Neo scMOS problem

[Lu Lei]

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Hi all,
We recently purchased a wide-field microscope system with a scMOS camera
(Neo, 5.5 Megapixel, by Andor). We are having quite some annoying problems
with this Neo scMOS camera. Though it is a 16-bit device, it does not have the
dynamic range it should have in our system.
1) In “Rolling” shutter mode, the intensity value that the camera could
generate is truncated at ~20K. In another word, the camera saturates at ~20K
instead of 65535.
2) In “Global” shutter mode, the camera saturates at ~57K—a little short of
65535.
The camera is controled by the latest MetaMorph. The cooling temperature of
the camera seems also normal as displayed by MetaMorph (-30C). We haven’t
received any explanation from Andor via local vendor yet. I am wondering what
is configured incorrectly here.
Does anyone have similar experience of this camera or suggestion to share?
Thanks a lot.
Regards,
Lei Lu
-------------------------------------------------------------------------
Lu Lei (Asst Prof) | School of Biological Sciences | Nanyang Technological
University SBS-03n-18, 60 Nanyang Drive, Singapore 637551
Tel: [phone] | Fax: [phone] | Email: [hidden email]
-------------------------------------------------------------------------

[John Oreopoulos]

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I'm almost certain there's a camera property that can turn on the high dynamic range digitizer. It's been a while since I had my hands on a NEO and back then I was using MicroManager to access this device property. Perhaps you can get access to it too from the Metamorph administrator as well? Try calling Molecular devices for details. Maybe the default can also be switched using the camera's native software too (Solis)?

John Oreopoulos
Staff Scientist
Spectral Applied Research
Richmond Hill, Ontario
Canada
www.soectral.ca

On 2013-07-26, at 3:56 AM, Lu Lei <[hidden email]> wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> Hi all,
> We recently purchased a wide-field microscope system with a scMOS camera
> (Neo, 5.5 Megapixel, by Andor). We are having quite some annoying problems
> with this Neo scMOS camera. Though it is a 16-bit device, it does not have the
> dynamic range it should have in our system.
> 1)    In “Rolling” shutter mode, the intensity value that the camera could
> generate is truncated at ~20K. In another word, the camera saturates at ~20K
> instead of 65535.
> 2)    In “Global” shutter mode, the camera saturates at ~57K—a little short of
> 65535.
> The camera is controled by the latest MetaMorph. The cooling temperature of
> the camera seems also normal as displayed by MetaMorph (-30&#61616;C). We haven’t
> received any explanation from Andor via local vendor yet. I am wondering what
> is configured incorrectly here.
> Does anyone have similar experience of this camera or suggestion to share?
> Thanks a lot.
> Regards,
> Lei Lu
> -------------------------------------------------------------------------
> Lu Lei (Asst Prof) | School of Biological Sciences | Nanyang Technological
> University SBS-03n-18, 60 Nanyang Drive, Singapore 637551
> Tel: [phone] | Fax: [phone] | Email: [hidden email]
> -------------------------------------------------------------------------

[simon walker (BI)-2]

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My understanding is that the Neo sCMOS sensor has two 11-bit (=2,048 grey level) analogue to digital converters, one with a high gain amplifier, one with a low gain amplifier.  In 16-bit readout mode the signal is a combined readout from the two amplifier/ADCs.  Presumably in rolling shutter mode you're just reading off from one of the amplifier/ADCs, choosing either the high or low gain option.  This is further confused by the chip being split into two halves with the top and bottom being read out independently, so presumably there are actually four amplier/ADCs in total.
Simon

-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Lu Lei
Sent: 26 July 2013 08:57
To: [hidden email]
Subject: Neo scMOS problem

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Hi all,
We recently purchased a wide-field microscope system with a scMOS camera (Neo, 5.5 Megapixel, by Andor). We are having quite some annoying problems with this Neo scMOS camera. Though it is a 16-bit device, it does not have the dynamic range it should have in our system.
1)      In "Rolling" shutter mode, the intensity value that the camera could
generate is truncated at ~20K. In another word, the camera saturates at ~20K instead of 65535.
2)      In "Global" shutter mode, the camera saturates at ~57K-a little short of
65535.
The camera is controled by the latest MetaMorph. The cooling temperature of the camera seems also normal as displayed by MetaMorph (-30&#61616;C). We haven't received any explanation from Andor via local vendor yet. I am wondering what is configured incorrectly here.
Does anyone have similar experience of this camera or suggestion to share?
Thanks a lot.
Regards,
Lei Lu
-------------------------------------------------------------------------
Lu Lei (Asst Prof) | School of Biological Sciences | Nanyang Technological University SBS-03n-18, 60 Nanyang Drive, Singapore 637551
Tel: [phone] | Fax: [phone] | Email: [hidden email]
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[David Baddeley]

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Following on from what others have said, it probably depends on how MetaMorph is reading the camera out (and what it is doing to the data afterwards - e.g. converting to photon counts etc ...). http://www.andor.com/learning-academy/dual-amplifier-dynamic-range-scmos-dynamic-range has some interesting info on how the Neo get's it's large dynamic range. Notable on that website is the following sentence "Due to the splicing together of the low and high gains, the transition region between them is not seamless but has been optimised as far as possible." To me this seems to suggest that if you're going to do deconvolution on the data (or any other form of quantitative data analysis), you might want to choose either the high or the low gain 11 bit mode, and live with the reduced dynamic range. It's quite possible that the MetaMorph engineers have made this choice when writing their camera code (It's certainly the safe default choice as it'll be sure not to
 generate artefacts whereas the combined mode might - knowing for sure would require a lot of testing, which might well be application specific).

best wishes,
David

________________________________
From: Lu Lei <[hidden email]>
To: [hidden email]
Sent: Friday, 26 July 2013 3:56 AM
Subject: Neo scMOS problem


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http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
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Hi all,
We recently purchased a wide-field microscope system with a scMOS camera
(Neo, 5.5 Megapixel, by Andor). We are having quite some annoying problems
with this Neo scMOS camera. Though it is a 16-bit device, it does not have the
dynamic range it should have in our system.
1)    In “Rolling” shutter mode, the intensity value that the camera could
generate is truncated at ~20K. In another word, the camera saturates at ~20K
instead of 65535.
2)    In “Global” shutter mode, the camera saturates at ~57K—a little short of
65535.
The camera is controled by the latest MetaMorph. The cooling temperature of
the camera seems also normal as displayed by MetaMorph (-30C). We haven’t
received any explanation from Andor via local vendor yet. I am wondering what
is configured incorrectly here.
Does anyone have similar experience of this camera or suggestion to share?
Thanks a lot.
Regards,
Lei Lu
-------------------------------------------------------------------------
Lu Lei (Asst Prof) | School of Biological Sciences | Nanyang Technological
University SBS-03n-18, 60 Nanyang Drive, Singapore 637551
Tel: [phone] | Fax: [phone] | Email: [hidden email]
-------------------------------------------------------------------------

[Christian Soeller]

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Seconding previous comments, I spoke with the local reps/engineers and they pointed out the switchover between amplifiers as well. Using Andor's own software (solis) you can select between all 3 modes (high gain, low gain, high dynamic range) and see what the effect is. Perhaps the local Andor people could get you demo access to solis and you could run some tests. That does not solve any metamorph related implementation questions though but might help answering which issues are truly camera related and which ones relate to the 3rd party driver.

Christian  

On Friday, 26 July 2013 at 3:39 PM, David Baddeley wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>  
> Following on from what others have said, it probably depends on how MetaMorph is reading the camera out (and what it is doing to the data afterwards - e.g. converting to photon counts etc ...). http://www.andor.com/learning-academy/dual-amplifier-dynamic-range-scmos-dynamic-range has some interesting info on how the Neo get's it's large dynamic range. Notable on that website is the following sentence "Due to the splicing together of the low and high gains, the transition region between them is not seamless but has been optimised as far as possible." To me this seems to suggest that if you're going to do deconvolution on the data (or any other form of quantitative data analysis), you might want to choose either the high or the low gain 11 bit mode, and live with the reduced dynamic range. It's quite possible that the MetaMorph engineers have made this choice when writing their camera code (It's certainly the safe default choice as it'll be sure not to
> generate artefacts whereas the combined mode might - knowing for sure would require a lot of testing, which might well be application specific).
>  
> best wishes,
> David
>  
> ________________________________
> From: Lu Lei <[hidden email] (mailto:[hidden email])>
> To: [hidden email] (mailto:[hidden email])  
> Sent: Friday, 26 July 2013 3:56 AM
> Subject: Neo scMOS problem
>  
>  
> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>  
> Hi all,
> We recently purchased a wide-field microscope system with a scMOS camera  
> (Neo, 5.5 Megapixel, by Andor). We are having quite some annoying problems  
> with this Neo scMOS camera. Though it is a 16-bit device, it does not have the  
> dynamic range it should have in our system.
> 1)    In “Rolling” shutter mode, the intensity value that the camera could  
> generate is truncated at ~20K. In another word, the camera saturates at ~20K  
> instead of 65535.
> 2)    In “Global” shutter mode, the camera saturates at ~57K—a little short of  
> 65535.
> The camera is controled by the latest MetaMorph. The cooling temperature of  
> the camera seems also normal as displayed by MetaMorph (-30C). We haven’t  
> received any explanation from Andor via local vendor yet. I am wondering what  
> is configured incorrectly here.  
> Does anyone have similar experience of this camera or suggestion to share?
> Thanks a lot.
> Regards,
> Lei Lu
> -------------------------------------------------------------------------
> Lu Lei (Asst Prof) | School of Biological Sciences | Nanyang Technological  
> University SBS-03n-18, 60 Nanyang Drive, Singapore 637551
> Tel: [phone] | Fax: [phone] | Email: [hidden email] (mailto:[hidden email])
> -------------------------------------------------------------------------
>  
>  

[Orla Hanrahan]

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Hi Lei,

Your Neo sCMOS camera has a dynamic range of 30,000:1 (e-s).  The dynamic range of a camera is typically defined as the full-well capacity divided by the camera noise and relates to the ability of a camera to record simultaneously very low light signals alongside bright signals.  From the dynamic range of the Neo, this means that a pixel can hold a maximum signal of 30,000 photoelectrons and will only have 1 electron noise.  

In order to convert these photoelectrons into counts the sensitivity and the read out speed of the camera have to be taken into account. The sensitivity of the Neo is dependent on the amplifier used (i.e. 11-bit or 16-bit) and the readout speed.  The Neo has both a Rolling shutter mode and a Global shutter mode and the sensitivity of the 11-bit and 16-bit amplifiers is different for each mode.  The performance sheet of your Neo will contain the sensitivity values for each amplifier in both Rolling shutter and Global shutter.  

In would be happy to discuss this with you further, so please mail me ([hidden email]).

Best wishes,

Orla Hanrahan, PhD
Application Specialist, Life Science Imaging




-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Lu Lei
Sent: 26 July 2013 08:57
To: [hidden email]
Subject: Neo scMOS problem

*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
*****

Hi all,
We recently purchased a wide-field microscope system with a scMOS camera (Neo, 5.5 Megapixel, by Andor). We are having quite some annoying problems with this Neo scMOS camera. Though it is a 16-bit device, it does not have the dynamic range it should have in our system.
1) In "Rolling" shutter mode, the intensity value that the camera could
generate is truncated at ~20K. In another word, the camera saturates at ~20K instead of 65535.
2) In "Global" shutter mode, the camera saturates at ~57K-a little short of
65535.
The camera is controled by the latest MetaMorph. The cooling temperature of the camera seems also normal as displayed by MetaMorph (-30&#61616;C). We haven't received any explanation from Andor via local vendor yet. I am wondering what is configured incorrectly here.
Does anyone have similar experience of this camera or suggestion to share?
Thanks a lot.
Regards,
Lei Lu
-------------------------------------------------------------------------
Lu Lei (Asst Prof) | School of Biological Sciences | Nanyang Technological University SBS-03n-18, 60 Nanyang Drive, Singapore 637551
Tel: [phone] | Fax: [phone] | Email: [hidden email]
-------------------------------------------------------------------------

[DENNIS Andrew]

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Dear Prof Lu,

I see from our records that Eric Tiw from ZUGO photonics, our Singapore distributor, sent you an explanatory email on this topic on the 17th of July. Maybe there was some issue with the mail getting through to your inbox (maybe spam filter issue).

The explanations from the other confocal LISTSERV contributors explains the operation of the sCMOS camera (there are some modes of operation which differ from traditional CCD styles of operation). I would like to thank those contributors who came forward with support.

I will resend the email of the 17th to you  again, and ensure that Eric follow up with you directly. Also, if you would like to speak directly please call me at [phone].

Kind regards,

Andrew Dennis
Director of Product Management
Andor Technology


On 26 Jul 2013, at 09:10, "Lu Lei" <[hidden email]<mailto:[hidden email]>> wrote:

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Hi all,
We recently purchased a wide-field microscope system with a scMOS camera
(Neo, 5.5 Megapixel, by Andor). We are having quite some annoying problems
with this Neo scMOS camera. Though it is a 16-bit device, it does not have the
dynamic range it should have in our system.
1)    In "Rolling" shutter mode, the intensity value that the camera could
generate is truncated at ~20K. In another word, the camera saturates at ~20K
instead of 65535.
2)    In "Global" shutter mode, the camera saturates at ~57K-a little short of
65535.
The camera is controled by the latest MetaMorph. The cooling temperature of
the camera seems also normal as displayed by MetaMorph (-30&#61616;C). We haven't
received any explanation from Andor via local vendor yet. I am wondering what
is configured incorrectly here.
Does anyone have similar experience of this camera or suggestion to share?
Thanks a lot.
Regards,
Lei Lu
-------------------------------------------------------------------------
Lu Lei (Asst Prof) | School of Biological Sciences | Nanyang Technological
University SBS-03n-18, 60 Nanyang Drive, Singapore 637551
Tel: [phone] | Fax: [phone] | Email: [hidden email]<mailto:[hidden email]>
-------------------------------------------------------------------------

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[Kate Luby-Phelps]

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We are also running a Neo with MetaMorph. Only some of the camera
properties show up in the Multidimensional Acquisition menu.  Others can only
be accessed from the Acquire menu. Perhaps you already know that since the
switch between Global and Rolling shutter is only available in the Acquire menu.
Have you tried running the camera with Andor software or with MicroManager
to see whether it is the camera vs. MetaMorph that is the issue?  

Kate