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