convert 12 bit to 8 bit images faithfully

[Hao Wu]

Hi, everyone!

I have been using ImageJ to export my 12 bit images for a long time. Today
I find out it is not a good idea because the "8  bit" function is not
working the way I thought. Instead of converting 0~4095 to 0~255, actually
it converts from min~max of that particular image to 0~255. I am wondering,
does anybody happen to know any plugins, macros or software to faithfully
do the conversion? Thank you very much!

Best,
Hao

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

[Michael Schmid]

Hi Hao,

you can simply set the display range to 0-4095 (Set in The Brighness&Contrast Panel). If you select "8-bit" then the 0-4095 range will be mapped to 0-255. You can easily have a macro for this. This is what the Macro recorder would tell you:
  setMinAndMax(0, 4095);
  run("8-bit");

(This assumes that Edit>Options>Conversions" has "Scale when converting" enabled; otherwise 0-255 will be mapped to 0-255 and everything from 256-2095 will become 255)

It should be noted that a conversion from 12 to 8 bits is never "faithful": You will always lose information; in your case 16 gray levels will be mapped to one!

Michael
________________________________________________________________
On Oct 21, 2014, at 19:09, Hao Wu wrote:

> Hi, everyone!
>
> I have been using ImageJ to export my 12 bit images for a long time. Today
> I find out it is not a good idea because the "8  bit" function is not
> working the way I thought. Instead of converting 0~4095 to 0~255, actually
> it converts from min~max of that particular image to 0~255. I am wondering,
> does anybody happen to know any plugins, macros or software to faithfully
> do the conversion? Thank you very much!
>
> Best,
> Hao

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

[Cammer, Michael]

I think this is what you want to do:

macro "Convert 12 to 8 bits linear" {
  setMinAndMax(0, 4095);
  call("ij.ImagePlus.setDefault16bitRange", 12);
  run("8-bit");
}

===========================================================================
Michael Cammer, Microscopy Core & Skirball Institute, NYU Langone Medical Center
Cell:  914-309-3270   note that we do not receive messages left at 212-263-3208
http://ocs.med.nyu.edu/microscopy & http://microscopynotes.com/


-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Hao Wu
Sent: Tuesday, October 21, 2014 1:09 PM
To: [hidden email]
Subject: convert 12 bit to 8 bit images faithfully

Hi, everyone!

I have been using ImageJ to export my 12 bit images for a long time. Today I find out it is not a good idea because the "8  bit" function is not working the way I thought. Instead of converting 0~4095 to 0~255, actually it converts from min~max of that particular image to 0~255. I am wondering, does anybody happen to know any plugins, macros or software to faithfully do the conversion? Thank you very much!

Best,
Hao

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

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

[Hao Wu]

Hi, Michael!

Thank you so much! It solves a big problem for me.

Best,
Hao

On Tue, Oct 21, 2014 at 1:46 PM, Michael Schmid <[hidden email]>
wrote:

> Hi Hao,
>
> you can simply set the display range to 0-4095 (Set in The
> Brighness&Contrast Panel). If you select "8-bit" then the 0-4095 range will
> be mapped to 0-255. You can easily have a macro for this. This is what the
> Macro recorder would tell you:
>   setMinAndMax(0, 4095);
>   run("8-bit");
>
> (This assumes that Edit>Options>Conversions" has "Scale when converting"
> enabled; otherwise 0-255 will be mapped to 0-255 and everything from
> 256-2095 will become 255)
>
> It should be noted that a conversion from 12 to 8 bits is never
> "faithful": You will always lose information; in your case 16 gray levels
> will be mapped to one!
>
> Michael
> ________________________________________________________________
> On Oct 21, 2014, at 19:09, Hao Wu wrote:
>
> > Hi, everyone!
> >
> > I have been using ImageJ to export my 12 bit images for a long time.
> Today
> > I find out it is not a good idea because the "8  bit" function is not
> > working the way I thought. Instead of converting 0~4095 to 0~255,
> actually
> > it converts from min~max of that particular image to 0~255. I am
> wondering,
> > does anybody happen to know any plugins, macros or software to faithfully
> > do the conversion? Thank you very much!
> >
> > Best,
> > Hao
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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

[Hao Wu]

Really nice! Thank you so much!

Best,
Hao

On Tue, Oct 21, 2014 at 1:47 PM, Cammer, Michael <[hidden email]
> wrote:

> I think this is what you want to do:
>
> macro "Convert 12 to 8 bits linear" {
>   setMinAndMax(0, 4095);
>   call("ij.ImagePlus.setDefault16bitRange", 12);
>   run("8-bit");
> }
>
> ===========================================================================
> Michael Cammer, Microscopy Core & Skirball Institute, NYU Langone Medical
> Center
> Cell:  914-309-3270   note that we do not receive messages left at
> 212-263-3208
> http://ocs.med.nyu.edu/microscopy & http://microscopynotes.com/
>
>
> -----Original Message-----
> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Hao
> Wu
> Sent: Tuesday, October 21, 2014 1:09 PM
> To: [hidden email]
> Subject: convert 12 bit to 8 bit images faithfully
>
> Hi, everyone!
>
> I have been using ImageJ to export my 12 bit images for a long time. Today
> I find out it is not a good idea because the "8  bit" function is not
> working the way I thought. Instead of converting 0~4095 to 0~255, actually
> it converts from min~max of that particular image to 0~255. I am wondering,
> does anybody happen to know any plugins, macros or software to faithfully
> do the conversion? Thank you very much!
>
> Best,
> Hao
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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