Import Image Sequence Contrast Bug (DM3)

[jumpfunky]

Hi,

I currently working with TEM image data. I imported a series of dm3
images via the Import -> Image Sequence command.

If I open a single image of that image series with Open -> Image it
seems to have another contrast:
https://dl.dropboxusercontent.com/u/560426/contrast_bug_16bit.png

But the pixel values are the same in left (sequence) and the right
(single) image, so there is not a problem. However, the images are 16bit
images and I have to convert them to 8 bit. I do that with  "Image ->
Type -> 8bit". But now the pixel values are DIFFERENT:
https://dl.dropboxusercontent.com/u/560426/contrast_bug_8bit.png

The marked pixel has in the left image a value of 22 and in the right
image a value 8. It think this must be a bug because this is not the
expected behaviour, isn't it?

Cheers,
Thorsten

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[Michael Schmid]

Hi Thorsten,

if you convert from 16 to 8 bits you can select in Edit>Options>Conversions:

"Scaled when converting"=off means that the 16-bit value will be transferred 1:1 to the 8-bit value, and everything above 255 will become 255 in the 8-bit image. Typically, this will lead to a lot of saturated pixels, so one would divide the 16-bit image by some number before conversion to 8 bits in that case, to get a reasonable 8-bit display.

"Scaled when converting"=on means that the current display range (as set in the Image>Adjust>Brightness&Contrast panel) determines the span from 0 to 255 of the 8-bit image.

If you have "Scaled when converting"=on and different B&C settings when converting, you get different results.

See the manual:

http://rsb.info.nih.gov/ij/docs/guide/146-28.html#toc-Subsection-28.1
http://rsb.info.nih.gov/ij/docs/guide/146-27.html#toc-Subsubsection-27.13.11


Michael
________________________________________________________________
On Sep 29, 2014, at 18:42, Thorsten Wagner wrote:

> Hi,
>
> I currently working with TEM image data. I imported a series of dm3
> images via the Import -> Image Sequence command.
>
> If I open a single image of that image series with Open -> Image it
> seems to have another contrast:
> https://dl.dropboxusercontent.com/u/560426/contrast_bug_16bit.png
>
> But the pixel values are the same in left (sequence) and the right
> (single) image, so there is not a problem. However, the images are 16bit
> images and I have to convert them to 8 bit. I do that with  "Image ->
> Type -> 8bit". But now the pixel values are DIFFERENT:
> https://dl.dropboxusercontent.com/u/560426/contrast_bug_8bit.png
>
> The marked pixel has in the left image a value of 22 and in the right
> image a value 8. It think this must be a bug because this is not the
> expected behaviour, isn't it?
>
> Cheers,
> Thorsten

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[jumpfunky]

Hi Michael,

I see! Thank you for your explanation.

Obviously ImageJ changes the brightness/contrast settings when opening
an 16bit image. Unfortunately it does not support different
brightness/contrast settings in stack (except by pressing "apply") and
therefor have to use the same settings for the whole stack (maybe based
on the global histogram?).

However, your answer clarified much for me. Thanks!

Regards,
Thorsten



Am Montag, den 29.09.2014, 19:27 +0200 schrieb Michael Schmid:

> Hi Thorsten,
>
> if you convert from 16 to 8 bits you can select in Edit>Options>Conversions:
>
> "Scaled when converting"=off means that the 16-bit value will be transferred 1:1 to the 8-bit value, and everything above 255 will become 255 in the 8-bit image. Typically, this will lead to a lot of saturated pixels, so one would divide the 16-bit image by some number before conversion to 8 bits in that case, to get a reasonable 8-bit display.
>
> "Scaled when converting"=on means that the current display range (as set in the Image>Adjust>Brightness&Contrast panel) determines the span from 0 to 255 of the 8-bit image.
>
> If you have "Scaled when converting"=on and different B&C settings when converting, you get different results.
>
> See the manual:
>
> http://rsb.info.nih.gov/ij/docs/guide/146-28.html#toc-Subsection-28.1
> http://rsb.info.nih.gov/ij/docs/guide/146-27.html#toc-Subsubsection-27.13.11
>
>
> Michael
> ________________________________________________________________
> On Sep 29, 2014, at 18:42, Thorsten Wagner wrote:
>
> > Hi,
> >
> > I currently working with TEM image data. I imported a series of dm3
> > images via the Import -> Image Sequence command.
> >
> > If I open a single image of that image series with Open -> Image it
> > seems to have another contrast:
> > https://dl.dropboxusercontent.com/u/560426/contrast_bug_16bit.png
> >
> > But the pixel values are the same in left (sequence) and the right
> > (single) image, so there is not a problem. However, the images are 16bit
> > images and I have to convert them to 8 bit. I do that with  "Image ->
> > Type -> 8bit". But now the pixel values are DIFFERENT:
> > https://dl.dropboxusercontent.com/u/560426/contrast_bug_8bit.png
> >
> > The marked pixel has in the left image a value of 22 and in the right
> > image a value 8. It think this must be a bug because this is not the
> > expected behaviour, isn't it?
> >
> > Cheers,
> > Thorsten
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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