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Displaying histogram in ImageJ with fixed limits

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Displaying histogram in ImageJ with fixed limits

V Byrd
I am trying to view a 16 bit image with min intensity value of 0 and max
intensity value of 32767.
When the image is displayed the max values "look" white however, for a 16
bit image it should be a shade of gray.
As I move the cursor over the image the correct intensity value is displayed
in the ImageJ window (that is x coordinate, y coordinate , value).
If I adjust the brightness and contrast and manually set min = 0 and max
= 32767 the display of the image is corrected so that the max intensity
values look to be a shade of gray.  Although the display is changed, the
histogram still shows min=0 and max = 32767. How do I get the histogram to
display fixed limits (0 to 65535) for 16 bit image even though the image
only contains two values zero and 32767?

I am able to force it to show the entire range (0 to 65535) by strategically
setting a single pixel value to 65535. When this is done the entire range is
displayed automatically, but I would like for the entire range to be
displayed in the histogram automatically without the need to tweak the image
to do so.

Does anyone know of a way to do this?

Thanks,
VByrd
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Re: Displaying histogram in ImageJ with fixed limits

Rasband, Wayne (NIH/NIMH) [E]
On Feb 20, 2010, at 9:42 PM, V Byrd wrote:

> I am trying to view a 16 bit image with min intensity value of 0 and max
> intensity value of 32767.
> When the image is displayed the max values "look" white however, for a 16
> bit image it should be a shade of gray.
> As I move the cursor over the image the correct intensity value is displayed
> in the ImageJ window (that is x coordinate, y coordinate , value).
> If I adjust the brightness and contrast and manually set min = 0 and max
> = 32767 the display of the image is corrected so that the max intensity
> values look to be a shade of gray.  Although the display is changed, the
> histogram still shows min=0 and max = 32767. How do I get the histogram to
> display fixed limits (0 to 65535) for 16 bit image even though the image
> only contains two values zero and 32767?
>
> I am able to force it to show the entire range (0 to 65535) by strategically
> setting a single pixel value to 65535. When this is done the entire range is
> displayed automatically, but I would like for the entire range to be
> displayed in the histogram automatically without the need to tweak the image
> to do so.
>
> Does anyone know of a way to do this?

Run the Histogram command by pressing alt-h and ImageJ will display a dialog box that allows you to specify the range.

-wayne
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Adding new Image type to ImageJ

Michael Ellis
In reply to this post by V Byrd
I create images comprising multiple colour channels (1 to  10) each  
channel has an associated LUT. Our own application renders these  
multiple channels as a RGB colour image whereby the blending of these  
multiple channels can be adjusted with a collection of sliders that  
adjust such things as brightness, contrast, thresholds and other  
parameters.

I'd like to reproduce this within ImageJ. The underlying Stack class  
can be used to hold the image data, but I want to create something  
that will allow the stack to be rendered under my own control (with a  
live palette of controls)

I would also like to be able to associate extra data with each slice  
of the stack and be able to save and retrieve this when opening these  
images.

Any suggestions gratefully appreciated


Sincerely yours - Michael Ellis
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Re: Adding new Image type to ImageJ

Michael Schmid-3
Hi Michael,

you need a Composite Image: Image>Color>Make Composite. Use the  
'More>>' button to set the color of each slice, and B&C for fine  
variation.

Extra data - you can have this in the metadata (Image Info), but this  
is for the stack (composite image) as a whole. You would need some  
custom annotation to determine which data are for which slice. This  
could be done in a macro.

Michael
________________________________________________________________

On 14 May 2010, at 12:25, Michael Ellis wrote:

> I create images comprising multiple colour channels (1 to  10) each  
> channel has an associated LUT. Our own application renders these  
> multiple channels as a RGB colour image whereby the blending of  
> these multiple channels can be adjusted with a collection of  
> sliders that adjust such things as brightness, contrast, thresholds  
> and other parameters.
>
> I'd like to reproduce this within ImageJ. The underlying Stack  
> class can be used to hold the image data, but I want to create  
> something that will allow the stack to be rendered under my own  
> control (with a live palette of controls)
>
> I would also like to be able to associate extra data with each  
> slice of the stack and be able to save and retrieve this when  
> opening these images.
>
> Any suggestions gratefully appreciated
>
>
> Sincerely yours - Michael Ellis
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Re: Adding new Image type to ImageJ

Michael Ellis
Michael (Schmid)

Thanks, the composite image gives me a lot of what I need, but not  
everything! I need more control over how the different colour planes  
are merged together to form the final colour result (inter colour  
plane arithmetic to improve the appearance). The underlying colour  
planes (and their data) needs to remain immutable, I just want to  
create an interactive rendering of this multi plane data.

I also need to be able to add a (less clunky) user interface that  
makes the colour balancing more interactive.

The ColourThresholder may be worth investigating but that seems to  
modify the underlying data.

Regards -- Michael Ellis


On 14 May 2010, at 13:51, Michael Schmid wrote:

> Hi Michael,
>
> you need a Composite Image: Image>Color>Make Composite. Use the  
> 'More>>' button to set the color of each slice, and B&C for fine  
> variation.
>
> Extra data - you can have this in the metadata (Image Info), but  
> this is for the stack (composite image) as a whole. You would need  
> some custom annotation to determine which data are for which slice.  
> This could be done in a macro.
>
> Michael
> ________________________________________________________________
>
> On 14 May 2010, at 12:25, Michael Ellis wrote:
>
>> I create images comprising multiple colour channels (1 to  10) each  
>> channel has an associated LUT. Our own application renders these  
>> multiple channels as a RGB colour image whereby the blending of  
>> these multiple channels can be adjusted with a collection of  
>> sliders that adjust such things as brightness, contrast, thresholds  
>> and other parameters.
>>
>> I'd like to reproduce this within ImageJ. The underlying Stack  
>> class can be used to hold the image data, but I want to create  
>> something that will allow the stack to be rendered under my own  
>> control (with a live palette of controls)
>>
>> I would also like to be able to associate extra data with each  
>> slice of the stack and be able to save and retrieve this when  
>> opening these images.
>>
>> Any suggestions gratefully appreciated
>>
>>
>> Sincerely yours - Michael Ellis

Michael Ellis
Managing Director
Digital Scientific UK Ltd.
http://www.digitalscientific.co.uk
[hidden email]
tel: +44(0)1223 329993
fax: +44(0)1223 370040

Sheraton House
Castle Park
Cambridge
CB3 0AX


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