Running Hamamatsu Camera on External Trigger Mode

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Running Hamamatsu Camera on External Trigger Mode

ranibar
Hi

I am using the microm-manager python wrapper to control the Hamamatsu ORCA
4.
I am able to do everything through code. however, I might be missing
something:
I set the camera properties to external trigger mode yet I get no images
although the trigger is active and the camera seems to be set right.
What I need to achieve eventually, is whenever a trigger comes in the camera
will take images.
Can anyone advise on this?

Thank you,
Rani



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Re: Running Hamamatsu Camera on External Trigger Mode

nanthony
Hi Ranibar,

Configuring the Hamamatsu camera can sometimes be complicated. It would be
helpful to see a simple code example where you attempt to get externally
triggered images.

--Nick



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Re: Running Hamamatsu Camera on External Trigger Mode

ranibar
Hi Nick

Thank you for your reply.

here is the code that I am using to control the camera and its
configuration:
import sys
import numpy as np
sys.path.append('C:\\Program Files\\Micro-Manager-2.0beta')
import MMCorePy

mmc = MMCorePy.CMMCore()
mmc.loadDevice('Camera', 'HamamatsuHam','HamamatsuHam_DCAM')
mmc.initializeAllDevices()
mmc.setProperty('Camera','TRIGGER ACTIVE','SYNCREADOUT')

The camera is fed with a square wave 20 ms which are 5 ms apart, the trigger
is fed through the EXT TRIG (1) at the back of the camera.

I am stuck at this point I don't know how to set up and which command to use
to start acquisition following the trigger.

When I use StartContinuousSequenceAcquisition I get images regardless of the
trigger. and when I use startSequenceAcquisition or snapImage I get
"Circular buffer is empty"

Thank you,
Rani




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Re: Running Hamamatsu Camera on External Trigger Mode

Nico Stuurman-2
Hi Rani,

> here is the code that I am using to control the camera and its
> configuration:
> import sys
> import numpy as np
> sys.path.append('C:\\Program Files\\Micro-Manager-2.0beta')
> import MMCorePy
>
> mmc = MMCorePy.CMMCore()
> mmc.loadDevice('Camera', 'HamamatsuHam','HamamatsuHam_DCAM')
> mmc.initializeAllDevices()
> mmc.setProperty('Camera','TRIGGER ACTIVE','SYNCREADOUT')
>
> The camera is fed with a square wave 20 ms which are 5 ms apart, the trigger
> is fed through the EXT TRIG (1) at the back of the camera.

You will need to set a property called something like 'TRIGGER_SOURCE'
to something like 'TRIGGER_SOURCE_EXTERNAL'. Hopefully the Property
Browser will show such a property and the values you can set it to.

Also, once you get this working, would be great if you could write up
how you accomplished it.

Best,

Nico



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Re: Running Hamamatsu Camera on External Trigger Mode

nanthony
Hi Rani,

I would second Nico's advice. There are many different properties related to triggering so you may need to set a few of them to get the behavior you expect. I'm not sure but I think the "TRIGGER ACTIVE" property that you are setting is actually configuring the camera to send TTL pulses of its own at the end of each exposure.

Once the triggering is configured you should be able to use `Snap`, `startSequenceAcquisition`, or `startContinuousAcquisition`. One confusing thing that I will warn you about is that Hamamatsu doesn't properly support the `intervalMs` argument for sequence acquisition so you need to set the `intervalMs` argument to 0.

--Nick

-----Original Message-----
From: Stuurman, Nico <[hidden email]>
Sent: Tuesday, February 25, 2020 11:20 AM
To: Micro-Manager General <[hidden email]>; ranibar <[hidden email]>
Subject: Re: [micro-manager-general] Running Hamamatsu Camera on External Trigger Mode

Hi Rani,

> here is the code that I am using to control the camera and its
> configuration:
> import sys
> import numpy as np
> sys.path.append('C:\\Program Files\\Micro-Manager-2.0beta') import
> MMCorePy
>
> mmc = MMCorePy.CMMCore()
> mmc.loadDevice('Camera', 'HamamatsuHam','HamamatsuHam_DCAM')
> mmc.initializeAllDevices()
> mmc.setProperty('Camera','TRIGGER ACTIVE','SYNCREADOUT')
>
> The camera is fed with a square wave 20 ms which are 5 ms apart, the
> trigger is fed through the EXT TRIG (1) at the back of the camera.

You will need to set a property called something like 'TRIGGER_SOURCE'
to something like 'TRIGGER_SOURCE_EXTERNAL'. Hopefully the Property Browser will show such a property and the values you can set it to.

Also, once you get this working, would be great if you could write up how you accomplished it.

Best,

Nico



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Re: Running Hamamatsu Camera on External Trigger Mode

ranibar
Hi all,

Thank you for your suggestions.

I am trying to find where the problem comes from and this is what I learned
thus far:

the command the list almost all properties available is
mmc.getDevicePropertyNames('Camera') which can be found in the MMCorePy.py.
also helpful are the commands mmc.getProperty, and
mmc.getAllowedPropertyValues
I tried changing various triggering properties
'TRIGGER ACTIVE' from 'EDGE' to 'SYNCREADOUT' or 'LEVEL'.
'TRIGGER EXPOSURE'
'ScanMode'

When I switch the TRIGGER SOURCE to EXTERNAL, the snapImage() is stuck until
timout (probably 10s of seconds and I get the error : Error in device
"Camera": Unknown error in the device (1). While when I switch the TRIGGER
to INTERNAL, the snapImage() works perfectly. Under EXTERNAL mode, when I
run the snapImage() command I see the status light of the camera turning
Orange (indicating data transfer is underway) and the status light keeps
orange even when the device returns an error, only when I switch trigger
source back to internal, the status light returns to green. However, note
that when the status light is 'stuck' on orange, the query deviceBusy
returns False.
so it seems to me that the snapImage function is waiting for the trigger and
it is not getting it?! So I tried to change the trigger timing, width,
voltage, etc. but nothing.
Might be there be any properties set that are conflicting and makes this
behavior? or is the camera somehow not getting the trigger signal right? or
is there another command that tells the camera to 'start' getting the
trigger?


Thank you,
I will keep trying and update and awaiting your advise.

Rani




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Re: Running Hamamatsu Camera on External Trigger Mode

nanthony
Hi Rani,

The freezing behavior you describe when using external triggering sounds consistent with the camera not receiving the trigger pulse, but it's hard to know with certainty. I would double check your wiring.

--Nick

-----Original Message-----
From: ranibar <[hidden email]>
Sent: Wednesday, February 26, 2020 3:29 AM
To: [hidden email]
Subject: Re: [micro-manager-general] Running Hamamatsu Camera on External Trigger Mode

Hi all,

Thank you for your suggestions.

I am trying to find where the problem comes from and this is what I learned thus far:

the command the list almost all properties available is
mmc.getDevicePropertyNames('Camera') which can be found in the MMCorePy.py.
also helpful are the commands mmc.getProperty, and mmc.getAllowedPropertyValues I tried changing various triggering properties 'TRIGGER ACTIVE' from 'EDGE' to 'SYNCREADOUT' or 'LEVEL'.
'TRIGGER EXPOSURE'
'ScanMode'

When I switch the TRIGGER SOURCE to EXTERNAL, the snapImage() is stuck until timout (probably 10s of seconds and I get the error : Error in device
"Camera": Unknown error in the device (1). While when I switch the TRIGGER to INTERNAL, the snapImage() works perfectly. Under EXTERNAL mode, when I run the snapImage() command I see the status light of the camera turning Orange (indicating data transfer is underway) and the status light keeps orange even when the device returns an error, only when I switch trigger source back to internal, the status light returns to green. However, note that when the status light is 'stuck' on orange, the query deviceBusy returns False.
so it seems to me that the snapImage function is waiting for the trigger and it is not getting it?! So I tried to change the trigger timing, width, voltage, etc. but nothing.
Might be there be any properties set that are conflicting and makes this behavior? or is the camera somehow not getting the trigger signal right? or is there another command that tells the camera to 'start' getting the trigger?


Thank you,
I will keep trying and update and awaiting your advise.

Rani




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Re: Running Hamamatsu Camera on External Trigger Mode

P.Almada
Hi Rani,

I can also confirm  that those settings are correct to set the camera to wait for a trigger:
"TRIGGER SOURCE" - "EXTERNAL"
"TRIGGER ACTIVE" - "SYNCREADOUT"

The orange light means it's waiting for a trigger. The 10 second time-out is from the Micro-Manager device adapter by the way and the camera's time-out is a bit longer. You'll have to wait a bit for it to clear.

Is the camera connected through USB? Is so, then it might not be able to keep up with the speed of your triggers and you'll see the behavior you describe.

Kind regards,
Pedro Almada

On Wed, 26 Feb 2020 at 17:41, Nicholas Michael Anthony <[hidden email]> wrote:
Hi Rani,

The freezing behavior you describe when using external triggering sounds consistent with the camera not receiving the trigger pulse, but it's hard to know with certainty. I would double check your wiring.

--Nick

-----Original Message-----
From: ranibar <[hidden email]>
Sent: Wednesday, February 26, 2020 3:29 AM
To: [hidden email]
Subject: Re: [micro-manager-general] Running Hamamatsu Camera on External Trigger Mode

Hi all,

Thank you for your suggestions.

I am trying to find where the problem comes from and this is what I learned thus far:

the command the list almost all properties available is
mmc.getDevicePropertyNames('Camera') which can be found in the MMCorePy.py.
also helpful are the commands mmc.getProperty, and mmc.getAllowedPropertyValues I tried changing various triggering properties 'TRIGGER ACTIVE' from 'EDGE' to 'SYNCREADOUT' or 'LEVEL'.
'TRIGGER EXPOSURE'
'ScanMode'

When I switch the TRIGGER SOURCE to EXTERNAL, the snapImage() is stuck until timout (probably 10s of seconds and I get the error : Error in device
"Camera": Unknown error in the device (1). While when I switch the TRIGGER to INTERNAL, the snapImage() works perfectly. Under EXTERNAL mode, when I run the snapImage() command I see the status light of the camera turning Orange (indicating data transfer is underway) and the status light keeps orange even when the device returns an error, only when I switch trigger source back to internal, the status light returns to green. However, note that when the status light is 'stuck' on orange, the query deviceBusy returns False.
so it seems to me that the snapImage function is waiting for the trigger and it is not getting it?! So I tried to change the trigger timing, width, voltage, etc. but nothing.
Might be there be any properties set that are conflicting and makes this behavior? or is the camera somehow not getting the trigger signal right? or is there another command that tells the camera to 'start' getting the trigger?


Thank you,
I will keep trying and update and awaiting your advise.

Rani




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Re: Running Hamamatsu Camera on External Trigger Mode

ranibar
In reply to this post by nanthony
Hi,

Thank you Almada and Nick for your replies.

I am still unable to make this work. I changed the rate and duty cycle of
the trigger signal (analog 3.3V square wave). I am working with a usb
connection of the camera so the rate is about 23Hz, and I am for sure giving
a trigger that is less than that.

I tried your suggestions checked cables and configurations.

Bu the way, also when using the micromanager software the same behavior. I
change the configurations to external trigger and when snapping the software
freezes.

Was anybody able to make this work with an ORCA flash 4.0?

moreover, where can I find what is the mapping between ScanMode property
values being 1,2, or 3 and what these actually mean. the ScanMode is
meanwhile at 2. and how do I change the mode of the camera between fast and
slow ? is this the ScanMode proeprty?

Thank you,
Rani



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Re: Running Hamamatsu Camera on External Trigger Mode

Matthijs
Hi Rani,

Just as a sanity-check, perhaps it is worth trying to hook up your TTL signal to an oscilloscope set to external trigger mode, just to see the signal makes it to your endpoint intact? 

I'm afraid we went the other direction with our Orca Flash 4.0: using an Arduino to send a trigger to our external acquisition boards when the camera starts recording to sync our electrophysiology with the camera, rather than the other way around. If I recall correctly, someone on this list makes dedicated sync boxes for applications like that. 

Yours,

  Matthijs


From: ranibar <[hidden email]>
Sent: Thursday, February 27, 2020 10:59 AM
To: [hidden email] <[hidden email]>
Subject: Re: [micro-manager-general] Running Hamamatsu Camera on External Trigger Mode
 
Hi,

Thank you Almada and Nick for your replies.

I am still unable to make this work. I changed the rate and duty cycle of
the trigger signal (analog 3.3V square wave). I am working with a usb
connection of the camera so the rate is about 23Hz, and I am for sure giving
a trigger that is less than that.

I tried your suggestions checked cables and configurations.

Bu the way, also when using the micromanager software the same behavior. I
change the configurations to external trigger and when snapping the software
freezes.

Was anybody able to make this work with an ORCA flash 4.0?

moreover, where can I find what is the mapping between ScanMode property
values being 1,2, or 3 and what these actually mean. the ScanMode is
meanwhile at 2. and how do I change the mode of the camera between fast and
slow ? is this the ScanMode proeprty?

Thank you,
Rani



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Re: Running Hamamatsu Camera on External Trigger Mode

P.Almada
In reply to this post by ranibar
Hi Ranibar

I did get the camera to work with triggering. Scan mode is indeed fast and slow, I forget which is which. I suggest trying to acquire a non triggered 1000 frames time lapse at 10 ms in either mode. Which ever takes longest will be the slow mode.

Kind regards, 
Pedro 

On Thu, 27 Feb 2020, 10:01 ranibar, <[hidden email]> wrote:
Hi,

Thank you Almada and Nick for your replies.

I am still unable to make this work. I changed the rate and duty cycle of
the trigger signal (analog 3.3V square wave). I am working with a usb
connection of the camera so the rate is about 23Hz, and I am for sure giving
a trigger that is less than that.

I tried your suggestions checked cables and configurations.

Bu the way, also when using the micromanager software the same behavior. I
change the configurations to external trigger and when snapping the software
freezes.

Was anybody able to make this work with an ORCA flash 4.0?

moreover, where can I find what is the mapping between ScanMode property
values being 1,2, or 3 and what these actually mean. the ScanMode is
meanwhile at 2. and how do I change the mode of the camera between fast and
slow ? is this the ScanMode proeprty?

Thank you,
Rani



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Re: Running Hamamatsu Camera on External Trigger Mode

ranibar
Hi Everybody,

I am still stuck with this.

It might be also indicative (maybe) of the nature of the problem is that I
am also unable to get a trigger from the camera. I hooked up the timing 1 to
an oscilloscope, opened the micromanager 2, started acquisition/snapped, but
I see nothing on the oscilloscope! tried changing configs. nothing.
Cable I guess is ok, I tried two already.

maybe there is some command to start triggering (whether from the camera or
into the camera) that is not fired? or maybe its a driver issue?

Best,
Rani



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Re: Running Hamamatsu Camera on External Trigger Mode

nanthony
Hi Rani,

It might be helpful to attach a screenshot or text readout of your device properties in micromanager. There are a few properties that affect the triggering behavior.

--Nick

> On Mar 3, 2020, at 1:58 AM, ranibar <[hidden email]> wrote:
>
> Hi Everybody,
>
> I am still stuck with this.
>
> It might be also indicative (maybe) of the nature of the problem is that I
> am also unable to get a trigger from the camera. I hooked up the timing 1 to
> an oscilloscope, opened the micromanager 2, started acquisition/snapped, but
> I see nothing on the oscilloscope! tried changing configs. nothing.
> Cable I guess is ok, I tried two already.
>
> maybe there is some command to start triggering (whether from the camera or
> into the camera) that is not fired? or maybe its a driver issue?
>
> Best,
> Rani
>
>
>
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Re: Running Hamamatsu Camera on External Trigger Mode

ranibar
Hi Nick,

here is a screenshot:
I tried all sort of things but maybe the combination of settings?


<http://micro-manager.3463995.n2.nabble.com/file/t397530/config.jpg>



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Re: Running Hamamatsu Camera on External Trigger Mode

nanthony
Hi Rani,

In order for "OUTPUT_TRIGGER_SOURCE" to have any effect you'll need to set "OUTPUT_TRIGGER_KIND" to "Programmable". Having it set as "Low" will mean that it is always at 0 volts.

--Nick

-----Original Message-----
From: ranibar <[hidden email]>
Sent: Tuesday, March 3, 2020 11:06 AM
To: [hidden email]
Subject: Re: [micro-manager-general] Running Hamamatsu Camera on External Trigger Mode

Hi Nick,

here is a screenshot:
I tried all sort of things but maybe the combination of settings?


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Re: Running Hamamatsu Camera on External Trigger Mode

ranibar
Hi Nick,

Thank you very much for this one. So now we established that the trigger
from the camera works. however I am still unable to get the camera work from
an external trigger! anything you see there that is not right?
or maybe the trigger needs to be in a very specific shape/duty
cycle/frequency?

Best,
Rani



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Re: Running Hamamatsu Camera on External Trigger Mode

Amit Cherian
Hello,

Hamamatsu Device property "Trigger polarity" is something that has not been
mentioned here in the discussion yet. By default it is negative. Try setting
it to positive.

Best,
Amit



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Re: Running Hamamatsu Camera on External Trigger Mode

塚田 祐基
In reply to this post by ranibar
Hi Rani,

Do you still have the problem? I have same problem and checked if
HCImage by Hamamatsu work with external trigger.
Then, it didn't work. After consulting with Hamamatsu engineer,
we are sending our camera to Hamamatsu if the external trigger circuit is working or not.
If you still have the problem, I would recommend you to check the hardware issue.
Best,

Yuki


On 2020/03/04 16:06, ranibar wrote:

> Hi Nick,
>
> Thank you very much for this one. So now we established that the trigger
> from the camera works. however I am still unable to get the camera work from
> an external trigger! anything you see there that is not right?
> or maybe the trigger needs to be in a very specific shape/duty
> cycle/frequency?
>
> Best,
> Rani
>
>
>
> --
> Sent from: http://micro-manager.3463995.n2.nabble.com/
>
>
> _______________________________________________
> micro-manager-general mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/micro-manager-general
>

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Yuki TSUKADA, Ph.D.
Neuroscience Institute,
Graduate School of Science,
Nagoya University

Furou-cho, Chikusa-ku
Nagoya 464-8602, Japan
TEL:+8152-789-4559
URL:http://elegans.bio.nagoya-u.ac.jp/~tsukada/


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