[Insight-users] histology stack registration

[Isaiah Norton]

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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