[Insight-users] histology stack registration

[Isaiah Norton]

Hi Dan,
That's very helpful, especially the paper link.. Thank you!
-Isaiah

On Fri, Jul 1, 2011 at 2:42 AM, Dan Mueller <dan.muel at gmail.com> wrote:

> Hi Isaiah,
>
> I have used elastix for histology stack registration:
>    http://elastix.isi.uu.nl/
> It does not support this "out-of-the-box", but it has all the required
> components which you can assemble with as simple control program
> calling the elastix executable.
>
> In theory, ITK also has all required components, but you must have a
> good knowledge of C++ (or one of the wrapped languages e.g. python).
>
> The general approach I recommend is as follows:
>
> (1) downsample all images
> (I use a similar size to you, namely 2K x 2K images)
>
> (2) choose a fixed image
> (I would suggest either the first slice or somewhere in the middle of the
> stack)
>
> (3) for each image next to the previously aligned slice
>
>    (a) set the initial transform to the transform of the previously
> aligned slice
>         if the previously aligned slice is the fixed image, use the
> identity transform
>
>    (b) execute the registration
>
>    (c) apply the resultant transform to this slice,
>         remember the transform when aligning the next slice,
>         write the transform to disk
>
>    (d) repeat until no more slices
>
> (at this point you have a transform per image)
> (4) apply the corresponding transform to each high-resolution image
> (you will need to employ either streaming (not sure if this is works),
> or use a x64 machine with lots of RAM)
>
> I should point out that I have never done step 4, as I always apply
> the transform on-the-fly when viewing, see here:
>     http://dx.doi.org/10.1016/j.compmedimag.2011.06.006
>
> For step 3b I used an elastix parameters file similar to below:
> (FixedInternalImagePixelType "float")and Paraview also ship
> (MovingInternalImagePixelType "float")
> (FixedImageDimension 2)
> (MovingImageDimension 2)
> (UseDirectionCosines "false")
> (HowToCombineTransforms "Compose")
> (DefaultPixelValue 0.0)
> (WriteResultImage "true")
> (ResultImagePixelType "float")
> (ResultImageFormat "mha")
> (Resampler "DefaultResampler")
> (FixedImagePyramid "FixedSmoothingImagePyramid")
> (MovingImagePyramid "MovingSmoothingImagePyramid")
> (NumberOfResolutions 5)
> (Registration "MultiMetricMultiResolutionRegistration")
> (Transform "BSplineTransform")
> (AutomaticScalesEstimation "true")
> (AutomaticTransformInitialization "true")
> (FinalGridSpacingInVoxels 8)
> (Metric "NormalizedCorrelation" "TransformRigidityPenalty")
> (Optimizer "AdaptiveStochasticGradientDescent")
> (MaximumNumberOfIterations 400)
> (Interpolator "Linear")
> (ResampleInterpolator "FinalLinear")
> (ImageSampler "Random")
>
> Good luck!
>
> Regards,
>
> Dan Mueller
> Senior Software Designer, Ph.D.
> Philips Digital Pathology, Healthcare Incubator
> Email: dan[dot]mueller[at]philips[dot]com
> Web: http://www.philips.com/digitalpathology
>
> On 29 June 2011 21:13, Isaiah Norton <isaiah.norton at gmail.com> wrote:
> > Hi,
> >
> > I'm looking for a tool to co-register a stack of microscope histology
> > sections to create a 3D volume. Sections are sliced roughly parallel,
> taken
> > in pairs with a 10 micron gap, followed by ~70-100 micron gap between
> each
> > pair, and H&E stained. The raw images are  ~28k*28k pixels and ~150mb but
> I
> > have down-sample to roughly 2500*2500 for the registration step.
> >
> > I've tried the register_pair/list tool in Farsight Toolkit but it threw
> some
> > itk memory exceptions, and in any case it seems geared to build adjacency
> > mosaics rather than z-stacks. Also looked at GoFigure2 and V3D but didn't
> > see this functionality in the release builds (apologies if I missed
> > something, please let me know).
> >
> > I noticed this discussion a while back:
> >
> http://itk-insight-users.2283740.n2.nabble.com/Constructing-3D-stack-from-2D-image-series-with-registration-td3832165.html
> >
> > Is this idea implemented anywhere now? I'd appreciate any suggestions,
> and
> > am happy to build from source...
> >
> > Thanks,
> > -Isaiah
>
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