Marking areas of like pixel values.

[D Williams]

I am taking pictures with a 12 bit camera in .FIT file format. When I open
them in Fiji it says

they are 32 bit and therefore it won't perform auto thresholding on them
because it says

this only works for 8 or 16 bit  images.

Why and how does it change my 12 bit image into something that it is not?

 

Dean


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[Cammer, Michael]

Don't know the answer, but perhaps would be easiest to set the grayscale from 0-4095 or 0-65535 and then convert type to 16 bit.

Michael Cammer, Research Scientist, DART Microscopy Laboratory
NYU Langone Health, 540 First Avenue, SK2 Microscopy Suite, New York, NY  10016
C: 914-309-3270  [hidden email]    http://microscopynotes.com/ 
https://med.nyu.edu/research/research-resources/scientific-cores-shared-resources/microscopy-laboratory



-----Original Message-----
From: D Williams [mailto:[hidden email]]
Sent: Monday, November 06, 2017 11:34 AM
To: [hidden email]
Subject: Marking areas of like pixel values.

I am taking pictures with a 12 bit camera in .FIT file format. When I open them in Fiji it says

they are 32 bit and therefore it won't perform auto thresholding on them because it says

this only works for 8 or 16 bit  images.

Why and how does it change my 12 bit image into something that it is not?

 

Dean


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[Gabriel Landini]

On Monday, 6 November 2017 16:33:39 GMT [hidden email] wrote:
> I am taking pictures with a 12 bit camera in .FIT file format. When I open
> them in Fiji it says they are 32 bit and therefore it won't perform auto
> thresholding on them because it says this only works for 8 or 16 bit
> images. Why and how does it change my 12 bit image into something that
> it is not?

I think you might be trying the Auto Threshold or Auto Local Threshold
commands. Those do not work on 32 bit images.
You could try the original Adjust Threshold command, that would rebin the
image into a smaller greyscale space and threshold it.

As to your other question, I have no idea. There are no 12 bit images in IJ,
so perhaps the importer, as a safety measure, might be opening them as 32bit.
Cheers

Gabriel

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[Kenneth Sloan-2]

Look at the .fit file header (it’s plain text).  What’s the value for “BITPIX”?

Your camera may take 12-bit images, but that doesn’t necessarily mean the file has 16-bits per pixel.

If the file DOES specify 16 bits per pixel, then something is wrong with the ImageJ reader (and it should be fixed).
But - as previously noted, that should be easy to fix by changing the image Type immediately after loading it.

Question: do you know the actual range of pixel values produced by the camera?  Do you know if the low-order bits are
significant?
—
Kenneth Sloan
[hidden email] <mailto:[hidden email]>
Vision is the art of seeing what is invisible to others.

> On Nov 6, 2017, at 10:33, D Williams <[hidden email]> wrote:
>
> I am taking pictures with a 12 bit camera in .FIT file format. When I open
> them in Fiji it says
>
> they are 32 bit and therefore it won't perform auto thresholding on them
> because it says
>
> this only works for 8 or 16 bit  images.
>
> Why and how does it change my 12 bit image into something that it is not?
>
>
>
> Dean
>
>
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> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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[Kenneth Sloan-2]

The .fit format allows 16-bit images.  One might assume that a camera producing 12-bit images
would store them as 16-bit images, but…stranger things have happened.

—
Kenneth Sloan
[hidden email] <mailto:[hidden email]>
Vision is the art of seeing what is invisible to others.

> On Nov 6, 2017, at 10:57, Gabriel Landini <[hidden email]> wrote:
>
> On Monday, 6 November 2017 16:33:39 GMT [hidden email] wrote:
>> I am taking pictures with a 12 bit camera in .FIT file format. When I open
>> them in Fiji it says they are 32 bit and therefore it won't perform auto
>> thresholding on them because it says this only works for 8 or 16 bit
>> images. Why and how does it change my 12 bit image into something that
>> it is not?
>
> I think you might be trying the Auto Threshold or Auto Local Threshold
> commands. Those do not work on 32 bit images.
> You could try the original Adjust Threshold command, that would rebin the
> image into a smaller greyscale space and threshold it.
>
> As to your other question, I have no idea. There are no 12 bit images in IJ,
> so perhaps the importer, as a safety measure, might be opening them as 32bit.
> Cheers
>
> Gabriel
>
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> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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