Re: not (yet) supported cameras in micro-manager - general

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Re: not (yet) supported cameras in micro-manager - general

Hazen Babcock-2
>
> There are now a couple of papers describing single molecule imaging with
> non-scientific CMOS cameras
> (https://www.biorxiv.org/content/early/2017/09/09/186544,
> https://www.nature.com/articles/s41598-017-14762-6).
>
There is also this paper describing how to correct the images from an
sCMOS camera:
https://dx.doi.org/doi:10.1038/nmeth.4379

Also, FWIW, in my experience the FLIR GS3-U3-51S5M-C actually has fewer
pixels with extreme variances compared to the Hamamatsu ORCA-Flash4.0
v2. Though the average variance is higher, 2.5e- vs 1.0e- at 50Hz. I can
provide a histogram to anyone who is interested.

best,
-Hazen

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Re: not (yet) supported cameras in micro-manager - general

Stuurman, Nico


On 12/13/17 9:02 AM, Hazen Babcock wrote:
>>
>> There are now a couple of papers describing single molecule imaging with
>> non-scientific CMOS cameras
>> (https://www.biorxiv.org/content/early/2017/09/09/186544,
>> https://www.nature.com/articles/s41598-017-14762-6).
>>
> There is also this paper describing how to correct the images from an
> sCMOS camera:
> https://dx.doi.org/doi:10.1038/nmeth.4379

Cool!  It would be nice to implement this as an "on-the-fly processor"
in Micro-manager.  Quite a bit of work since the original code is
Matlab.  If I only had more time...

> Also, FWIW, in my experience the FLIR GS3-U3-51S5M-C actually has
> fewer pixels with extreme variances compared to the Hamamatsu
> ORCA-Flash4.0 v2. Though the average variance is higher, 2.5e- vs
> 1.0e- at 50Hz. I can provide a histogram to anyone who is interested.

Would be fun to see.  If you do not have an online site yourself, you
are welcome to add it to the Micro-Manager Point Grey page:
https://micro-manager.org/wiki/Point_Grey_Research.


Best,

Nico


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Re: not (yet) supported cameras in micro-manager - general

Hazen Babcock-2
On 12/13/2017 01:40 PM, Nico Stuurman wrote:
>
>> Also, FWIW, in my experience the FLIR GS3-U3-51S5M-C actually has
>> fewer pixels with extreme variances compared to the Hamamatsu
>> ORCA-Flash4.0 v2. Though the average variance is higher, 2.5e- vs
>> 1.0e- at 50Hz. I can provide a histogram to anyone who is interested.
>
> Would be fun to see.  If you do not have an online site yourself, you
> are welcome to add it to the Micro-Manager Point Grey page:
> https://micro-manager.org/wiki/Point_Grey_Research.

Sure, but apparently I need a 50 word biography to create an account for
the wiki? Or am I doing something wrong? I can't find any other user
biographies to use as templates.

-Hazen

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Re: not (yet) supported cameras in micro-manager - general

Stuurman, Nico


On 12/13/17 12:21 PM, Hazen Babcock wrote:

> On 12/13/2017 01:40 PM, Nico Stuurman wrote:
>>
>>> Also, FWIW, in my experience the FLIR GS3-U3-51S5M-C actually has
>>> fewer pixels with extreme variances compared to the Hamamatsu
>>> ORCA-Flash4.0 v2. Though the average variance is higher, 2.5e- vs
>>> 1.0e- at 50Hz. I can provide a histogram to anyone who is interested.
>>
>> Would be fun to see.  If you do not have an online site yourself, you
>> are welcome to add it to the Micro-Manager Point Grey page:
>> https://micro-manager.org/wiki/Point_Grey_Research.
>
> Sure, but apparently I need a 50 word biography to create an account
> for the wiki? Or am I doing something wrong? I can't find any other
> user biographies to use as templates.

Sorry for that hurdle.  We have had spam bots creating thousands of
pages pointing to pharmacy websites in the Ukraine, and needed a system
to prevent those from signing up (I ended up paying my kids to help
clicking the delete key, since for whatever reason it was hard to do
mass removal).  So, anything that makes clear that you are you is fine
there (I don't think that the text is visible anywhere else).

Best,

Nico



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Re: not (yet) supported cameras in micro-manager - general

GeoffP
Hi Nico. 

I tried to post the following but probably got it wrong:

Could someone please help with the following:

PROBLEM 1
I have been using ImageJ’s (Ver 1.51i and r) very useful Plot Profile on a linear series of objects in still images to measure 8-bit gray levels for some time. I recently bought a new camera (AmScope MU503B) so I could do the same analysis on live images using Micromanager (Ver 2.0.0-beta 3 20171122) with its embedded ImageJ (Ver <a href="x-apple-data-detectors://1" dir="ltr" x-apple-data-detectors="true" x-apple-data-detectors-type="calendar-event" x-apple-data-detectors-result="1" style="-webkit-text-decoration-color: rgba(0, 0, 0, 0.258824);">1.49h).
When using MicroManager and ImageJ’s Plot Profile in ‘live’ mode, I have been using the ImageJ cursor to find the base and the peak grey levels (usually 150 and 130 respectively) of the linear objects. However, when I change the focus or change the selected area, the ‘y’ range changes and causes an immediate loss of 1:1 correlation between the cursor values and the corresponding ‘y’ values. For example, the ‘y’ value may be 150, but the cursor is saying it is say 130. The same with the height of any drawn rectangle on the Profile - e.g. the real height (difference in ‘y’ values) may be 10 gray levels, but the cursor is saying it is 3 gray levels depending upon the windows history since making it ‘live’. I have to quit and restart Plot Profile to correct this problem which is then useless if I make any focus or selected area change.
I have tested stand-alone versions of ImageJ (Ver 1.49v, 1.50i, 1.50r) and ImageJ2 (Ver 2.0.0-rc-43/1/1.51r) on still images and any change of the selected area making a major change in the ‘y’ value of the Plot does NOT create the problems listed above - the ‘y’ values and differences are accurately reflected in the cursor values.
Can anyone please assist me in fixing this problem?

PROBLEM 2
When I try to update ImageJ within MicroManager, using the Help/Update menu, the message comes up ‘Release Notes are not in the expected format’. I have located the ImageJ file in the MicroManager Directory but cannot see how to update it directly. Is anyone please able to sort this out and perhaps give me instructions on how to do it?

PROBLEM 3
I am trying to use a Tucsen ISH500 camera with Micromanager but can see any device configurations to do this, even in the Ver 2.0.0-beta 3 20171122.  Does anyone know how to do this please?
Many thanks


Geoff Pickford


Pickford Resources Pty Ltd
<a href="x-apple-data-detectors://3/1" dir="ltr" x-apple-data-detectors="true" x-apple-data-detectors-type="address" x-apple-data-detectors-result="3/1" style="-webkit-text-decoration-color: rgba(0, 0, 0, 0.258824);">PO Box 618, Wollongong, NSW, 2500
Laboratory Fax:  <a href="tel:02%204227%206673" dir="ltr" x-apple-data-detectors="true" x-apple-data-detectors-type="telephone" x-apple-data-detectors-result="3/2" style="-webkit-text-decoration-color: rgba(0, 0, 0, 0.258824);">02 4227 6673.  Mobile:  <a href="tel:0417%20417%20507" dir="ltr" x-apple-data-detectors="true" x-apple-data-detectors-type="telephone" x-apple-data-detectors-result="3/3" style="-webkit-text-decoration-color: rgba(0, 0, 0, 0.258824);">0417 417 507

On 14 Dec 2017, at 8:13 am, Nico Stuurman <[hidden email]> wrote:



On 12/13/17 12:21 PM, Hazen Babcock wrote:
On 12/13/2017 01:40 PM, Nico Stuurman wrote:

Also, FWIW, in my experience the FLIR GS3-U3-51S5M-C actually has fewer pixels with extreme variances compared to the Hamamatsu ORCA-Flash4.0 v2. Though the average variance is higher, 2.5e- vs 1.0e- at 50Hz. I can provide a histogram to anyone who is interested.

Would be fun to see.  If you do not have an online site yourself, you are welcome to add it to the Micro-Manager Point Grey page: https://micro-manager.org/wiki/Point_Grey_Research.

Sure, but apparently I need a 50 word biography to create an account for the wiki? Or am I doing something wrong? I can't find any other user biographies to use as templates.

Sorry for that hurdle.  We have had spam bots creating thousands of pages pointing to pharmacy websites in the Ukraine, and needed a system to prevent those from signing up (I ended up paying my kids to help clicking the delete key, since for whatever reason it was hard to do mass removal).  So, anything that makes clear that you are you is fine there (I don't think that the text is visible anywhere else).

Best,

Nico



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Re: not (yet) supported cameras in micro-manager - general

Hazen Babcock-2
In reply to this post by Stuurman, Nico
On 12/13/2017 01:40 PM, Nico Stuurman wrote:
>
>> Also, FWIW, in my experience the FLIR GS3-U3-51S5M-C actually has
>> fewer pixels with extreme variances compared to the Hamamatsu
>> ORCA-Flash4.0 v2. Though the average variance is higher, 2.5e- vs
>> 1.0e- at 50Hz. I can provide a histogram to anyone who is interested.
>
> Would be fun to see.  If you do not have an online site yourself, you
> are welcome to add it to the Micro-Manager Point Grey page:
> https://micro-manager.org/wiki/Point_Grey_Research.

I've added the plots to this page.

best,
-Hazen

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Re: not (yet) supported cameras in micro-manager - general

Micro-Manager mailing list
In reply to this post by Stuurman, Nico
On 12/13/17 1:40 PM, Nico Stuurman wrote:
> On 12/13/17 9:02 AM, Hazen Babcock wrote:
>>>
>> There is also this paper describing how to correct the images from an
>> sCMOS camera:
>> https://dx.doi.org/doi:10.1038/nmeth.4379
>
> Cool!  It would be nice to implement this as an "on-the-fly processor"
> in Micro-manager.  Quite a bit of work since the original code is
> Matlab.  If I only had more time...

There is now a C version of this which might be of interest:
https://github.com/HuanglabPurdue/NCS/pull/1

It is pretty fast, but I'm not sure it is quite fast enough for
"on-the-fly". On my laptop it can process 128x128 images at about 10Hz.

best,
-Hazen


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Re: not (yet) supported cameras in micro-manager - general

Micro-Manager mailing list
I have a 

CARL ZEISS AXIOSKOP 20 FLUORESCENCE MICROSCOPE

Dos the software work with this model?

Thanks in advance.

Stephen
--
203-675-9010
PO Box 230
Guilford, CT 06437





On May 6, 2019, at 1:26 PM, Hazen Babcock via micro-manager-general <[hidden email]> wrote:

On 12/13/17 1:40 PM, Nico Stuurman wrote:
On 12/13/17 9:02 AM, Hazen Babcock wrote:

There is also this paper describing how to correct the images from an
sCMOS camera:
https://dx.doi.org/doi:10.1038/nmeth.4379

Cool!  It would be nice to implement this as an "on-the-fly processor"
in Micro-manager.  Quite a bit of work since the original code is
Matlab.  If I only had more time...

There is now a C version of this which might be of interest:
https://github.com/HuanglabPurdue/NCS/pull/1

It is pretty fast, but I'm not sure it is quite fast enough for
"on-the-fly". On my laptop it can process 128x128 images at about 10Hz.

best,
-Hazen


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[hidden email]
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Re: not (yet) supported cameras in micro-manager - general

Micro-Manager mailing list
On 5/6/19 3:23 PM, Stephen J. Arpie wrote:
> I have a 
>
> CARL ZEISS AXIOSKOP 20 FLUORESCENCE MICROSCOPE
>
> Dos the software work with this model?

The software will work to correct for the noise in any CMOS camera
image, so if you have such a camera then yes.

However in it's current state this will take some work. First you will
need to acquire calibration data for your camera following for example
the procedure in the supplement of this paper:

https://www.nature.com/articles/nmeth.2488

Then you'd need to feed the calibration data, your image and an estimate
of your microscopes OTF to the software.

-Hazen

>> On May 6, 2019, at 1:26 PM, Hazen Babcock via micro-manager-general
>> <[hidden email]
>> <mailto:[hidden email]>> wrote:
>>
>> On 12/13/17 1:40 PM, Nico Stuurman wrote:
>>> On 12/13/17 9:02 AM, Hazen Babcock wrote:
>>>>>
>>>> There is also this paper describing how to correct the images from an
>>>> sCMOS camera:
>>>> https://dx.doi.org/doi:10.1038/nmeth.4379
>>>
>>> Cool!  It would be nice to implement this as an "on-the-fly processor"
>>> in Micro-manager.  Quite a bit of work since the original code is
>>> Matlab.  If I only had more time...
>>
>> There is now a C version of this which might be of interest:
>> https://github.com/HuanglabPurdue/NCS/pull/1
>>
>> It is pretty fast, but I'm not sure it is quite fast enough for
>> "on-the-fly". On my laptop it can process 128x128 images at about 10Hz.
>>
>> best,
>> -Hazen
>>
>>
>> _______________________________________________
>> micro-manager-general mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/micro-manager-general
>



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