Tudor DICOM compressed images

[Peter Sebastian Masny]

Hi all,

Hope this isn't too much of a FAQ. I tried to find the solution, but no
luck.

Basically I want to view compressed DICOM images.

I have the windows version of ImageJ 1.41o bundled with JRE 1.6.0
I have the tudor jar and libraries in my plugins and they start fine

When I try to upen a DICOM CD (with a patient MRI) , I get:
java.io.IOexception
ImageJ cannot open compressed DICOM images

I have tried with the IJ-imageIO jar in my plugins, but no luck

I have tried downloading jai_imageio-1_1-lib-windows-i586-jre.exe
and running it to install in the the ImageJ/jre folder, with no luck
(selected all install components).

I still get the same error.

Any ideas? or a link to the answer?

Thanks,
Peter Sebastian Masny

[Johannes Hermen]

I just updated the TUDOR DICOm Tools to version 0.9.2, now opening
compressed images  should work within the imagej-plugins too.

      Johannes

-----------------------------------------------------------------
Johannes Hermen  -  Ingenieur de Recherche
[hidden email]
-----------------------------------------------------------------
CRP Henri Tudor  http://www.santec.tudor.lu
29, Avenue John F. Kennedy
L-1855 Luxembourg
-----------------------------------------------------------------

[Hugo A. M. Torres]

Hello dear colleagues,

ImageJ seems to be displaying some files incorrectly here.  Please check
this link: http://imagebin.ca/view/6z_mf8hh.htmler 

There I have the imageJ and another application (nautilus) displaying
the same TIF file. The imageJ display seems more grainy and darker.
 
The interesting thing is that it does not happen to every file! Specimen
photos are displayed as expected.
It only happens to the photos which I took without a specimen, that is,
only an empty glass slide was placed on the microscope, so I can
subtract light path aberrations from the specimen photos.

I can't subtract these photos the way it is being displayed. (I
understand I have to convert photos to 8bit grayscale in order to
accomplish this, but this issue would have to be solved first.)

I am using imageJ 1.42h in ubuntu 64bits.

Any clues?

Thanks

--
Hugo Arruda de Moura Torres
==================================
Departamento de Biofísica
Universidade Federal de São Paulo
Rua Botucatu 862 7o. andar
CEP 04023-062 Vila Clementino
São Paulo - SP - Brasil
Tel:[phone] r.220
Fax: [phone]

["Janne Hyötylä"]

On Mon, 09 Feb 2009 14:43:44 +0100, Hugo A. M. Torres
<[hidden email]> wrote:

> Hello dear colleagues,
>
> ImageJ seems to be displaying some files incorrectly here.  Please check
> this link: http://imagebin.ca/view/6z_mf8hh.htmler
>
> There I have the imageJ and another application (nautilus) displaying
> the same TIF file. The imageJ display seems more grainy and darker.
> The interesting thing is that it does not happen to every file! Specimen
> photos are displayed as expected.

Hello,

ImageJ changes the value for white and and black according to the maximal
and minimal intensities in an image. This only affects how the image is
displayed, not the raw data itself. You can check this yourself by going
to Image > Adjust > Brightness/Contrast. You will see that in your case
the histogram does not go from 0 to 255 (or 0-65535 in 16bit) but a subset
of it. But when you change the sliders the raw intensity of each pixel
does not change. Any operation (subtraction etc.) will act on the raw
values so this will not be a problem.

Nautilus on the other hand seems to fix black = 0 and white = 255 (or
65535).


Best regards,
Janne

--
Janne Hyötylä
Biozentrum / Swiss Nanoscience Institute
University of Basel
--
Jetzt 1 Monat kostenlos! GMX FreeDSL - Telefonanschluss + DSL
für nur 17,95 Euro/mtl.!* http://dsl.gmx.de/?ac=OM.AD.PD003K11308T4569a

[Nicola B.]

Hi all,
I've a little problem with zoom..
When I create a little image (e.g. 30x30), what should I do to display
it bigger on screen? (e.g 1/5 of total screen height)
I try with:

-----------
        ImagePlus imp = new ImagePlus("testZoom", new
ColorProcessor(30,30));
        imp.show();
        double _newImpHeight =
Toolkit.getDefaultToolkit().getScreenSize().getHeight() / 5;
        double _displayMagn = _newImpHeight/imp.getHeight();

        imp.getCanvas().setMagnification(_displayMagn);

        imp.updateAndDraw();
        imp.updateAndRepaintWindow();
-----------

but it doesn't work..
Best regards,
    -nicola

[Hugo A. M. Torres]

Hi Janne Hyötylä,

This sounds reassuring!

However, I've done a subtraction exercise and it seemed to affect the
outcome: the resulting image was darkened all over (is this expected?)
-- maybe I am doing it wrong: what I am trying to do is remove a couple
of dark spots present in the lightpath picture from the specimen picture
(darkspots are also present there).

An important question that stems from this is whether I really should do
a subtraction operation to accomplish what I want. Considering that
darker pixels have lower values, should I be adding  the pictures to one
another instead? Either way, I did not get what I expected. Can anyone
advise me on this?

I was reading some imageJ documentation and it seems it might be
important to calibrate the grayscale with a grayscale steptablet before
doing the subtraction operation.
http://rsbweb.nih.gov/ij/docs/examples/calibration/index.html
Maybe thats the root cause of my problem?

Here is what I did: 1 - convert the 16bit RGB to RGB, then to 8 bit,
then process > image calculator and subtracted the blank file (lightpath
background photo) from the specimen image file.

 Any help is welcome =]



On Mon, 2009-02-09 at 15:26 +0100, "Janne Hyötylä" wrote:

> On Mon, 09 Feb 2009 14:43:44 +0100, Hugo A. M. Torres
> <[hidden email]> wrote:
>
> > Hello dear colleagues,
> >
> > ImageJ seems to be displaying some files incorrectly here.  Please check
> > this link: http://imagebin.ca/view/6z_mf8hh.htmler
> >
> > There I have the imageJ and another application (nautilus) displaying
> > the same TIF file. The imageJ display seems more grainy and darker.
> > The interesting thing is that it does not happen to every file! Specimen
> > photos are displayed as expected.
>
> Hello,
>
> ImageJ changes the value for white and and black according to the maximal
> and minimal intensities in an image. This only affects how the image is
> displayed, not the raw data itself. You can check this yourself by going
> to Image > Adjust > Brightness/Contrast. You will see that in your case
> the histogram does not go from 0 to 255 (or 0-65535 in 16bit) but a subset
> of it. But when you change the sliders the raw intensity of each pixel
> does not change. Any operation (subtraction etc.) will act on the raw
> values so this will not be a problem.
>
> Nautilus on the other hand seems to fix black = 0 and white = 255 (or
> 65535).
>
>
> Best regards,
> Janne
>
> --
> Janne Hyötylä
> Biozentrum / Swiss Nanoscience Institute
> University of Basel

--
Hugo Arruda de Moura Torres
==================================
Departamento de Biofísica
Universidade Federal de São Paulo
Rua Botucatu 862 7o. andar
CEP 04023-062 Vila Clementino
São Paulo - SP - Brasil
Tel:[phone] r.220
Fax: [phone]

[Gabriel Lapointe]

Hello Hugo,
When you convert a 16 bit image to 8bit ImageJ take use the minimum and
maximum displayed as the limits for the scaling down. So you either have
to adjust the brightness and contrast before the conversion (make sure
it is the same for all sample) or avoid the conversion and substract the
16 bit image directly. As long as both image are the same depth (8 or 16
bit) it should work.

Gabriel

Hugo A. M. Torres wrote:

> Hi Janne Hyötylä,
>
> This sounds reassuring!
>
> However, I've done a subtraction exercise and it seemed to affect the
> outcome: the resulting image was darkened all over (is this expected?)
> -- maybe I am doing it wrong: what I am trying to do is remove a couple
> of dark spots present in the lightpath picture from the specimen picture
> (darkspots are also present there).
>
> An important question that stems from this is whether I really should do
> a subtraction operation to accomplish what I want. Considering that
> darker pixels have lower values, should I be adding  the pictures to one
> another instead? Either way, I did not get what I expected. Can anyone
> advise me on this?
>
> I was reading some imageJ documentation and it seems it might be
> important to calibrate the grayscale with a grayscale steptablet before
> doing the subtraction operation.
> http://rsbweb.nih.gov/ij/docs/examples/calibration/index.html
> Maybe thats the root cause of my problem?
>
> Here is what I did: 1 - convert the 16bit RGB to RGB, then to 8 bit,
> then process > image calculator and subtracted the blank file (lightpath
> background photo) from the specimen image file.
>
>  Any help is welcome =]
>
>
>
> On Mon, 2009-02-09 at 15:26 +0100, "Janne Hyötylä" wrote:
>
>  
>> On Mon, 09 Feb 2009 14:43:44 +0100, Hugo A. M. Torres
>> <[hidden email]> wrote:
>>
>>    
>>> Hello dear colleagues,
>>>
>>> ImageJ seems to be displaying some files incorrectly here.  Please check
>>> this link: http://imagebin.ca/view/6z_mf8hh.htmler
>>>
>>> There I have the imageJ and another application (nautilus) displaying
>>> the same TIF file. The imageJ display seems more grainy and darker.
>>> The interesting thing is that it does not happen to every file! Specimen
>>> photos are displayed as expected.
>>>      
>> Hello,
>>
>> ImageJ changes the value for white and and black according to the maximal
>> and minimal intensities in an image. This only affects how the image is
>> displayed, not the raw data itself. You can check this yourself by going
>> to Image > Adjust > Brightness/Contrast. You will see that in your case
>> the histogram does not go from 0 to 255 (or 0-65535 in 16bit) but a subset
>> of it. But when you change the sliders the raw intensity of each pixel
>> does not change. Any operation (subtraction etc.) will act on the raw
>> values so this will not be a problem.
>>
>> Nautilus on the other hand seems to fix black = 0 and white = 255 (or
>> 65535).
>>
>>
>> Best regards,
>> Janne
>>
>> --
>> Janne Hyötylä
>> Biozentrum / Swiss Nanoscience Institute
>> University of Basel
>>    
>
>  

[ctrueden]

Hi Peter,

Basically I want to view compressed DICOM images.
>

You can also try Bio-Formats:
http://www.loci.wisc.edu/ome/formats.html

If you want to read DICOMs compressed with lossless JPEG, you'll need to
follow the directions at:
http://www.loci.wisc.edu/ome/formats-native.html

HTH,
Curtis

On Sat, Feb 7, 2009 at 6:54 PM, Peter Sebastian Masny <[hidden email]>wrote:

> Hi all,
>
> Hope this isn't too much of a FAQ. I tried to find the solution, but no
> luck.
>
> Basically I want to view compressed DICOM images.
>
> I have the windows version of ImageJ 1.41o bundled with JRE 1.6.0
> I have the tudor jar and libraries in my plugins and they start fine
>
> When I try to upen a DICOM CD (with a patient MRI) , I get:
> java.io.IOexception
> ImageJ cannot open compressed DICOM images
>
> I have tried with the IJ-imageIO jar in my plugins, but no luck
>
> I have tried downloading jai_imageio-1_1-lib-windows-i586-jre.exe
> and running it to install in the the ImageJ/jre folder, with no luck
> (selected all install components).
>
> I still get the same error.
>
> Any ideas? or a link to the answer?
>
> Thanks,
> Peter Sebastian Masny
>

[Hugo A. M. Torres]

Thanks Gabriel,

I will try to do the operation before the conversion, now if I had to do
it later, how would I ensure the contrast is the same? Should I worry
only about the slope and position of the line displayed over the
histogram  in the b/c dialogue box? Sorry if this is basic, I am new at
this.

Hugo

On Mon, 2009-02-09 at 12:55 -0500, Gabriel Lapointe wrote:

> Hello Hugo,
> When you convert a 16 bit image to 8bit ImageJ take use the minimum and
> maximum displayed as the limits for the scaling down. So you either have
> to adjust the brightness and contrast before the conversion (make sure
> it is the same for all sample) or avoid the conversion and substract the
> 16 bit image directly. As long as both image are the same depth (8 or 16
> bit) it should work.
>
> Gabriel
>

[Gabriel Lapointe]

In the Brightness and contrast dialog ther is a "set" button where you
can enter the values manually.

Hope this help,

Gabriel

Hugo A. M. Torres wrote:

> Thanks Gabriel,
>
> I will try to do the operation before the conversion, now if I had to do
> it later, how would I ensure the contrast is the same? Should I worry
> only about the slope and position of the line displayed over the
> histogram  in the b/c dialogue box? Sorry if this is basic, I am new at
> this.
>
> Hugo
>
> On Mon, 2009-02-09 at 12:55 -0500, Gabriel Lapointe wrote:
>
>  
>> Hello Hugo,
>> When you convert a 16 bit image to 8bit ImageJ take use the minimum and
>> maximum displayed as the limits for the scaling down. So you either have
>> to adjust the brightness and contrast before the conversion (make sure
>> it is the same for all sample) or avoid the conversion and substract the
>> 16 bit image directly. As long as both image are the same depth (8 or 16
>> bit) it should work.
>>
>> Gabriel
>>
>>    
>
>  

[Hugo A. M. Torres]

The Wayne Rasband's "Shading Corrector" plugin does exactly what I need
in a very straightforward way! All I have to do is rename my light path
image to "blank-field" without  the  file extension, open both images
and click on its menu entry.

Hope this helps others


On Mon, 2009-02-09 at 15:20 -0500, Gabriel Lapointe wrote:

> In the Brightness and contrast dialog ther is a "set" button where you
> can enter the values manually.
>
> Hope this help,
>
> Gabriel
>
> Hugo A. M. Torres wrote:
> > Thanks Gabriel,
> >
> > I will try to do the operation before the conversion, now if I had to do
> > it later, how would I ensure the contrast is the same? Should I worry
> > only about the slope and position of the line displayed over the
> > histogram  in the b/c dialogue box? Sorry if this is basic, I am new at
> > this.
> >
> > Hugo
> >
> > On Mon, 2009-02-09 at 12:55 -0500, Gabriel Lapointe wrote:
> >
> >  
> >> Hello Hugo,
> >> When you convert a 16 bit image to 8bit ImageJ take use the minimum and
> >> maximum displayed as the limits for the scaling down. So you either have
> >> to adjust the brightness and contrast before the conversion (make sure
> >> it is the same for all sample) or avoid the conversion and substract the
> >> 16 bit image directly. As long as both image are the same depth (8 or 16
> >> bit) it should work.
> >>
> >> Gabriel
> >>
> >>    
> >
> >  

--
Hugo Arruda de Moura Torres
==================================
Departamento de Biofísica
Universidade Federal de São Paulo
Rua Botucatu 862 7o. andar
CEP 04023-062 Vila Clementino
São Paulo - SP - Brasil
Tel:[phone] r.220
Fax: [phone]