Background Subtraction On The Fly: Different from Flat-Field Correction

[Micro-Manager mailing list]

Hi,

 

I would like to use something similar to flat-field correction on some polarization contrast imaging. Currently, flat-field correction calculates on-the-fly:

 

Resulting image = (acquired image – background) / (flatfield image – background)

 

I want:

 

Resulting image = acquired image – background

 

Here the background would be the topographic information of my sample, and the resulting image after subtraction would highlight the polarization contrast due to strain/magnetic contrast/etc. Is there a plugin available to do that? Or would there be a way to massage the chosen flatfield image to enable that anyway?

 

I am using a Thorlabs camera, by the way.

 

Thanks,

 

Dan

 

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[Vikram Kopuri]

Hi Dan, 

OpenCv has tools for subtracting background. Check this out https://docs.opencv.org/3.4/db/d5c/tutorial_py_bg_subtraction.html 

On Thu, Feb 7, 2019 at 10:08 AM Gopman, Daniel (Fed) via micro-manager-general <[hidden email]> wrote:

Hi,

 

I would like to use something similar to flat-field correction on some polarization contrast imaging. Currently, flat-field correction calculates on-the-fly:

 

Resulting image = (acquired image – background) / (flatfield image – background)

 

I want:

 

Resulting image = acquired image – background

 

Here the background would be the topographic information of my sample, and the resulting image after subtraction would highlight the polarization contrast due to strain/magnetic contrast/etc. Is there a plugin available to do that? Or would there be a way to massage the chosen flatfield image to enable that anyway?

 

I am using a Thorlabs camera, by the way.

 

Thanks,

 

Dan

 

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[Vikram Kopuri]

On second thought, opencv is an overkill. Looks like image calculator in Fiji will do basic image subtraction. 

"Fiji > Process > Image Calculator "

Have a look at this thread , http://imagej.1557.x6.nabble.com/Subtracting-Images-td5019039.html

On Thu, Feb 7, 2019 at 10:12 AM Vikram G Kopuri <[hidden email]> wrote:

Hi Dan, 

OpenCv has tools for subtracting background. Check this out https://docs.opencv.org/3.4/db/d5c/tutorial_py_bg_subtraction.html 

On Thu, Feb 7, 2019 at 10:08 AM Gopman, Daniel (Fed) via micro-manager-general <[hidden email]> wrote:

Hi,

 

I would like to use something similar to flat-field correction on some polarization contrast imaging. Currently, flat-field correction calculates on-the-fly:

 

Resulting image = (acquired image – background) / (flatfield image – background)

 

I want:

 

Resulting image = acquired image – background

 

Here the background would be the topographic information of my sample, and the resulting image after subtraction would highlight the polarization contrast due to strain/magnetic contrast/etc. Is there a plugin available to do that? Or would there be a way to massage the chosen flatfield image to enable that anyway?

 

I am using a Thorlabs camera, by the way.

 

Thanks,

 

Dan

 

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[Stuurman, Nico]

Hi Dan,

> I would like to use something similar to flat-field correction on some
> polarization contrast imaging. Currently, flat-field correction
> calculates on-the-fly:
>
> Resulting image = (acquired image – background) / (flatfield image –
> background)
>
> I want:
>
> Resulting image = acquired image – background
>

At least in 2.0-gamma, simply leave out the flatfield image, and you
will get on the fly background subtraction.  It can even be carried out
on the GPU (first GPU accelerated code in MM, more to follow). I don't
know/remember behavior in older MM versions, but you can easily test. 
Switching to gamma should be a good thing in any case.


Best,


Nico



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