Re: anomalous (?) display

Posted by Hugo A. M. Torres on Feb 09, 2009; 4:41pm
URL: http://imagej.273.s1.nabble.com/Tudor-DICOM-compressed-images-tp3693776p3693780.html

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
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CEP 04023-062 Vila Clementino
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Tel:[phone] r.220
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