Maximum entropy thresholding for 16-bit images

[Sanneke Brinkers]

Dear all,
 
The current maximum entropy threshold plugin needs 8-bit images as input.
However, my images are 16-bit TIFF. When I convert the images to 8-bit a lot
of information is lost, so my question is: Is there a maximum entropy
thresholding plugin available for 16-bit images?
 
Or can the writer of the current plugin give me tips on how to convert the
plugin, or rewrite it himself to include 16-bit images?
 
Thanks in advance!
 
Sanneke
 

===========================

Sanneke Brinkers

BioPhysical Engineering (BPE)

Faculty of Science and Technology

University of Twente

P.O. Box 217

7500 AE Enschede

The Netherlands

P: [phone]

F: [phone]

E:  <mailto:[hidden email]> [hidden email]

I:  <http://bpe.tnw.utwente.nl/> http://bpe.tnw.utwente.nl

 

[dscho]

Hi,

On Mon, 1 May 2006, Sanneke Brinkers wrote:

> The current maximum entropy threshold plugin needs 8-bit images as input.
> However, my images are 16-bit TIFF. When I convert the images to 8-bit a lot
> of information is lost, so my question is: Is there a maximum entropy
> thresholding plugin available for 16-bit images?

That's easy. Just change the line

   return PlugInFilter.DOES_8G | PlugInFilter.DOES_STACKS;

to

   return PlugInFilter.DOES_16 | PlugInFilter.DOES_8G | PlugInFilter.DOES_STACKS;

Be warned! A small test with a 256x256 image on my computer said that for
8-bit, the time was 0.051 seconds, but for 16-bit it was 101 seconds!

Also, the difference it makes should be negligible in most cases. It might
be necessary to adjust he contrast a little before 16-bit to 8-bit
conversion, but you should be able to come close to the result of the
16-bit thresholding.

Ciao,
Dscho

[Wayne Rasband]

> The current maximum entropy threshold plugin needs 8-bit images
> as input. However, my images are 16-bit TIFF. When I convert the
> images to 8-bit a lot of information is lost, so my question is: Is
> there a maximum entropy thresholding plugin available for 16-bit
> images?
>
> Or can the writer of the current plugin give me tips on how to
> convert the plugin, or rewrite it himself to include 16-bit images?

The MultiThresholder plugin at

     http://rsb.info.nih.gov/ij/plugins/multi-thresholder.html

does maximum entropy thresholding on 16-bit images.

-wayne

[Sanneke Brinkers]

I tried the MultiThresholder but got different results with the same images.
Does the plugin use actual 16-bit max entropy thresholding or does it do 1
to 8-bit conversion, but you just can't see it?

 Also, sometimes the thresholder selects the background in stead of the
cells. Did I do something wrong? Or are there more settings I just haven't
found yet? How can I control this plugin better?  

Thanks,

Sanneke

P.S. I will also try to adjust the max entropy plugin with the suggestion
from Johannes Schindelin and see if it fits my needs


-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Wayne
Rasband
Sent: maandag 1 mei 2006 23:38
To: [hidden email]
Subject: Re: Maximum entropy thresholding for 16-bit images

> The current maximum entropy threshold plugin needs 8-bit images as
> input. However, my images are 16-bit TIFF. When I convert the images
> to 8-bit a lot of information is lost, so my question is: Is there a
> maximum entropy thresholding plugin available for 16-bit images?
>
> Or can the writer of the current plugin give me tips on how to convert
> the plugin, or rewrite it himself to include 16-bit images?

The MultiThresholder plugin at

     http://rsb.info.nih.gov/ij/plugins/multi-thresholder.html

does maximum entropy thresholding on 16-bit images.

-wayne