagakis,

When you first define a group, MM asks you to create the first preset. In cretaing that preset, you are allowed to club together any number of properties of all of the defined devices. In this way, you define a certain change in the state of the microscope when that preset is selected. For all subsequent presets, you can alter the properties of the devices already clubbed as a 'group' previously.

When you perform multi-D acquisition, you can pick up any group as 'channel'. The presets in the group are the individual channels that you can acquire with suitable exposures and x,y,z settings.

Therefore, to me it seems optimum that  everything (e.g., turning on the source, activating right shutter, right settings of light-path including the diachroic) but stage positions and exposure is what should be 'grouped'. You could call this group 'Fluorescence'. Each preset of this group can have different settings (e.g. different diachronic) for different fluorescent channels.

You may also wish to define some 'low-level' groups of properties that you most often manipulate from the Device Property Browser.

btw, is there any performance penalty when too many groups are defined?

Hope this helps,
Shalin

On Mon, Jan 18, 2010 at 7:29 PM, S. Pagakis <[hidden email]> wrote:
Hello

I was looking for a manual/short document which could explain to me how to use the features of GROUPS and PRESETS.
Is there such a document?

If not, could someone please explain briefly?

For example could a group be the dichroic filter wheel of the microscope and each preset could be a specific filter position?  Or a group could be something more comprehensive such as a specific filter, a stage position and a camera exposure time as well?

Some info on the optimum usage of these features would be appreciated.


Thanks in advance


S. Pagakis



*********************************

Stamatis Pagakis Ph.D.

Biological Imaging Unit

Biomedical Research Foundation, Academy of Athens

Soranou Efessiou 4, Athens 115 27 - Greece

M:     +306946644955                 

W:     +302106597481

FAX: +302106597545

http://www.bioacademy.gr/Faculty/core.php?cr=17



------------------------------------------------------------------------------
Throughout its 18-year history, RSA Conference consistently attracts the
world's best and brightest in the field, creating opportunities for Conference
attendees to learn about information security's most important issues through
interactions with peers, luminaries and emerging and established companies.
http://p.sf.net/sfu/rsaconf-dev2dev
_______________________________________________
micro-manager-general mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/micro-manager-general



------------------------------------------------------------------------------
Throughout its 18-year history, RSA Conference consistently attracts the
world's best and brightest in the field, creating opportunities for Conference
attendees to learn about information security's most important issues through
interactions with peers, luminaries and emerging and established companies.
http://p.sf.net/sfu/rsaconf-dev2dev
_______________________________________________
micro-manager-general mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/micro-manager-general
Reply | Threaded
Open this post in threaded view
|

Re: Help on how to use groups and presets... (attempt to answer question about groups performance)

Hoover, Karl
Hi Pagakis & Shalin,

Reviewing the source code, I see that a loop over AvailableConfigGroups is executed, for example, in MicroscopeModel.createSetupConfigsFromHardware (called from MMStudioMainFrame.saveConfigPresets), GroupEditor.writeGroup, and  MMAcquisitionEnginer.getAvailableGroups (called when the Acquisition dialog is loaded). Thus a large number of groups will have some performance impact on the pre-set editor, the group editor and the the launching of the acquisition dialog. In my understanding, a large number of Groups should have NO performance impact on the run-time operation of the software.

Best Regards,

Karl

________________________________
From: Shalin Mehta [[hidden email]]
Sent: Monday, January 18, 2010 03:46
To: Micro-Manager General
Subject: Re: [micro-manager-general] Help on how to use groups and presets...

Hi Pagakis,

When you first define a group, MM asks you to create the first preset. In cretaing that preset, you are allowed to club together any number of properties of all of the defined devices. In this way, you define a certain change in the state of the microscope when that preset is selected. For all subsequent presets, you can alter the properties of the devices already clubbed as a 'group' previously.

When you perform multi-D acquisition, you can pick up any group as 'channel'. The presets in the group are the individual channels that you can acquire with suitable exposures and x,y,z settings.

Therefore, to me it seems optimum that  everything (e.g., turning on the source, activating right shutter, right settings of light-path including the diachroic) but stage positions and exposure is what should be 'grouped'. You could call this group 'Fluorescence'. Each preset of this group can have different settings (e.g. different diachronic) for different fluorescent channels.

You may also wish to define some 'low-level' groups of properties that you most often manipulate from the Device Property Browser.

btw, is there any performance penalty when too many groups are defined?

Hope this helps,
Shalin

On Mon, Jan 18, 2010 at 7:29 PM, S. Pagakis <[hidden email]<mailto:[hidden email]>> wrote:
Hello

I was looking for a manual/short document which could explain to me how to use the features of GROUPS and PRESETS.
Is there such a document?

If not, could someone please explain briefly?

For example could a group be the dichroic filter wheel of the microscope and each preset could be a specific filter position?  Or a group could be something more comprehensive such as a specific filter, a stage position and a camera exposure time as well?

Some info on the optimum usage of these features would be appreciated.


Thanks in advance


S. Pagakis




*********************************

Stamatis Pagakis Ph.D.

Biological Imaging Unit

Biomedical Research Foundation, Academy of Athens

Soranou Efessiou 4, Athens 115 27 - Greece

M:     +306946644955

W:     +302106597481

FAX: +302106597545

http://www.bioacademy.gr/Faculty/core.php?cr=17


------------------------------------------------------------------------------
Throughout its 18-year history, RSA Conference consistently attracts the
world's best and brightest in the field, creating opportunities for Conference
attendees to learn about information security's most important issues through
interactions with peers, luminaries and emerging and established companies.
http://p.sf.net/sfu/rsaconf-dev2dev
_______________________________________________
micro-manager-general mailing list
[hidden email]<mailto:[hidden email]>
https://lists.sourceforge.net/lists/listinfo/micro-manager-general



------------------------------------------------------------------------------
Throughout its 18-year history, RSA Conference consistently attracts the
world's best and brightest in the field, creating opportunities for Conference
attendees to learn about information security's most important issues through
interactions with peers, luminaries and emerging and established companies.
http://p.sf.net/sfu/rsaconf-dev2dev
_______________________________________________
micro-manager-general mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/micro-manager-general