Hamamastu Orca R2 and multidimensional acquisition

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Hamamastu Orca R2 and multidimensional acquisition

Laurent.Boitard
Hello all,

I have several questions regarding multidimensional acquisition with
hamamatsu orca R2.
I'm trying to make a simple timelapse with two channels (fluo and trans).
Each shutter is independantely controlled by a Labview program.
I set my camera to positive edge trigger. To start acquisition I send a
TTL with a period of 750ms between each rise. For hamamastu Orca R2 the
read out time is 117,36ms and interval trigger time 100ms hence I
shouldn't have any trouble triggering an acquisition every 750ms.
It happens that during the acquisition some images are not acquired.
Weather I record on the ram or directly on disk I still need at least
750ms between each TTL. Why so ? Even if i leave 1s between each TTL i
still miss some images after several 1000.
I've been working with hamamatsu support team but so far we haven't
figured out how to solve this issue.
Does anybody have the same problem ?
I'd be most greatful for any help.

Laurent Boitard
PhD student
LCMD-ESPCI


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Re: Hamamastu Orca R2 and multidimensional acquisition

Nico Stuurman
Administrator
Hi Laurent,


> I have several questions regarding multidimensional acquisition with
> hamamatsu orca R2.
> I'm trying to make a simple timelapse with two channels (fluo and  
> trans).
> Each shutter is independantely controlled by a Labview program.

What is the reason to control your shutters by Labview instead of  
Micro-Manager?  Your acquisition protocol would be trivially simple if  
you would control both shutters and camera by Micro- Manager.

> I set my camera to positive edge trigger. To start acquisition I  
> send a
> TTL with a period of 750ms between each rise. For hamamastu Orca R2  
> the
> read out time is 117,36ms and interval trigger time 100ms hence I
> shouldn't have any trouble triggering an acquisition every 750ms.
> It happens that during the acquisition some images are not acquired.
> Weather I record on the ram or directly on disk I still need at least
> 750ms between each TTL. Why so ? Even if i leave 1s between each TTL i
> still miss some images after several 1000.

I assume that you are using "Burst" mode to collect the images?

Is the camera not triggered or is the software missing the image?  I  
think that the R2 has a TTL that goes high during exposure, so you  
could check by hooking up an oscilloscope.

If the software is "skipping" images, there is most likely something  
going on in the functions "svc" and "PushImage" in the Hamamatsu  
code.  We have not tested this with external triggers, and it would  
not surprise me if there is something going on with timing.  That code  
was tested extensively with internal triggering.


Best,

Nico


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Re: Hamamastu Orca R2 and multidimensional acquisition

Laurent.Boitard
Hi Nico,

> Hi Laurent,
>
>
>> I have several questions regarding multidimensional acquisition with
>> hamamatsu orca R2.
>> I'm trying to make a simple timelapse with two channels (fluo and
>> trans).
>> Each shutter is independantely controlled by a Labview program.
>
> What is the reason to control your shutters by Labview instead of
> Micro-Manager?  Your acquisition protocol would be trivially simple if
> you would control both shutters and camera by Micro- Manager.

I'm controlling the shutters by Labview because I also have to control my
X/Y stage (Thorlabs) that is not supported yet by micro-manager. So I made
a program that control everything and send TTLs to the camera to start the
acquisition.

>> I set my camera to positive edge trigger. To start acquisition I
>> send a
>> TTL with a period of 750ms between each rise. For hamamastu Orca R2
>> the
>> read out time is 117,36ms and interval trigger time 100ms hence I
>> shouldn't have any trouble triggering an acquisition every 750ms.
>> It happens that during the acquisition some images are not acquired.
>> Weather I record on the ram or directly on disk I still need at least
>> 750ms between each TTL. Why so ? Even if i leave 1s between each TTL i
>> still miss some images after several 1000.
>
> I assume that you are using "Burst" mode to collect the images?

Actually I'm using "Multi dimensional acquisition" mode to collect the
images. Weather I use a function generator or my Labview program there are
always images missing.
>
> Is the camera not triggered or is the software missing the image?  I
> think that the R2 has a TTL that goes high during exposure, so you
> could check by hooking up an oscilloscope.

I did that and it's software related since with the HCImage software given
with the camera it works just fine.
>
> If the software is "skipping" images, there is most likely something
> going on in the functions "svc" and "PushImage" in the Hamamatsu
> code.  We have not tested this with external triggers, and it would
> not surprise me if there is something going on with timing.  That code
> was tested extensively with internal triggering.

Anything that can be done about it ?

Finally an other question. Is it possible to change the name of the
images. Right now I set the name prefix it gives the name of the directory
in which the images will be recorded but the name of the images is
img_#########_config_000.tif where config is the the configuration of the
group that I created. I'd like to be able to record in two different
directories: 1 for transmission images 1 for fluorescence images with the
following name: img_config_#########.tif


Thanks again.

Laurent


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> developing skills, take BlackBerry mobile applications to market and stay
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Re: Hamamastu Orca R2 and multidimensional acquisition

Nico Stuurman
Administrator
Hi Laurent,

I have several questions regarding multidimensional acquisition with
hamamatsu orca R2.
Each shutter is independantely controlled by a Labview program.

I'm controlling the shutters by Labview because I also have to control my
X/Y stage (Thorlabs) that is not supported yet by micro-manager. So I made
a program that control everything and send TTLs to the camera to start the
acquisition.

Do you need programmatic control of the XY stage during acquisition, i.e. are you acquiring at multiple positions simultaneously?  If not, I would let Micro-Manager control the shutters and use software triggering.  The nicest solution would be to write a Micro-Manager adapter for the Thorlabs stage.

I set my camera to positive edge trigger. To start acquisition I
send a
TTL with a period of 750ms between each rise. For hamamastu Orca R2
the
read out time is 117,36ms and interval trigger time 100ms hence I
shouldn't have any trouble triggering an acquisition every 750ms.
It happens that during the acquisition some images are not acquired.
Weather I record on the ram or directly on disk I still need at least
750ms between each TTL. Why so ? Even if i leave 1s between each TTL i
still miss some images after several 1000.

Actually I'm using "Multi dimensional acquisition" mode to collect the
images. Weather I use a function generator or my Labview program there are
always images missing.

That means that the function "SnapImage()" in the adapter is called, followed by "GetImageBuffer()".  These functions have been written with software triggers in mind, and no testing has been done with external triggering.  Also, the Multi-Dimensional Acquisition has no clue about external triggers, so it is not strange that things do not work as expected.  How do you now set set up your MDF acquisition (channels, intervals, etc...)?

I would try to use sequence acquisition ("Burst" mode) and see if that works better.  If it does, you could either use Burst mode directly, or you could write a Beanshell script that saves the incoming images with the file names that you want (which would solve the problem you describe below)
 

If the software is "skipping" images, there is most likely something
going on in the functions "svc" and "PushImage" in the Hamamatsu
code.  We have not tested this with external triggers, and it would
not surprise me if there is something going on with timing.  That code
was tested extensively with internal triggering.

Forget that comment, since you are using the SnapImage functionality rather than "Burst" mode.  

Finally an other question. Is it possible to change the name of the
images. Right now I set the name prefix it gives the name of the directory
in which the images will be recorded but the name of the images is
img_#########_config_000.tif where config is the the configuration of the
group that I created. I'd like to be able to record in two different
directories: 1 for transmission images 1 for fluorescence images with the
following name: img_config_#########.tif

Best,

Nico

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