Things done in the name of science…. (and the even greater things to be done)

Accomplishments (1/3) NetOStat Client –Now available in 3 forms, a Webstart application, a standalone application, and a SDK. –Includes the BIRN atlas interoperability API (XML streaming-AJAX like capabilities). –Navigation through atlas (voxel map and VOIs) robust on MacOS and Linux. Windows soon. –Co-navigation with aligned 2D dataset (to be demonstrated tomorrow). –Lots and lots of nice features…. NeuroTerrain Server –Support the BIRN atlas interoperability API (XML streaming-AJAX like capabilities). –Robust scalable architecture to support multiple simultaneous sessions on single or multiple 3D datasets. –Multiresolutional support nearly complete.

Accomplishments (2/3) Macrovoxelizer –Reslice on client side nearly complete. –Submission of resliced sections along with ROI masks allows conversion into macrovoxel format and generation of VOIs. –GluClose (macrovoxel builder) now supports incremental builds and can except any binary TIFF files. Instructions will be posted on Wiki Registration –Atlas as 2D sequence now available in TIFF format. –Lots of new stuff on registration. Automated coarse and fine alignment with subsequent atlas-driven segmentation (to be demonstrated this afternoon). Surface smoothing –Collaboration with David Breen has yielded surface smoothing –Transmogifier concept, though, not working.

Accomplishments (3/3) Publications –Gefen S., Bertrand L., Kiryati N, Nissanov J Localization of sections within the brain via 2D to 3D image registration. IEEE Proceedings Acoustics, Speech, and Signal Processing, : –Gefen S., Kiryati N., Nissanov, J. Submitted. Level-set-based image to surface alignment. IEEE Trans Image Process –Braude, I., Marker, J., Museth, K., Nissanov, J., Breen, D. Submitted. Contour- based surface reconsdtruction using MPU implicit models. Graph Models –Gustafson, C., Bug, W., Nissanov, J. Submitted. NeuroTerrain-a client-server system for browsing 3D biomedical image data sets. BMC Bioinformatics –Bug, W., Gustafson, C., Shahar, A., Gefen, S., Fan, Y., Bertrand, L., Nissanov, J. Brain spatial normalization: indexing neuroanatomical databases In: Neuroinformatics (C. Crasto, ed). Humana Press. –Gefen, N. Kiryati, L. Bertrand, and Nissanov, J. In Press. Planar-to-curved-surface image registration. Mathematical Methods in Biomedical Image Analysis (MMBIA), New-York City, –SFN BIRN abstracts (3).

Goals Workflow Framework: Adapt pipeline to utilize BIRN-CC Cluster and open pipeline to the BIRNcommunity to use in 2D-3D and 3D-3D alignment. Incorporate Web-based submission (Spring 2007). NeuroTerrain QC Client: QC client allows rapid examination and correction of 2D datasets particularly prior to alignment. Distribution with additional support for access of images on SRB(Spring 2007). Incorporation of atlas and netOStat into MBAT (our end ready now, and we are ready to assist MBAT programmers. Web service access to Drexel image repository-MBL plus whatever else we align (Winter 07). Speed up of atlas navigation(Summer 06)-Two options: –Install Atlas server in UCSD. –Get our server on Internet 2 at Drexel. Incorporate “BIRN enhanced Neuronames” to ID VOIs (Winter 06). Developmental atlas (ongoing) Continued participation in working groups ( BONFIRE Extension, BIRN Ontology Task Force, Mouse BIRN Global Schema