Undesirable conversion of 16-bit to 8-bit/RGB using ImageJ

[Shanna Banman]

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Hello all,

Would anyone be able to tell me how to save a 16-bit image (3channels) as a tiff
file or equivalent using ImageJ? Every time I save the file (either as separate
channels or composite image) in tiff format using ImageJ/FIJI I get three black
images.  If I convert to RGB or save as PNG, it becomes 8-bit image. Is there
any way around this?

Thank you!

 Shanna

[mmodel]

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A strange problem indeed. Can you save a single image in 16 bit? I suggest you make your own image/images within ImageJ and try to save them.

-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Shanna Banman
Sent: Monday, May 06, 2013 11:00 AM
To: [hidden email]
Subject: Undesirable conversion of 16-bit to 8-bit/RGB using ImageJ

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Hello all,

Would anyone be able to tell me how to save a 16-bit image (3channels) as a tiff file or equivalent using ImageJ? Every time I save the file (either as separate channels or composite image) in tiff format using ImageJ/FIJI I get three black images.  If I convert to RGB or save as PNG, it becomes 8-bit image. Is there any way around this?

Thank you!

 Shanna

[Tim Feinstein-2]

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It is possible that the 'black' images are just your original 16-bit pics with the lookup tables reset.  A lot of imaging data is collected by 12- or 14-bit platforms and then saved in a 16-bit format, and thus appears blank if you view the image with its full 16-bit range on an 8-bit monitor.  To check whether your original data is there, reduce the max display value in brightness/contrast and see whether something comes up.  

All the best,


TF

Timothy Feinstein, PhD
Visiting Research Associate
Laboratory for GPCR Biology
Dept. of Pharmacology & Chemical Biology
University of Pittsburgh, School of Medicine
BST W1301, 200 Lothrop St.
Pittsburgh, PA  15261

On May 6, 2013, at 11:28 AM, MODEL, MICHAEL wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> A strange problem indeed. Can you save a single image in 16 bit? I suggest you make your own image/images within ImageJ and try to save them.
>
> -----Original Message-----
> From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Shanna Banman
> Sent: Monday, May 06, 2013 11:00 AM
> To: [hidden email]
> Subject: Undesirable conversion of 16-bit to 8-bit/RGB using ImageJ
>
> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> Hello all,
>
> Would anyone be able to tell me how to save a 16-bit image (3channels) as a tiff file or equivalent using ImageJ? Every time I save the file (either as separate channels or composite image) in tiff format using ImageJ/FIJI I get three black images.  If I convert to RGB or save as PNG, it becomes 8-bit image. Is there any way around this?
>
> Thank you!
>
> Shanna

[Pedro Almada]

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Hi Shanna,

If you're trying to view them with the default Windows and OSX viewers,
they don't scale tif files. Your images will look black if your signal is
in the very low end of the bitrange (as with cases Tim mentions). If you
open those tifs again in ImageJ you'll see your images are fine because
ImageJ autoscales on opening. Photoshop also will understand those 16bit
files if I remember correctly.

Best,
Pedro


On 6 May 2013 15:59, Shanna Banman <[hidden email]> wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> Hello all,
>
> Would anyone be able to tell me how to save a 16-bit image (3channels) as
> a tiff
> file or equivalent using ImageJ? Every time I save the file (either as
> separate
> channels or composite image) in tiff format using ImageJ/FIJI I get three
> black
> images.  If I convert to RGB or save as PNG, it becomes 8-bit image. Is
> there
> any way around this?
>
> Thank you!
>
>  Shanna
>