[Insight-users] Question on registration of cryogenic RGB images

[Luis Ibanez]

Hi Fucang,

0) It looks like a single slice will have take
    around 26Mb. (asuming 1 byte/ per RGB component)
    Is this right ?

1) It is not a problem to register images
    with different resolutions. Just make sure
    that the values of spacing are set correctly
    (that is, the distance in millimeter between
    pixel centers). Registration is performed in
    physical space coordinates.

2) Don't worry about your old computer. It fits
    the initial requirement set for the toolkit.
    It may be slow, but it should be possible to
    do it.

3) For visuallization you may want to reduce the
    resolution but probably some experimentation
    will be needed here to find the right resolution
    to visualize.
    Note that you could use the multiresolution
    framework

4) About registering RGB color images. Bill Lorensen
    made some validation studies and found that using
    only the red channel is in general sufficient for
    registering color images.

    We haven't implemented RGB metrics yet. It is in
    fact a matter of demand. If you find that a single
    channel registration is not good enough, please
    let us know so we can move the RGB metrics up in
    the list of priorities.

5) By differences in intensities do you mean that
    the brightness in the center one slice is different
    from the brightness on the borders ?
    or do you mean that the brightness of one slice
    is different from the brightness of the next slice ?

    If one image has a different brightness scale than
    the others. The effect varies depending on the Metric.

    a- MutualInformation is insensitive to brightness
       changes.

    b- MeanSquares will is sensitive to differences
       in brightness between the two images being
       registered

    c- NormalizedCorrelation will compensate for
       *multiplicative* changes in intensity but not
       for additive changes in intensity

    d- PatternIntensity will be sensitive to the
       intensity changes. More sensitive to additive
       changes than multiplicative changes.

    BTW How big are the differences in brightness ?
    a factor of 1.5 ? 1.2 ?

6) You don't need to segment the images before
    registration.


Please let us know if you have futher questions,


Thanks


    Luis


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

Fucang Jia wrote:

> Hi, everyone,
> 
> At first I thank Luis's help.
> 
> Recently I obtained 1399 cryogemic RGB color image, which were produced 
> with a high-precision scanner.
> These images have different resolution, which are as follows:
> 
> 1-66         2733 x 3179
> 67-89        2417 x 3010
> 90-544       2240 x 3010
> 545-644      2241 x 3011
> 645-673      2178 x 3011
> 674-682      2105 x 3041
> 683-702      2071 x 3041
> 703-989      2105 x 3041  ( same with 674-682th )
> 990-1034     2148 x 3086
> 1035-1286    2155 x 3110
> 1287         2163 x 3110
> 1288-1290    2294 x 3071
> 1291-1399    2155 x 3110
> 
> The image difference is mainly translation and rotation. I want to align 
> the second image to the first image, the third to the second, etc. So 
> this is a 2D registration problem.
> 
> The computer is somewhat old, PIII 500 with 640Mb Ram.
> 
> Here is several problem I concern:
> 
> 1. The resolution is different, should I downsampled the image to the 
> minimum 2071 x 3010? Or a smaller resolution
> such as 500 x 750, because finally I want to visualize the three 
> dimensional structure by Marching Cubes or Dividing Cubes in this computer.
> 
> 2. The image is RGB color, but most of registration algorithm is useful 
> for gray scale image, the simplest method is convert RGB image to gray 
> image, or only use one channel (red, green, blue), which method is more 
> accurate? I noticed that Dr.Luis once said that he would like to 
> implement a registration for color image, but I do not know whether this 
> method was included in ITK already.
> 
> 3. The images were not homogenous in brightness, that is to say, the 
> brightness of each image have more or least
> difference, I think this will induce difficulty in registration. And the 
> target area is very small contrast to the entire image. So should I 
> first segment the image before registration?
> 
> I am confused by these huge images, any advice would be very appreciated!
> 
> Fucang
> 
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