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DarenLee - 14 Jan 2009
Spring 2009 AHM Deliverables (May 21, 2009)
This document lists the deliverables for each institution to be delivered by the Spring MouseBIRN AHM Meeting on May 21, 2009. CalTech: AIR workflow
Goal
- develop MBAT registration plugin to execute CalTech AIR workflows
Requirements Specification
- select and preview multiple input data
- launch LONI Pipeline registration workflows from MBAT registration workspace
- view and save multiple results
Technical Specification
- implement as mbRegistration workspace plugin
- using Pipeline Java client, invoke LONI pipeline through command line, connecting to LONI pipeline server remotely
- need way to display preview images of multiple input data in registration workspace
CalTech: Electronic Lab Notebook
Goal
- develop MBAT search plugin to access Electronic Lab Notebook (ELN) database
Requirements Specification
- keyword search of ELN database
- view Nifti compressed data
Technical Specification
- implement as mbDataSource plugin
MBAT core Open Issues
- mbViewer: open compressed Nifti files
- mbSearch: Image3D annotated object definition
- mbSecurity: specify credentials
UCSD: AIDB plugin
Goal
- develop MBAT search plugin to access Animal Imaging Database (AIDB) database
Requirements Specification
- keyword search of AIDB database
- query term search of AIDB database
- view 3D volume data
Technical Specification
- implement as mbDataSource plugin
MBAT core Open Issues
- mbSearch: Image3D annotated object definition
- mbViewer: specify returned 3D image format (Analyze/Nifti/etc)
UT
Goal
- develop MBAT search plugin to access GeneNetwork (GN) database
Requirements Specification
- keyword search of GN database
- query term search of GN database
- return gene expression and classical phenotype datasets
Technical Specification
- implement as mbDataSource plugin
- returned results include multiple datasets
- return statistics diagram as a thumbnail image in the phenotype dataset result
MBAT core Open Issues
- mbSearch: add additional annotated objects for new data sets(mbPhenotype, mbProtein??, mbMRI??)
- mbSearchPlugin: Support other datasets (after May AHM): MRI dataset, protein dataset
- mbViewer: (after May AHM) develop plugin to view gene/gene expression data/phenotype data/protein data painting on an atlas
- mbViewer: map the GeneNetwork anatomical structures to the common atlas used in MBAT (e.g. Allen's atlas, ABA atlas)
Duke CIVM
Goal
- develop MBAT rendering plugin to load and display large data sets that do not fit in system memory with atlasing features
Requirements Specification
- view and navigate CIVM MR data in the MBAT comparison viewer workspace at full resolution
- load data from local files
- load data from network
- view 3 orthogonal planes
- view and navigate CIVM atlas with MR data
- write CIVM anatomical hierarchies in MBAT hierarchy format (OWL,ILF,BGX)
- view CIVM anatomical labels
Technical Specification
- implement as mbViewer plugin
- inherit from JLayerImage3DLabelled from mbViewer API (gets you for free):
- atlas labelling (requires 3D MR volume, 3D label volume, hierarchy file)
- hierarchy viewer - image viewer linkage
- need to customize update of image data
- inherit GUI controls from JLayerImage3DGUI
- Orthogonal plane controls (ie: navigate in plane and switch to another plane)
MBAT core Open Issues
- mbViewer: Coordinate system (stereotaxic?)
- mbViewer: Standardize image axes
- mbViewer: Customized dlLayerGUI necessary?
- what other GUI controls are needed?
Drexel
Goal
- develop MBAT rendering plugin to display data from NeuroTerrain (NT) server
Requirements Specification
- view and navigate Macro-voxel data in MBAT comparison viewer workspace at full resolution
- load data from NT server
- arbitrary slice plane
- view and navigate Drexel NT atlas
- write NT anatomical hierarchies in MBAT hierarchy format (OWL,ILF,BGX)
- view NT anatomical labels
Technical Specification
- implement as mbViewer plugin
- inherit from JLayerImage3DLabelled from mbViewer API (gets you for free):
- atlas labelling (requires 3D MR volume, 3D label volume, hierarchy file)
- hierarchy viewer - image viewer linkage
- need to customize update of image data (ie: stream from NT)
- customize GUI control:
- add controls to specify arbitrary slice plane
MBAT core Open Issues
- mbViewer: Coordinate system (stereotaxic?)
- mbViewer: Standardize image axes
UCLA LONI
Goal
- develop robust and flexible bioinformatics and atlasing framework that is scalable and extensible via plugins
- supply core functionality that can be customized by end users
Requirements Specification
- Complete Viewer API (Nov 2008 - Jan 2009)
- mbManagerIO (ImageJ)
- Image Manipulation
- Brightness, Contrast, LUT
- Rendering plugin API
- handle 2D images, 3D images of arbitrary/limitless size
- Atlas Painting API
- Atlas rendering plugins
- Load .atlas files
- Interactive label picking
- Planar views
- mbManagerIO (ImageJ)
- Hierarchy Viewer (Nov 2008-Feb 2009)
- Linked with atlas
- Multiple instances -> multiple atlases
- Multiple ancestors
- Literature Search (Nov 2008 - Feb 2009)
- pop up browser with publication results (ie: Google scholar, PubMed?, etc)
- Linked to atlas
- Integration (Mar 2009 – Apr 2009)
- Comparison Viewer + Hierarchy Viewer
- Hierarchy Viewer + Literature search
- Upload workspace API (Nov 2008 - Dec 2008)
- Web browser based
- Security API (Feb 2009 – Mar 2009)
- Database credentials
- Saving work API (Feb 2009 – Apr 2009)
- working image to file
- cart contents
- viewer workspace state
- analysis results
- Analysis plugin API (TBD?)
- user defined ROI
- apply analysis plugin to selected image or ROI
Technical Specification
- mbManagerIO: use ImageJ file I/O plugin architecture
- mbViewer: use ImageJ analysis plugin architecture for analysis plugins
MBAT core Open Issues
DarenLee - 14 Jan 2009