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Registration Workflows

Registration Workflows. D-09. Workflow steps. 2. 3. Interpolation. 4. Packaging and downsampling. Alignment. 1. Segmentation. 5. Validation. 3D reconstruction. nifti. Atlas hub. iRODS. Hub-in a-box. 6. 11. M asking, validation. Compute cluster. Atlas service update. 10. 7.

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Registration Workflows

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  1. Registration Workflows D-09

  2. Workflow steps 2 3 Interpolation 4 Packaging anddownsampling Alignment 1 Segmentation 5 Validation 3D reconstruction nifti Atlas hub iRODS Hub-ina-box 6 11 Masking, validation Computecluster Atlas serviceupdate 10 7 Lookup, forward and inverse 9 ListSRSs Alignment to WHS(affine) DescribeSRS 8 Computation, mesh generation ListTransformation Fine registration TransformPOI Warped Dataset

  3. ITK scripts for steps 5,7,8 https://github.com/INCF/ImageRegistration/tree/master/Scripts • SimpleImageReconstruction.sh • RoughVolumetricRegistration.sh • WarpReferenceAfterRoughVolumetricRegistration.sh

  4. 2 Segmenting and packaging for processing 5 Visualize in WIB 1 Warping, computingtransformations Registeringbased on landmarks, using Jibber 3 Setting up in DAI 6 Atlas Service Update: new SRS: BrainStem, new transformations(from and to BrainStem SRS): ListSRSs, DescribeSRS ListTransformations TransformPOI iRODS 4 Computecluster – Jetsam Transformation Matrix

  5. Computed Transformations From BrainStem to ABA Reference: http://tirebiter.ucsd.edu/cgi-bin/brainstem_transform.pl?inputsrsname=Mouse_BrainStem_1.0&outputsrsname=Mouse_ABAreference_1.0&x=1.1&y=0&z=0 From ABAReference to BrainStem http://tirebiter.ucsd.edu/cgi-bin/brainstem_transform.pl?outputsrsname=Mouse_BrainStem_1.0&inputsrsname=Mouse_ABAreference_1.0&x=1.1&y=0&z=0

  6. Atlas Services D-10

  7. Links • Portal: http://incf-dev-local.crbs.ucsd.edu/incfportal/ • Wiki: http://code.google.com/p/incf-dai/ • Specification, WaxML schema and examples, services and sample calls • INCF Atlasing: http://www.incf.org/programs/atlasing • WPS: http://en.wikipedia.org/wiki/Web_Processing_Service • Deegree WPS: http://wiki.deegree.org/deegreeWiki/deegree3/ProcessingService

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