sCMOS Cameras

[Claire Brown]

*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
Post images on http://www.imgur.com and include the link in your posting.
*****

We are looking to purchase new sCMOS cameras for our SD confocal. We are looking at the Flash4 and the new Photometrics 95B.

I am partial to the Flash4. Using 2x2 binning is gives good sensitivity and resolution and for bright samples the resolution is superior with no binning.
The 95B is more sensitive for low light samples at the cost of resolution but I'm not convinced the improved sensitivity is worth the higher price tag.

The speeds both seem reasonable for our applications.

Anyone have any thoughts? You can respond offline if you prefer.


Sincerely,

Claire

[Eric Marino]

*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
Post images on http://www.imgur.com and include the link in your posting.
*****

Hi Claire,

I’ve had some experience with both cameras, let’s discuss off-line. My email is below.

Eric Marino
[hidden email]

On 3/1/18, 1:21 PM, "Confocal Microscopy List on behalf of Claire Brown, Dr." <[hidden email] on behalf of [hidden email]> wrote:

    *****
    To join, leave or search the confocal microscopy listserv, go to:
    http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
    Post images on http://www.imgur.com and include the link in your posting.
    *****
   
    We are looking to purchase new sCMOS cameras for our SD confocal. We are looking at the Flash4 and the new Photometrics 95B.
   
    I am partial to the Flash4. Using 2x2 binning is gives good sensitivity and resolution and for bright samples the resolution is superior with no binning.
    The 95B is more sensitive for low light samples at the cost of resolution but I'm not convinced the improved sensitivity is worth the higher price tag.
   
    The speeds both seem reasonable for our applications.
   
    Anyone have any thoughts? You can respond offline if you prefer.
   
   
    Sincerely,
   
    Claire
   

*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
Post images on http://www.imgur.com and include the link in your posting.
*****

From our experience with our Laser Free Confocal system, the Orca is a great choice as you can use binning to get more sensitivity.
Phillipa
Aurox

Sent from my iPhone

> On 1 Mar 2018, at 18:49, Eric Marino <[hidden email]> wrote:
>
> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> Post images on http://www.imgur.com and include the link in your posting.
> *****
>
> Hi Claire,
>
> I’ve had some experience with both cameras, let’s discuss off-line. My email is below.
>
> Eric Marino
> [hidden email]
>
> On 3/1/18, 1:21 PM, "Confocal Microscopy List on behalf of Claire Brown, Dr." <[hidden email] on behalf of [hidden email]> wrote:
>
>    *****
>    To join, leave or search the confocal microscopy listserv, go to:
>    http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
>    Post images on http://www.imgur.com and include the link in your posting.
>    *****
>
>    We are looking to purchase new sCMOS cameras for our SD confocal. We are looking at the Flash4 and the new Photometrics 95B.
>
>    I am partial to the Flash4. Using 2x2 binning is gives good sensitivity and resolution and for bright samples the resolution is superior with no binning.
>    The 95B is more sensitive for low light samples at the cost of resolution but I'm not convinced the improved sensitivity is worth the higher price tag.
>
>    The speeds both seem reasonable for our applications.
>
>    Anyone have any thoughts? You can respond offline if you prefer.
>
>
>    Sincerely,
>
>    Claire
>

[lechristophe]

*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
Post images on http://www.imgur.com and include the link in your posting.
*****

Hi,

There is a newer Prime BSI that has the same 95% efficiency as the Prime
95B with 4 million 6.5 um pixels, so similar to the Flash4 in this regard:
https://www.photometrics.com/products/scmos/primeBSI

Maybe a way to get the best of both? I have no direct experience with it
though.

Christophe

Le 1 mars 2018 19:21, "Claire Brown, Dr." <[hidden email]> a écrit :

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> Post images on http://www.imgur.com and include the link in your posting.
> *****
>
> We are looking to purchase new sCMOS cameras for our SD confocal. We are
> looking at the Flash4 and the new Photometrics 95B.
>
> I am partial to the Flash4. Using 2x2 binning is gives good sensitivity
> and resolution and for bright samples the resolution is superior with no
> binning.
> The 95B is more sensitive for low light samples at the cost of resolution
> but I'm not convinced the improved sensitivity is worth the higher price
> tag.
>
> The speeds both seem reasonable for our applications.
>
> Anyone have any thoughts? You can respond offline if you prefer.
>
>
> Sincerely,
>
> Claire
>

[Tim Feinstein]

*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
Post images on http://www.imgur.com and include the link in your posting.
*****

We use both with CameraLink PCI cards, though we use them for different purposes so it's hard to directly compare.  The speed of a Flash4 is fantastic for our light sheet...however!  We have not been able to get close to its max speed using Micro-Manager!  So far I have not found a solution in the usual discussion forums.  For very high speed recordings we have to use the proprietary software that comes with the camera, which can make some experiments awkward.  Software from the major scope makers might have drivers that make better use of the Hamamatsu's speed; I don't know.  

The 95b's back-thinned chip is great if sensitivity matters.  We noticed quite a difference in brightness between the two; for applications like TIRF that's a big deal for us.  I would rather use the 95b at 1x binning than the Flash at 2x.  

I don't know whether this matters, but the 95b generates a little heat during use (but no vibration) while the Flash4 does not.  

Considering they have released a model with comparable resolution to the Flash4, it mostly comes down to whether speed or sensitivity matters more for your needs.  

Best,


T

Timothy Feinstein, Ph.D.
Research Scientist
Department of Developmental Biology
University of Pittsburgh

 



On 3/1/18, 1:21 PM, "Confocal Microscopy List on behalf of Claire Brown, Dr." <[hidden email] on behalf of [hidden email]> wrote:

    *****
    To join, leave or search the confocal microscopy listserv, go to:
    https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Flists.umn.edu%2Fcgi-bin%2Fwa%3FA0%3Dconfocalmicroscopy&data=01%7C01%7Ctnf8%40PITT.EDU%7C6a6a64d57f594f94654b08d57fa14d0e%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=sfPBvKj7%2BWBUUjqKtKl26ss%2BO78FBaoRfeoRvkTwedE%3D&reserved=0
    Post images on https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.imgur.com&data=01%7C01%7Ctnf8%40PITT.EDU%7C6a6a64d57f594f94654b08d57fa14d0e%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=KsvFFrXYdUJtuDw5UbG8On7SFcPxFiB8A0IBkDG6apo%3D&reserved=0 and include the link in your posting.
    *****
   
    We are looking to purchase new sCMOS cameras for our SD confocal. We are looking at the Flash4 and the new Photometrics 95B.
   
    I am partial to the Flash4. Using 2x2 binning is gives good sensitivity and resolution and for bright samples the resolution is superior with no binning.
    The 95B is more sensitive for low light samples at the cost of resolution but I'm not convinced the improved sensitivity is worth the higher price tag.
   
    The speeds both seem reasonable for our applications.
   
    Anyone have any thoughts? You can respond offline if you prefer.
   
   
    Sincerely,
   
    Claire
   

[Talley Lambert]

*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
Post images on http://www.imgur.com and include the link in your posting.
*****

There seems to be a misunderstanding about binning on an sCMOS:
binning on an sCMOS will NOT gain you the same SNR bump that you are used to on a CCD.  Because the charge-to-voltage conversion in an sCMOS happens at the pixel, binning is not performed on chip but rather after analog to digital conversion.  This means that the gain in SNR that you might see by binning on an sCMOS is no different from what you would get if you simply downsampled (with averaging) the full resolution image in ImageJ or something post-acquisition.  I believe the option to bin on software driving on sCMOS cameras is mostly there because in some rare cases where the connection between the camera and the computer is bandwidth limited, you might be able to increase speed by binning to decrease the data flow.  (either that or it's there because people are "used to it" and don't understand the difference between CCD).  searching around online, there's a lot of misinformation about this, but there is a brief explanation of this point about SNR and binning here: http://camera.hamamatsu.com/jp/en/technical_guides/relative_snr/index.html

So don't make your decision based on the presence or absence of the binning feature.  If sensitivity is your primary need, you will not be able to compensate for a smaller pixel size or low QE simply by binning (and of course, you'll never be able to recover the sampling rate offered by a small pixel on a camera with a larger pixel without some additional magnification in the light path).  In that regard, you must chose "up front" what your pixel size needs are.  But it's also not safe to assume that the noise characteristics and fixed pattern idiosyncrasies of each camera model are equivalent.  As always, the best advice remains to demo anything that you're considering prior to purchase, to evaluate it for your specific system and samples.

[RJ3]

*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
Post images on http://www.imgur.com and include the link in your posting.
*****

Talley Lambert is correct, binning on an sCMOS has very limited usage. Mainly:
1) Increasing frame rate if you are limited by the link between the camera and the computer (eg. USB).
2) If you have limited post-acquisition capabilities, and you know you'll bin the images anyway.

It is not like binning on an EMCCD, in that, you will not gain readout speed or improve the SNR. The improvement in SNR you are seeing is from image blurring which can be performed at any time.

We were in the same situation a couple years ago choosing between the Zyla 4.2 PLUS/ Orca Flash and the Prime 95B. Ultimately we went with the Zyla but have since moved it to another system and bought a Prime 95B for the spinning disk. Here's my two cents:

1) The chips are almost physically identical in size, but the prime's resolution is only 1200 instead of 2048, so it's pixels are a lot bigger. Is this important for your application?
2) The sensitivity of the Prime 95B is noticeably better which led us to get it for the spinning disk.
3) The Prime 95B has some quirks. It doesn't have an acquisition card but a PCIe expander, so it's cheaper, but you need to have the camera turned on before the computer.
4) Lastly, the Zyla is significantly faster and why I love it for our other application. While the Prime claims 82 full frame, you have to keep in mind that's only at 12-bit, 4096 points of digitization is not very good. At the full 16-bit it runs at half speed, whereas with a dual link cam card with the Zyla you can get the full frame rate at full bit depth.

I can also comment on EMCCDs, if you're interested in making your decision even more complicated.

[Claire Brown]

*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
Post images on http://www.imgur.com and include the link in your posting.
*****

Thank you to everyone for you online and offline comments.

We did demo the cameras but I wanted input from the community because I was still having issues deciding.
For the pixel binning issue I appreciate all of the clarification. It is good to remember the differences with sCMOS and CCDs.
My main point with the binning was sensitivity versus resolution. So binning offline is fine.

This is a core facility microscope so as I'm sure many of you are aware it is difficult to pick components for one application since some users need speed, others need sensitivity and others resolution. For my own work the Flash 4 is fine. For others they may need the improved sensitivity.

We are actually upgrading two microscopes. A SD/TIRF and a SD so I think we will put two Flash 4 on one and two Prime on the other. This will give us the option to move people between systems depending on their needs.

Thanks again for all the information.

Claire

[Gerhard Holst]

*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
Post images on http://www.imgur.com and include the link in your posting.
*****

Dear Claire,

Like Talley Lambert I would like to emphasize that "Binning" in CMOS or sCMOS image sensors never has the some impact like in CCD image sensors. In CCDs it means summing up charges before readout, that means increasing signal before charge to voltage conversion which helps with the signal-to-noise-ratio. In CMOS and sCMOS "Binning" is always averaging either done in the camera (less data to transfer) or in the computer, and it comes with the usual improvement of signal-to-noise-ratio by averaging. Maybe in the future there will be some options to do a charge domain summing in CMOS image sensors as well, but it is not yet available.

Concerning the comparison between "front side illuminated (FSI)" and "back side illuminated (BSI)" there are some major differences:
FSI: lower dark current, lower quantum efficiency, better MTF, lower NIR sensitivity
BSI: higher dark current, higher quantum efficiency, lower MTF, better NIR sensitivity

Dark current - matters mostly in case of long exposure times
Quantum efficiency - if your signal is always near to the detection limit, QE helps
MTF - this is more complex, because it belongs to the whole setting of objective (magnification & aperture), used wavelength, magnification of camera adapter and pixel size
Pixel size - see above (there is a nice free app for the Android smartphones called "Resolution" which can give a nice start to figure out what a good pixel size is

Further, there are some new sCMOS image sensors around which show a nice noise behavior ("nice" for me means less high noise pixels, since the distribution of noise in sCMOS is anyhow not Gaussian).
Some of them even allow to use even non-cooled sCMOS cameras:
GSENSE400BSI => cameras: Prime 95B, Kuro (I assume) & Dhyana 95 (11µm pitch, BSI, QE = 95%)
GSENSE2020e => cameras: pco.panda 4.2, Prime, Dhyana 400D (6.5µm pitch, FSI, QE = 75%)
GSENSE2020BSI => cameras: pco.panda 4.2 bi, Prime BSI, Dhyana 400 BSI (6.5µm pitch, BSI, QE = 95%)

In comparison to the other established cameras with the sCMOS image sensors:
CIS2521 => cameras: pco.edge 5.5 (various), Zyla 5.5 and Neo 5.5 (6.5µm pitch, FSI, QE > 60%)
CIS2020A => cameras : pco.edge 4.2 (various), Zyla 4.2 and Orca Flash 4.0 (6.5µm pitch, FSI, QE > 80%)

with best regards,

Gerhard


Dr. Gerhard Holst
Head of Science & Research
[phone]
[phone]

PCO AG, Donaupark 11, 93309 Kelheim, Germany, www.pco.de
USt. ID-Nr. / VAT: DE128590843, Registergericht / Register court: Regensburg HRB 9157
Sitz der Gesellschaft / Registered office: Kelheim, Vorstand / Chairman: Dr. Emil Ott
Vorsitzender des Aufsichtsrats / Chairman of the supervisory board: Johann Plöb

-----Ursprüngliche Nachricht-----
Von: Confocal Microscopy List [mailto:[hidden email]] Im Auftrag von Claire Brown, Dr.
Gesendet: Donnerstag, 1. März 2018 19:21
An: [hidden email]
Betreff: sCMOS Cameras

*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
Post images on http://www.imgur.com and include the link in your posting.
*****

We are looking to purchase new sCMOS cameras for our SD confocal. We are looking at the Flash4 and the new Photometrics 95B.

I am partial to the Flash4. Using 2x2 binning is gives good sensitivity and resolution and for bright samples the resolution is superior with no binning.
The 95B is more sensitive for low light samples at the cost of resolution but I'm not convinced the improved sensitivity is worth the higher price tag.

The speeds both seem reasonable for our applications.

Anyone have any thoughts? You can respond offline if you prefer.


Sincerely,

Claire

[Sylvie Le Guyader]

*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
Post images on http://www.imgur.com and include the link in your posting.
*****

Dear list

I think that binning an sCMOS has great advantages that are often overlooked but that we use a lot at our facility:

One advantage is that when one has a very large sample and needs to find the regions to be imaged, acquiring and especially reconstructing a tiled image of the whole sample is much faster with bin 2, 4 or even 8 (depending on what one does with the images afterwards).

But the greatest advantage is that automated image analysis is also much faster. This allows us to routinely use high throughput / slide scanner type of imaging pipelines even if we do not have tons of sample. We use the Jobs module in the Nikon NIS software.

For example let's say we have 3 glass slide and 10 brain sections on each slide. On each sections there are a few ROIs that are fluorescent and need to be imaged. There is no need to sit by the microscope and look with fluorescence in the eyepiece to find (bleach) each ROI.

Instead, using high binning and a low magnification, we quickly scan the 3 slides at once, then analysis is run automatically, the ROI positions are recorded in a list, then the system changes to a higher magnification /NA objective, refocuses, revisits all the positions and reimages with different settings (no binning, maybe z stack and a small tile)...

All this without the user having to sit there which means that this can be done during the night to increase microscope usage.

I do not think that this would work if we were not binning the first tiled image. It would be much slower or would require a much more powerful computer.

This of course also applies for MW plates but it can be used for all samples.

Med vänlig hälsning / Best regards

Sylvie

@@@@@@@@@@@@@@@@@@@@@@@@

Sylvie Le Guyader, PhD
Live Cell Imaging Facility Manager

Karolinska Institutet- Bionut Dpt
Hälsovägen 7C
Room 7362/7840
14157 Huddinge
Sweden

mobile: [phone]
office: [phone]
LCI website

---- Gerhard Holst wrote ----

*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
Post images on http://www.imgur.com and include the link in your posting.
*****

Dear Claire,

Like Talley Lambert I would like to emphasize that "Binning" in CMOS or sCMOS image sensors never has the some impact like in CCD image sensors. In CCDs it means summing up charges before readout, that means increasing signal before charge to voltage conversion which helps with the signal-to-noise-ratio. In CMOS and sCMOS "Binning" is always averaging either done in the camera (less data to transfer) or in the computer, and it comes with the usual improvement of signal-to-noise-ratio by averaging. Maybe in the future there will be some options to do a charge domain summing in CMOS image sensors as well, but it is not yet available.

Concerning the comparison between "front side illuminated (FSI)" and "back side illuminated (BSI)" there are some major differences:
FSI: lower dark current, lower quantum efficiency, better MTF, lower NIR sensitivity
BSI: higher dark current, higher quantum efficiency, lower MTF, better NIR sensitivity

Dark current - matters mostly in case of long exposure times
Quantum efficiency - if your signal is always near to the detection limit, QE helps
MTF - this is more complex, because it belongs to the whole setting of objective (magnification & aperture), used wavelength, magnification of camera adapter and pixel size
Pixel size - see above (there is a nice free app for the Android smartphones called "Resolution" which can give a nice start to figure out what a good pixel size is

Further, there are some new sCMOS image sensors around which show a nice noise behavior ("nice" for me means less high noise pixels, since the distribution of noise in sCMOS is anyhow not Gaussian).
Some of them even allow to use even non-cooled sCMOS cameras:
GSENSE400BSI => cameras: Prime 95B, Kuro (I assume) & Dhyana 95 (11µm pitch, BSI, QE = 95%)
GSENSE2020e => cameras: pco.panda 4.2, Prime, Dhyana 400D (6.5µm pitch, FSI, QE = 75%)
GSENSE2020BSI => cameras: pco.panda 4.2 bi, Prime BSI, Dhyana 400 BSI (6.5µm pitch, BSI, QE = 95%)

In comparison to the other established cameras with the sCMOS image sensors:
CIS2521 => cameras: pco.edge 5.5 (various), Zyla 5.5 and Neo 5.5 (6.5µm pitch, FSI, QE > 60%)
CIS2020A => cameras : pco.edge 4.2 (various), Zyla 4.2 and Orca Flash 4.0 (6.5µm pitch, FSI, QE > 80%)

with best regards,

Gerhard


Dr. Gerhard Holst
Head of Science & Research
[phone]
[phone]

PCO AG, Donaupark 11, 93309 Kelheim, Germany, www.pco.de
USt. ID-Nr. / VAT: DE128590843, Registergericht / Register court: Regensburg HRB 9157
Sitz der Gesellschaft / Registered office: Kelheim, Vorstand / Chairman: Dr. Emil Ott
Vorsitzender des Aufsichtsrats / Chairman of the supervisory board: Johann Plöb

-----Ursprüngliche Nachricht-----
Von: Confocal Microscopy List [mailto:[hidden email]] Im Auftrag von Claire Brown, Dr.
Gesendet: Donnerstag, 1. März 2018 19:21
An: [hidden email]
Betreff: sCMOS Cameras

*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
Post images on http://www.imgur.com and include the link in your posting.
*****

We are looking to purchase new sCMOS cameras for our SD confocal. We are looking at the Flash4 and the new Photometrics 95B.

I am partial to the Flash4. Using 2x2 binning is gives good sensitivity and resolution and for bright samples the resolution is superior with no binning.
The 95B is more sensitive for low light samples at the cost of resolution but I'm not convinced the improved sensitivity is worth the higher price tag.

The speeds both seem reasonable for our applications.

Anyone have any thoughts? You can respond offline if you prefer.


Sincerely,

Claire