JPEG 2000

[Jason NoSpam]

Hi,

I was hoping someone could tell me if there is a plugin for ImageJ to handle Jpeg2000?  I reviewed the IMageJ web site, and didn't see anything.

Thanks!

Jason

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[Liu, Dongfang (NIH/NIAID) [F]]

Dear Friends:

I am a new user of Image J. I appreciate that you can tell me how to write a macro to do intensity tracking in ImageJ.
I have 500 slides in one .tiff. I want to know the change of "center of mass" and "mean Gray value" of single plot from 1 to 500 slide. Thank you very much.

 

> ----------
> From: Jason NoSpam
> Reply To: List IMAGEJ
> Sent: Friday, February 17, 2006 12:48 PM
> To: List IMAGEJ
> Subject: JPEG 2000
>
> Hi,
>
> I was hoping someone could tell me if there is a plugin for ImageJ to handle Jpeg2000?  I reviewed the IMageJ web site, and didn't see anything.
>
> Thanks!
>
> Jason
>
> __________________________________________________
> Do You Yahoo!?
> Tired of spam?  Yahoo! Mail has the best spam protection around
> http://mail.yahoo.com 
>
>

[michael shaffer]

 
Jason writes ...

> I was hoping someone could tell me if there is a plugin for
> ImageJ to handle Jpeg2000?  I reviewed the IMageJ web site,
> and didn't see anything.

  I don't believe the JPEG2000 format is in the public domain(?)

Genuinely, Michael Shaffer  :o)

SEM/MLA Research Coordinator
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Inco Innovation Centre
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P.O. Box 4200
St. John's, NL A1C 5S7

[Mikhail Umorin]

I think it's in the encoding standard: ISO/IEC[2000]
Gonzalez and Woods 2002 talk about it. I think it's public.


>
>   I don't believe the JPEG2000 format is in the public domain(?)
>

[William Macy]

Try this site for a free JPEG 2000 plugin. I use it frequently to  
store large images more compactly.

William K. Macy, Ph.D.
Associate Marine Research Scientist
Graduate School of Oceanography
University of RI
South Ferry Rd.
Narragansett RI 02882     tel: [phone]
[hidden email]       fax: [phone]

[Gabriel Landini]

On Saturday 18 February 2006 02:10, William Macy wrote:
> Try this site for a free JPEG 2000 plugin. I use it frequently to
> store large images more compactly.

Which site?

G.

[William Macy]

Sorry for the missing link to the jpeg 2000 plugin. Here it is:  
http://www.fnordware.com/index.html

I had needed to change my e-mail address with the ListServer and in  
the shuffle of getting it corrected the crucial part of my reply went  
missing.
Sorry again, Bill

[Jason NoSpam]

Thanks for the help.

However, it is a Photoshop plugin.  Will it work with ImageJ?

http://www.fnordware.com/j2k/

William Macy <[hidden email]> wrote: Sorry for the missing link to the jpeg 2000 plugin. Here it is:  
http://www.fnordware.com/index.html

I had needed to change my e-mail address with the ListServer and in  
the shuffle of getting it corrected the crucial part of my reply went  
missing.
Sorry again, Bill


               
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[Jason NoSpam]

I was just told that ImageJ can't use this plugin.  Therefore, is there any way for ImageJ to read (which is all I need) JPEG2000 images?

Thanks!

Jason NoSpam <[hidden email]> wrote: Thanks for the help.

However, it is a Photoshop plugin.  Will it work with ImageJ?

http://www.fnordware.com/j2k/

William Macy  wrote: Sorry for the missing link to the jpeg 2000 plugin. Here it is:  
http://www.fnordware.com/index.html

I had needed to change my e-mail address with the ListServer and in  
the shuffle of getting it corrected the crucial part of my reply went  
missing.
Sorry again, Bill


 
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[Wayne Rasband]

> I was just told that ImageJ can't use this plugin.  Therefore, is
> there any way for ImageJ to read (which is all I need) JPEG2000
> images?

Write a plugin to do this using the JAI (Java Advanced Imaging) Image
I/O Tools library at

     
http://java.sun.com/products/java-media/jai/downloads/download-iio.html

Or contact Jarek Sacha and ask him if this library will work with his
ImageIO plugins at

      http://ij-plugins.sourceforge.net/plugins/imageio/index.html


-wayne

[Andrew Phillips-2]

Is there any way that ImageJ could use the JJ2000 codec at the link
below.  I'm not yet proficient enough at Java to figure it out, but if
so, I would be interested in how to do it.

http://www.jpeg.org/jpeg2000/testlinks.html

Thanks,

Andy Phillips


-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
Wayne Rasband
Sent: Friday, February 24, 2006 6:28 AM
To: [hidden email]
Subject: Re: JPEG 2000-missing URL


> I was just told that ImageJ can't use this plugin.  Therefore, is
> there any way for ImageJ to read (which is all I need) JPEG2000
> images?

Write a plugin to do this using the JAI (Java Advanced Imaging) Image
I/O Tools library at

     
http://java.sun.com/products/java-media/jai/downloads/download-iio.html

Or contact Jarek Sacha and ask him if this library will work with his
ImageIO plugins at

      http://ij-plugins.sourceforge.net/plugins/imageio/index.html


-wayne

[Jason NoSpam]

I actually would be interested in having JPEG2000 functionality added to the core ImageJ application.  What would be involved to do this?  I may have the ability to dedicate time to working on coding this provided I can get some help from the community?

"Phillips, Andrew (DPI-Corvallis)" <[hidden email]> wrote: Is there any way that ImageJ could use the JJ2000 codec at the link
below.  I'm not yet proficient enough at Java to figure it out, but if
so, I would be interested in how to do it.

http://www.jpeg.org/jpeg2000/testlinks.html

Thanks,

Andy Phillips


-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
Wayne Rasband
Sent: Friday, February 24, 2006 6:28 AM
To: [hidden email]
Subject: Re: JPEG 2000-missing URL


> I was just told that ImageJ can't use this plugin.  Therefore, is
> there any way for ImageJ to read (which is all I need) JPEG2000
> images?

Write a plugin to do this using the JAI (Java Advanced Imaging) Image
I/O Tools library at

     
http://java.sun.com/products/java-media/jai/downloads/download-iio.html

Or contact Jarek Sacha and ask him if this library will work with his
ImageIO plugins at

      http://ij-plugins.sourceforge.net/plugins/imageio/index.html


-wayne


                       
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[Gabriel Landini]

On Friday 24 February 2006 16:11, Phillips, Andrew (DPI-Corvallis) wrote:
> Is there any way that ImageJ could use the JJ2000 codec at the link
> below.  I'm not yet proficient enough at Java to figure it out, but if
> so, I would be interested in how to do it.

Can I ask why do you want to use JPEG 2000?
Surely if you want to do image processing, only the lossless version makes sense.
What are the advantages over Tiff?

Cheers,

Gabriel

[Andrew Phillips-2]

The reason is that I am using ImageJ to evaluate the behavior of image
processing algorithms (i.e. the pixel by pixel changes when comparing
the source content with the transmitted or processed result.  I realize
that ImageJ is intended for the medical community, and what I am doing
is certainly outside that scope, but it turns out that ImageJ's ability
to handle process stacks and macro language makes it easy for me to work
with small video clips and simulate a complete image pipeline in a very
"visual" way.  Currently JPEG 2000 is part of my image pipeline - hence
my interest.

Hope that answers your question.

By the way - ImageJ is great program!

Thanks,

Andy Phillips (Hewlett-Packard).





-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
Gabriel Landini
Sent: Friday, February 24, 2006 8:27 AM
To: [hidden email]
Subject: Re: JPEG 2000-missing URL


On Friday 24 February 2006 16:11, Phillips, Andrew (DPI-Corvallis)
wrote:
> Is there any way that ImageJ could use the JJ2000 codec at the link
> below.  I'm not yet proficient enough at Java to figure it out, but if

> so, I would be interested in how to do it.

Can I ask why do you want to use JPEG 2000?
Surely if you want to do image processing, only the lossless version
makes sense. What are the advantages over Tiff?

Cheers,

Gabriel

[No Name-4]

I don't know what the needs are for other users but I am interested in
JPEG2000 data interchange because our lab is a heavy user of the Aperio
slide scanner which produces files in a flavor of the JPEG2000 format
(contain several scaled versions of the original image and some header
data). These files have an ".svs" naming extension but my understanding is
that they are JPEG2000 format. There is a pretty nice white paper on their
file format here: http://www.aperio.com/documents/

This company is very open to data interchange with third parties and can
provide an SDK for developing algorithms within their ImageScope analysis
tool. They do offer a way to break the larger images up into tiles which
can be fed through ImagePro Plus - it would be interesting to see
something similar for ImageJ

Jim Deeds





Gabriel Landini <[hidden email]>
Sent by: ImageJ Interest Group <[hidden email]>
02/24/2006 11:26 AM
Please respond to ImageJ Interest Group

 
        To:     [hidden email]
        cc:     (bcc: James Deeds/PH/Novartis)
        Subject:        Re: JPEG 2000-missing URL


On Friday 24 February 2006 16:11, Phillips, Andrew (DPI-Corvallis) wrote:
> Is there any way that ImageJ could use the JJ2000 codec at the link
> below.  I'm not yet proficient enough at Java to figure it out, but if
> so, I would be interested in how to do it.

Can I ask why do you want to use JPEG 2000?
Surely if you want to do image processing, only the lossless version makes
sense.
What are the advantages over Tiff?

Cheers,

Gabriel

[Jon Harman]

Hi,

jpeg2000 does a much better job of compression on color images.  jpeg is
crude by comparison.  It is a shame that digital cameras (and everywhere
else) universally use jpeg instead of jpeg 2000.  Image processing can
be done on lossy images and that does make sense, especially if they are
the only images you have.  My Canon S400 only has jpeg output.

I am no expert in the history of jpeg, but I guess this is the
unfortunate price jpeg2000 paid for starting out as proprietary.  Now
that the battle is lost it is becoming freely available.

Maybe there are others that know the history of this better than I do.

Jon


Gabriel Landini wrote:

> On Friday 24 February 2006 16:11, Phillips, Andrew (DPI-Corvallis) wrote:
>  
>> Is there any way that ImageJ could use the JJ2000 codec at the link
>> below.  I'm not yet proficient enough at Java to figure it out, but if
>> so, I would be interested in how to do it.
>>    
>
> Can I ask why do you want to use JPEG 2000?
> Surely if you want to do image processing, only the lossless version makes sense.
> What are the advantages over Tiff?
>
> Cheers,
>
> Gabriel
>
>  

[Gabriel Landini]

On Friday 24 February 2006 16:43, Phillips, Andrew (DPI-Corvallis) wrote:
> The reason is that I am using ImageJ to evaluate the behavior of image
> processing algorithms (i.e. the pixel by pixel changes when comparing
> the source content with the transmitted or processed result.

I see. I was curious as to why to use a lossy  format. Only in its losless
version would be useful to evaluate any image processing. But obviously you
must have your reasons.

Just in case you do not find an encoder/decoder to add to IJ, you can always
do the processing in a non-lossy format and then (if this is what you need)
save it in tiff, encode with an external programme, convert it back to an IJ
supported file format and load it back to evaluate the result.
ImageJ can send commands out to the OS (I wrote a little plugin to control my
laptop backlight and sound volume in linux; I guess it is similar in the
other OSs), so if you find an executable that does the job, you could save
your image to disk and call the encoder with the saved file name, call the
decoder and load back the reult all from a plugin.

Cheers,

Gabriel

[Gabriel Landini]

On Friday 24 February 2006 17:04, Jon Harman wrote:
> jpeg2000 does a much better job of compression on color images.  jpeg is
> crude by comparison.  It is a shame that digital cameras (and everywhere
> else) universally use jpeg instead of jpeg 2000.

Yes, I have seen some examples and it is noticeably better than jpeg.

> Image processing can
> be done on lossy images and that does make sense, especially if they are
> the only images you have.  My Canon S400 only has jpeg output.

That is unfortunate. Why wouldn't they allow raw format output?

Lossy Jpegs are good for throwing away information that they eye cannot
notice. Sure one can do image processing in any image, but results depend on
the application and how rigorous one wants to be.

If one wants to increase contrast and retouch red eyes in a photo, then that
may be fine but if one wants to estimate cell ploidy or nuclear texture in a
histological image, I do not think it is sensible at all. One ends up
partially characterising the compression artifact instead.
Furthermore, in each cycle of decompression and compression one introduces yet
more artifacts.

For those who do not believe this, just convert a colour jpeg to HSB colour
space and look at the Hue channel. It is frightening!

[DeBarr, Gabriel]

FYI:

You can download a java implementation of the jpeg 2000 codec @ http://jj2000.epfl.ch/jj_download/index.html
from there, you should be able to hack out a plug-in version.

        -gd

For the record, I happen to prefer lossless compression, myself (Material science, not medical image analysis, but still...)

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