Histogram Equalization

[Marcos Nieves]

Hi everyone!

I am having a kind of frustrating problem with the Histogram Equalization function of ICY.

I am used to the "Image > Adjust > Brightness/Contrast > Auto" function of ImageJ. Just to give you an example of the images I deal with, this is how the image would look when you first open it:

And this would be it after automatic histogram equalization with ImageJ...

When I use ICY, the first time I open the same image, it looks like this:

And after applying the Histogram Equalization plugin, it looks like this:

Clearly the visualization of the image doesn't improve at all. I have also try to adjust manually the max and min limits of the histogram, without much succes. The image keeps looking like a pseudo-binary image.

If somebody can help me with this I would really apreciate it.

Marcos.

[Stephane]

Hi Marcos,

Can you provide a sample of your image ? I tried with a screen shot of your image but it was not relevant as i don't have the correct original pixel value. Also the plugin Histogram Equalization plugin is not an auto adjust contrast as the ImageJ feature you used, it will "flatten" the whole histogram which is different.
In Icy the histogram is automatically adjusted when you open the image and then you can manually modify it if required.
Still if you don't have the same "view" you can then adjust the colormap itself, it's made for that (improve displaying and contrast in general). Hope that helps.

Best,

- Stephane

[Marcos Nieves]

Thanks for the quick answer!... Then, if the histogram is automatically adjusted when I open the image it doesn't seem to be working for me... As you can see in the third screenshot I pasted in my message, it doesn't look like the histogram was adjusted. I didn't understand what the equalization plugin does...

I uploaded the original image here: http://goo.gl/EWQWkt. It is actually a movie. I realized that if I extract only one frame and I open it independently in ICY, the histogram seems to be adjusted automaically, but when I open the whole movie it doesn't work.... I have no clue about why.

[Alexandre Dufour]

Dear Marcos,

Here are a few points that might clarify things a bit:

 — The brightness auto-adjust functions (of ImageJ and Icy) will *visually* adjust the minimum and maximum histogram range used to convert pixel data into pixel brightness (In Icy, this range is represented by the blue and red bars in the histogram panel). The difference between ImageJ and Icy is that ImageJ will calculate this range independently on each image of a sequence, whereas Icy takes the minimum and maximum values of the entire sequence. This is probably why loading up a single image will give you the same adjustment in both software, and not on a sequence.

 — Histogram equalisation (http://en.wikipedia.org/wiki/Histogram_equalization) is an image processing technique that will spread out the contents of the histogram equally throughout, but doing so will *replace* pixel values by adjusted ones, therefore the pixel data will be different from the original image (this is therefore *not* a method to use if you intend to perform intensity measurements down the line).

Hope this helps,

Alexandre

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[Marcos Nieves]

Thank you very much.