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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. - PowerPoint PPT Presentation
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Registration Workflows
D-09
Workflow steps
iRODS
1Segmentation
2Packaging anddownsampling
3Alignment 4 Interpolation
53D reconstruction
7Alignment to WHS(affine)8
Fine registration
9
Computation,mesh generation
6Masking, validation
10
Lookup, forward and inverse
11
Atlas serviceupdate
Validation
Computecluster
Atlas hub
Hub-ina-box
nifti
ListTransformationTransformPOIWarped Dataset
DescribeSRSListSRSs
ITK scripts for steps 5,7,8
https://github.com/INCF/ImageRegistration/tree/master/Scripts• SimpleImageReconstruction.sh• RoughVolumetricRegistration.sh• WarpReferenceAfterRoughVolumetricRegistra
tion.sh
2
3
5
Atlas Service Update: new SRS: BrainStem,new transformations (from and to BrainStem SRS):ListSRSs, DescribeSRS ListTransformationsTransformPOI
6
Registeringbased on landmarks, using Jibber
Warping, computing
transformations
Visualize in WIB
Setting up in DAI
Transformation
Matrix
Segmenting and packaging for processing
1
Computecluster – Jetsam
4
iRODS
Computed TransformationsFrom 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
Atlas Services
D-10
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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