Working plan: June 2009-October 2009

The MBAT team has identified several features for delivery by October 2009 (Society for Neuro Science Annual Meeting: Oct. 17-21)). The following list are goals for the workspaces. Priorities have not yet been assigned and it is not expected that all goals will be met.

User Documentation

1. Tutorial videos
2. User Manual pdf

Saving

1. Save/cache to local file

Viewer workspace:

1. synchronized cross-hair
2. Layer controls: expand/collapse all
3. Layer controls: slider fix
4. Multi-resolution image layering (different resolutions for label image and template image).
5. Atlas coloring
   • by label (paint by number)
   • by voxel
6. Set image origin and orientation (generic mechanism which can support Waxholm Space (WHS))
   • Sept deadline?

1. Dynamic loading of multi-resolution data (eg: zoomify).
   • NT/MBL
   • CCDB

• Auto arrange (tile) viewer panes.
• Oblique view/arbitrary plane of section through an image volume.
• Image painting (segmentation)

Plugin API:

1. inter-plugin communication
   1. ABA rendering plugin
   2. GENSAT rendering plugin

Hierarchy display

1. Implement tree view.
2. Add search hierarchy (research feasibility)

• Look into other libraries, methods and layouts for graph display.

User customization:

1. "My MBAT" preferences such as:
   1. unload plugins
      1. workspaces
      2. tool plugins per workspace
   • MBAT login security
   • orientation
   • transformations
   • coordinate system

Registration workspace:

1. Rigid body alignment
   1. FLIRT

• Generic Pipeline plugin
  • Pipeline team create integrated UI to plugin MBAT workspace
  • Distribution (LONI License) concerns for Pipeline.jar
    • provide link to LONI download site

Analysis Plugin API

• ImageJ image processing evaluation

Search Workspace:

• Design but not included in Oct release

1. UMD server to XML (use ontology)
2. Query term plugin API

• Boolean logic for keyword search (and/or)

Editors:

• Atlas assembly (eg: open .ilf, label image and image data-> save .atlas file or select files to assemble to write .atlas)
• Hierarchy editor (.ilf) similar to the BrainGraph editor.

Partner Requests

• Java WebStart^? (UCSD)
• SmartAtlas^?/ArcIMS plugin (UCSD)

Working plan: October 2009 -

Viewer workspace

• Annotation tools
  • arrow/text per slice
• Analysis Tools
  • measure
  • angle
  • ROI/VOI
    • polygon selection
    • painting
    • automatic (ie: region growing)
  • ROI/VOI stats
• Coordinate axis
  • Radiological v. Neurological (MIPAV)
  • Arbirary assignment (Slicer)
• compare a VOI stat over time/data sets (ie: growth over development)
• Volume Rendering
  • with lighting

Use Cases

Create/annotate/upload

• Stage 1:
  1. Search gene
  2. Download images
  3. Discovery: any anatomical structures with same set of gene expression?
  4. annotate/re-annotate/tag image(s)
     • create a) hierarchical graphs, b) anatomical tree
     • (goal: assemble info together)
  5. link to ontology(-ies)

• Stage 2:
  1. curate the save info/annotated images
  2. compare with existing data set/experiment
  3. save results in some sort of xml format
  4. submit to another datasource (processed data)