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Center for Bioimaging Informatics BISQUIK Internals Kristian Kvilekval Center for Bioimaging Informatics BISQUIK Internals Kristian Kvilekval

Center for Bioimaging Informatics Bisque/OME lessons learned • New data sets take significant resources Center for Bioimaging Informatics Bisque/OME lessons learned • New data sets take significant resources to incorporate. – Schema, tool, and interface modifications • Changing experiments also require effort. – Per experiment metadata may also require significant changes • Building analysis should be straight forward. – Researchers balk at learning complex software – Simpler is better May 2007

Center for Bioimaging Informatics Bisque/OME Challenges • Automatic and semi-automatic analysis are needed: – Center for Bioimaging Informatics Bisque/OME Challenges • Automatic and semi-automatic analysis are needed: – Our problems are less about bulk processing – High value images may need intervention • Semi-automatic (interactive) analysis requires rich set of user tools • Google, flickr, etc have raised the bar May 2007

Center for Bioimaging Informatics Motivation: • Current metadata model is inflexible – Adding new Center for Bioimaging Informatics Motivation: • Current metadata model is inflexible – Adding new experimental images requires: • Changes to Digital notebook • Changes to Bisque interface • Changes to OME/postgres schema • Shouldn’t this be easier? – “Add my images with this experimental data” – “Find images tagged with rod-opsin and GFAP ” – “Create a region and specify an object type there” – “Try my new segmentation algorithm given …” May 2007

Center for Bioimaging Informatics New project: Bisquik • Easily support new image collections and Center for Bioimaging Informatics New project: Bisquik • Easily support new image collections and experimental data and allow rapid prototyping of new analyses – Metadata is often a (changing) list of experimental parameters – New analysis often requires DB changes • Support cross-server/lab collections/queries – Support multiple data sources and server types (OME, PSLID) • Integrate different labs metadata • Support semi-automatic analysis May 2007

Center for Bioimaging Informatics • • • Bisquik Basics Everything is a web accessible Center for Bioimaging Informatics • • • Bisquik Basics Everything is a web accessible resource Image Server (slice, thumb, etc) Data server (store, query) Module Server: Execute code Web client server (aggregate, distribute)

Center for Bioimaging Informatics Simple deployment Rich Client interface • Image/Blob Service • (Meta) Center for Bioimaging Informatics Simple deployment Rich Client interface • Image/Blob Service • (Meta) Data Service • Web Server • Module Engine IS HTML XML Web Service Image Server Data Server Module Engine RC – Rich Client WS-web server IS - Image Server DS – Data Server MS - Module Scheduler ME – Module Engine May 2007

Center for Bioimaging Informatics Scalable services IS IS IS DS WS HTML XML DS Center for Bioimaging Informatics Scalable services IS IS IS DS WS HTML XML DS XML ME ME RC – Rich Client WS-web server IS - Image Server DS – Data Server MS - Module Scheduler ME – Module Engine May 2007 ME

Center for Bioimaging Informatics Scalable/distributed deployment • Component services – Image/Blob Server • Manipulations Center for Bioimaging Informatics Scalable/distributed deployment • Component services – Image/Blob Server • Manipulations (slice, format, etc) – Data Service (query, storage) – Module Engine (Analysis Executions) – Web Service (browser, aggregation support) May 2007

Center for Bioimaging Informatics Remote services IS OMEIS WS OME/DS HTML XML PSLID/DS XML Center for Bioimaging Informatics Remote services IS OMEIS WS OME/DS HTML XML PSLID/DS XML DS RC – Rich Client WS-web server IS - Image Server DS – Data Server MS - Module Scheduler ME – Module Engine May 2007

Center for Bioimaging Informatics Remote Access • All basic services are web accessible: – Center for Bioimaging Informatics Remote Access • All basic services are web accessible: – RESTful (simple web model, caching, auth, etc) – Dough. DB, Image server, Module engines • Cluster Database support – Image collections are split across machines – Unified view – Query engine distributes and resolves • Already supports access to ‘foreign’ data sources: – multiple BISQUE/PSLID/OME sources May 2007

Center for Bioimaging Informatics Service Examples • http: //host/images <response> <image uri=“/images/1/” imgurl=“/imgsrv/2” /> Center for Bioimaging Informatics Service Examples • http: //host/images • http: //host/images/1? view=full May 2007

Center for Bioimaging Informatics Service Examples • GET http: //host/modules/1? view=full <response> <module uri=“/modules/1/” Center for Bioimaging Informatics Service Examples • GET http: //host/modules/1? view=full • POST http: //host/modules/1 • May 2007

Center for Bioimaging Informatics Programming Toolkit • Goal: Allow vision researcher to easily test Center for Bioimaging Informatics Programming Toolkit • Goal: Allow vision researcher to easily test and incorporate new analysis • Image/Object/Tag query/creation • Implemented as web services – Resources exposed through web interfaces – Libraries provided for python, matlab access • Support for data provenance • Module execution from any environment May 2007

Center for Bioimaging Informatics Programming Toolkit • get. Image. List(url, from=0, count=-1) – Return Center for Bioimaging Informatics Programming Toolkit • get. Image. List(url, from=0, count=-1) – Return a list of images availabe • get. Image. Data(url) – Return image info (x, y, z, t) • get. Image. Tags(url) – Get a list tags xml document • get. Tag. Value(url) – Get list of values based on the url • add. Tag(url, tag, val, type) – Tag an object with a value • put. Image(server) – Save an image on the server • query. Images(url, querystring) – Return list of images based on tag query May 2007

Center for Bioimaging Informatics Components Web Services Metadata Annotation Query Web UI May 2007 Center for Bioimaging Informatics Components Web Services Metadata Annotation Query Web UI May 2007 Analysis Blob/Image Server Flexible Database Remote Data Proxy Analysis Engine

Center for Bioimaging Informatics Flexible Metadata • Support rapid addition of new datasets including Center for Bioimaging Informatics Flexible Metadata • Support rapid addition of new datasets including experimental metadata • Support new experimental protocols • Allow analysis to create new metadata structures without a lot of work • Extendible list of tagged values seems to be simplest model May 2007

Center for Bioimaging Informatics Bisquik: Dough. DB OID 4 OID 1 Name GH 1020 Center for Bioimaging Informatics Bisquik: Dough. DB OID 4 OID 1 Name GH 1020 Foo 2 pixels image OID 1 Feature f 1 […] [OID 2 OID 3] OID 2 image data Server: //… Pixel-type May 2007 OID 1 raw

Center for Bioimaging Informatics Dough. DB requirements • Add new tag/value pairs to any Center for Bioimaging Informatics Dough. DB requirements • Add new tag/value pairs to any db object – (Foo, 2) – (visible-cell, rod) • Allow multiple tags with same value – (visible-cell, rod) – (visible-cell, muller) • Support fine-grained tag permission/visibility – Tags have creators and access control • Support update semantics & preserve history – Timestamp tags – No deletes (except under restricted conditions) May 2007

Center for Bioimaging Informatics Dough. DB key features • Open ended data model – Center for Bioimaging Informatics Dough. DB key features • Open ended data model – tag/value pairs – Templates for common sets • • Pair values have ts, owner, acl Preserves history of annotations SQL like query language Simple keyword queries – Antibody: rod-opsin AND antibody: gfap – Rod-opsin AND glial fibrillary acid protein May 2007

Center for Bioimaging Informatics Dough. DB Implementation • Taggable super type – Ts, mex, Center for Bioimaging Informatics Dough. DB Implementation • Taggable super type – Ts, mex, user, perm • Derive Image, module, user, etc – Each has local fields but is also ‘taggable’ • Tag – Parent (taggable), name, type, indx • Value – FK tag, index PK, str, num, object – Or graphical point

Center for Bioimaging Informatics Dough. DB Implementation • Tags for image 1 – Select Center for Bioimaging Informatics Dough. DB Implementation • Tags for image 1 – Select * from tags where parent=1 • Images where some tag has value= retinal* – Select * from images as i, tags as t , values as v where t. parent = i. id, and t. id = v. id and v. str like ‘retinal%’

Center for Bioimaging Informatics Dough. DB Implementation • Gobject : Extensible graphical objects • Center for Bioimaging Informatics Dough. DB Implementation • Gobject : Extensible graphical objects • Examples : mt_track – polyline in time and origin • > …

Center for Bioimaging Informatics Bisquik ontology support • Unstructured tag/value – Great for taggers Center for Bioimaging Informatics Bisquik ontology support • Unstructured tag/value – Great for taggers – Unhappy searchers • Different labs use different terms for the same object. • Permit soft schema integration based on conceptual map (project here) May 2007

Center for Bioimaging Informatics Bisquik ontology support • Dictionary of terms and relations • Center for Bioimaging Informatics Bisquik ontology support • Dictionary of terms and relations • Require (or strongly suggest) that tags and value are defined before use • Drop into ontology editor when new values and tags are encountered. • Integrated into search system – Permit (or offer) ‘alias’ ‘part-of’ ‘related-to’ searches May 2007

Center for Bioimaging Informatics Module Scheduler/Engine • Track free computational resources • Execution engine Center for Bioimaging Informatics Module Scheduler/Engine • Track free computational resources • Execution engine – Schedule executions on module engines – Automatic component placement • Permit development outside cluster environment • Permit scalable deployment inside cluster environment May 2007

Center for Bioimaging Informatics Bisquik interface • Current Bisque functionality – Browse/Organize/Analyze • Supports Center for Bioimaging Informatics Bisquik interface • Current Bisque functionality – Browse/Organize/Analyze • Supports 5 D images • Flickr-like interface for image/region tagging • Complex region definition and tagging May 2007

Center for Bioimaging Informatics May 2007 Simple annotation Center for Bioimaging Informatics May 2007 Simple annotation

Center for Bioimaging Informatics May 2007 Region annotation Center for Bioimaging Informatics May 2007 Region annotation

Center for Bioimaging Informatics May 2007 Search (metadata) Center for Bioimaging Informatics May 2007 Search (metadata)

Center for Bioimaging Informatics May 2007 Segmentation Analysis Center for Bioimaging Informatics May 2007 Segmentation Analysis

Center for Bioimaging Informatics May 2007 Local and remote access Center for Bioimaging Informatics May 2007 Local and remote access

Center for Bioimaging Informatics Bisquik Metadata Annotation • Unified offline (Digital Notebook) and online Center for Bioimaging Informatics Bisquik Metadata Annotation • Unified offline (Digital Notebook) and online manipulation. • Easy to build annotation forms/templates • Allow “schema” modification “in field” • Permit annotation templates to be shared between DN and Bisquik • Graphical geometry annotator May 2007

Center for Bioimaging Informatics Blob+Image server • Extensible server for read-only objects – Pixels Center for Bioimaging Informatics Blob+Image server • Extensible server for read-only objects – Pixels – Features • Pluggable transforms – Thumbnails, slices – pixel transforms (watermarks) – Graphical metadata renderers • Feature server May 2007

Center for Bioimaging Informatics Bisquik Status: • Web UI – Uploading, Tagging, simple searches Center for Bioimaging Informatics Bisquik Status: • Web UI – Uploading, Tagging, simple searches – Demo at http: //biodev. ece. ucsb. edu: 8080/bisquik • Dough. DB – Prototype based on SQL/Berkely. DB – Multi node storage aggregation and queries • Analysis – Layer segmentation (Lucca, Nhat/Pratim) – Cell Counting • In Development – Ontology support, advanced query/indexing May 2007

Center for Bioimaging Informatics Bisquik: Initial impressions • Focus : Ease of Use – Center for Bioimaging Informatics Bisquik: Initial impressions • Focus : Ease of Use – For biologists: simple data model, easy searching – For analysis developers: develop in comfortable environment • Web UI – Tools developed for semi-automatic analysis • Dough. DB – Performance needs to be tested on large sets • ** Analysis ** – < 1 day for researcher to use tool kit – ~1 day for interface improvements • Development – Rapid development tools – Agile language and methods (python) – Lots of progress in little time (march 15 -Now) May 2007

Center for Bioimaging Informatics Conclusion/Vision • Prototype data model and analysis in Bisquik • Center for Bioimaging Informatics Conclusion/Vision • Prototype data model and analysis in Bisquik • Use data and analysis from multiple sources • Migrate to backend systems (OME/PSLID) as needed May 2007

Center for Bioimaging Informatics Bisquik plans • Release 0. 1 : April 2007 – Center for Bioimaging Informatics Bisquik plans • Release 0. 1 : April 2007 – – Bisquik Tagging + Dough. DB Bisque/OME Bridge (image + metadata) Simple queries (antibody: vimentin and ‘cross section’) Blob server • Release 0. 2 : May 2007 – Web + DN Metadata annotations (text, graphical) – Distributed queries – Several analyses (retinal segmentation, MT) • Release 0. 3 : June 2007 – – – Access to ‘foreign’ analysis BISQUE/PSLID Segmentation Test bed. Digital Notebook integration Full Permission system UCSB deployment • Release 0. 4 : July 2007 – Analysis engine scheduling + performance tests – Other analysis from local researchers (MT body) May 2007

Center for Bioimaging Informatics Bisquik plan • Release 0. 5 : August 2007 – Center for Bioimaging Informatics Bisquik plan • Release 0. 5 : August 2007 – Ontology support (Dough. DB + UI + query support) – Remote deployments (Utah? ) • Release 0. 6 : September 2007 – Integration of distributed information – Unification with existing databases. – Biological Mashup design • Release 0. 7 : October 2007 – Ontology Inference engine – Other analysis from local researchers • Release 0. 8 : November 2007 – Automated hardening of schema – Possible move to column-store in-core db. – Mashup demo • Release 1. 0 : December 2007 – Website, polishing May 2007

Center for Bioimaging Informatics Bisquik project areas – Flexible database schemas • Organization and Center for Bioimaging Informatics Bisquik project areas – Flexible database schemas • Organization and Querying of soft–schema databases • Hardening (template detection) – Analysis and visualization development • Evaluation test beds (segmentation, etc) • Rich data immersion – UI Enhancements • Semi-automated (interactive) analysis • Data exploration • Visualization integration – Distributed computation • Cluster based computation system • External resources (Amazon EC 3, grid) – Ontology support and schema integration • Programmatic maintenance and query • Integrating soft schemas – Biological Data integration • Combining data (XML) resources • Building web-based biological services – Dataset modeling and Ontology development • Building new datasets and ontologies May 2007