[Insight-users] Question on registration of cryogenic RGB images
Fucang Jia
jiafucang@hotmail.com
Wed, 11 Dec 2002 22:35:16 +0800
Hi, Luis,
Thank you very much! Your reply let me understand the key of registration.
>From: Luis Ibanez <luis.ibanez@kitware.com>
>To: Fucang Jia <jiafucang@hotmail.com>
>CC: insight-users@public.kitware.com
>Subject: Re: [Insight-users] Question on registration of cryogenic RGB
>images
>Date: Mon, 09 Dec 2002 08:27:15 -0500
>
>Hi Fucang,
>
>0) It looks like a single slice will have take
> around 26Mb. (asuming 1 byte/ per RGB component)
> Is this right ?
Yes, the images are 1byte per RGB component.
>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.
After looking up the maillists, I see (the translation in mm, not numbers of
pixels).
>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.
Yes, I make a MultiResMIRegistration on a Red component, the result is good
enough. Though it needs about 900 Mb RAM, but it works, about 15 minutes,
which is acceptable.
>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
Yes
>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.
Yes, after I look the red, green and blue component of the original image, I
find them are similar, so red component is enough. The pixels' red , green
and blue component has a high correlation, which make sure that one
component is acceptable.
>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 ?
I have not test the difference in brightness, but I will compute the
correlation of two images to make it clear. But here is a problem, when I
use ImageRegistration to register two image, the registered image is all
black, does ImageRegistration need two unsigned-short images?
>6) You don't need to segment the images before
> registration.
Yes. I do.
>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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