[Insight-users] Histoligical images registration

[Luis Ibanez]

Hi Delphine,


    Your registration problem sounds quite interesting.

    One possible way of preventing the holes in the histological sample
    from affecting the registration results is to take advantage of the
    Masks.

    You can define Masks in the Fixed image and in the Moving image
    for selecting what pixels you want to participate in the
    registration. If you create masks where the holes are excluded
    from the mask, then the registration metric will be computed without
    considering such holes.

    It seems that you have already look at the ITK Software Guide

              http://www.itk.org/ItkSoftwareGuide.pdf

    in particular section 8.11.3
    "Registration using masks constructed with Spatial Objects"
    pdf-page 464-466.

    What you want to do is to create Masks where all the pixels
    corresponding to holes of the histological sample, are set to
    Zero, and the others are set to non zero.  Note that you could
    also take advantage of the mask to remove all the pixels outside
    of the mouse body to count on the registration process. It is
    usually advisable to leave a small border outside the body, as
    a way of making sure the that transition between body and air
    contributes to the registration process.


    The trick now, is to find an easy way of building the Mask.
    Hopefully the holes in your images are clear enough for using
    simple segmentation methods.

    If now, we may need to take a look at your images in order to
    give you better advice.



     Please let us know if you have more questions,


         Thanks


            Luis




------------------------------
delphine.ribes at epfl.ch wrote:
> Dear all,
> 
> I am doing Image registration of histological images. My goal is to align brain
> mice in the same space coordinate to compare them. To do so I am using a
> reference volume.
> During the sectioning, some part of the brain is lost which create holes. To
> align volume, I am using 4 following registration : land mark, rigid, affine
> and a non rigid one which is Bspline. the last one is used to align internal
> organs. The alignment is good. But if the external border is cut, artifacts
> appear.
> 
> Do you know if there is a way to mask the hole to avoid those artifacts ?
> 
> I read in the itk book that you can pass the mask to the metric, but as far as I
> understand it, it helps to improve computational cost ( as the metric is
> focusing on pixel mask).  But I might misunderstood it...
> 
> Thanks a lot
> Delphine
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