Download Atlasstatus11_05

MBAT Status as of 11/17/2005
I. WORKSPACE DEVELOPMENT
A. Viewing: Visualization/gross comparisons of atlases or data
1. Goals:
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Access a free brain atlas to learn about brain anatomy (offering MRI,
Compare different methods of visualizing brain structure, e.g., Nissl, MRI, DTI imaging
View and manipulate individual 2D images or 3D volumes, e.g., reslice
View and compare different types of data that is spatially registered to the atlas
2. Currently available:
Images:
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DT MRI volume (fairly low resolution)
Access to CCDB high resolution volumes that are registered to the Paxinos plates
(currently 6 volumes), includes information about the image (including web-link) and
SRB download
Atlases:
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Segmentations of MRI volume based on Paxinos (30 structures)
Segmentations of MRI volume based on Swanson (31 structures), includes a hierarchy,
and direct connection to BAMS
3D surfaces (71 structures) based on Swanson delineations (access from computer)
Contours created from these surfaces (access from computer or web)
3. To do:
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Offer higher resolution MRI volume(s) (option to download or access over server)
Drexel: Offer Drexel Nissl + delineations (currently ~70 structures)
Drexel: Ability to navigate multiple volumes simultaneously (i.e. one atlas, one new
image)
UCLA: Offer ALL spatially registered common specimen images
UCSD: Offer surfaces (and contours?) from Maryann based on common specimen study,
registered to Duke MRI
UCLA: Improve the interface for viewing data in PIC format, includes both better
resolution and automatically able to find best plane to view cell
UCLA: Link ontology viewer, label tool and labels on image
UCLA/UCSD: Improve registration of Paxinos space to 3D MRI volume
UCLA-All: Offer the ability to get more information about images, i.e. acquision
parameters, staining, etc. (perhaps this would come from an associated XML file?)
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MBAT Status as of 11/17/2005
B. Query and interface:
1. Goals:
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Use the brain atlas interface to retrieve data indexed to a particular location
Use the brain atlas interface to examine patterns of gene expression
Retrieve data linked to spatial location or ontology:
o Higher resolution images (i.e. EM, other microscopy)
o Images with additional information than spatial (i.e. gene expression)
o Publications on that area (perhaps with the ability to combine with genes
expressed there, or with disease model, etc.)
o Other text based information (i.e. BAMS etc)
2. Currently available:
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Spatial query of EM/Cell data available to public from CCDB
Limited search of WebQTL based on gene of interest
BAMS connection
Ontology viewer linked to appropriate label file
3. To do:
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Redesign the interface for spatial query of available EM/Cell data (how do we handle
more images and types?)
UCLA: Link ontology viewer to querying tools
Add color map for expression level to current WebQTL search return
Revise the output of spatial information for WebQTL search return
Expand query ability for gene or protein expression patterns (query based on specific
gene or protein, spatial, region, structure, expression level) (i.e. like SmartAtlas,
and EMAGE/EMAP)
o Microarray
o In situ hybridization tissues
Add query that shows the user what data is available for them to examine or download
UCLA: Add query that gives results of relevant literature from Pubmed
UCLA: Check BAMS cell search option, is it working properly?
C. Processing, analysis and quantification:
1. Goals:
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Offer tools to measure signal intensities
Offer tools to delineate anyone’s own images
Offer tools for volumetric comparisons between chosen images, atlases, or populations
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MBAT Status as of 11/17/2005
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Offer tools for measuring certain parts of images (i.e. volumes, distances, thicknesses,
etc)
Offer tools for statistical comparisons or output to a file that can be used in other
programs
2. Currently available:
None in MBAT
3. To do:
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UCLA: Integrate tools for delineation (from SHIVA)
UCLA: Integrate tools for measuring volumes (from SHIVA)
UCSD/UCLA: Integrate tools for measuring signal intensities (SmartAtlas?)
Add tools for measuring distances, thicknesses, etc.
Add tools for statistical comparison or output of information to file
D. Integration of registration tools:
1. Goals:
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Intuitive registration tools for 2D images to 3D space (MBL registration by Drexel,
generalize to other data? Jibber for manual 2D registration to Paxinos plate)
Intuitive registration tools to generate 3D volumes from 2D slices (Drexel and LONI
registration, both use AIR?)
Intuitive registration tools for 3D MRI and histological volumes to 3D space (LONI
registration, AIR tools and others?)
Allow the user to spatially reference microarray, physiological, biochemical, etc.
information (UCSD registers cells using stereotaxic coordinates using Paxinos
framework? UTHSC microarray information can be mapped to structure. Others?)
2. Currently available:
None in MBAT (although WebQTL microarray gene expression information is mapped to
structure)
3. To do:
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Evaluate currently available registration tools for each method
Determine feasibility and potential design of creating workflows for each method
Determine order of implementation
Implement methods
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MBAT Status as of 11/17/2005
E. Contribute data:
1. Goals:
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Implement tools for people to easily add their data to the mouse BIRN infrastructure,
including:
o Registration of data to common space
o Upload to database so it is traceable and transparent to anyone else (i.e.
hierarchy/XML file)
o Adding appropriate metadata
2. Currently available:
None in MBAT, although it is possible to open many of the image types using this viewer
3. To do:
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Implement registration methods
Determine information needed to add data types to database
Establish mouse BIRN protocols for how to handle data upload to database
Create tools to make this process as simple as possible for a user for each data type
Access to an ontology editor?
Add ability to save modified file both locally and to remote database
F. Anatomical forum: Compare and debate
The Anatomical Forum will allow users to compare different views of brain anatomy, using both
conceptual and spatial frameworks. For example, the concept browsers from Brain Info and
BAMS allow users to view alternate nomenclatures for anatomical structures. The goal is to
allow users to explore these alternate views within the spatial context of the atlas browsers.
II. DATA:
The goal is for many different types of data to be available through this infrastructure. The
specific items need to be addressed in order to facilitate this goal.
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For all data that is added to the mouse BIRN, how do we manage quality control?
For all high resolution images, what is necessary to serve images remotely will be
examined as well as options for not having to use the network for a specific image.
A better system for examining different scales of information needs to be implemented
Protocols for uploading data need to be established: includes SRB hierarchy, conceptual
global schema, and XML data file
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MBAT Status as of 11/17/2005
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Atlases:
o How do we differentiate so the user can choose what works best for them?
o What are the most useful ways to view multiple atlases?
o Specific atlases offered for sharing:
 Drexel Nissl C57BL/6J
 MBL C57BL/6J
 UCSD structures (and conversions to contours) delineated from Duke scan
of common specimen
Whole brain volumes
o Do we have the ability to allow view both a large file locally and a remote
volume?
o Data sets offered for sharing:
 Set up a tag or protocol for identifying data sets on SRB that people are
willing to share
 Duke has offered to share some data
 Drexel Nissl C57BL/6J (goes with atlas)
 Susumu Mori: Diffusion tensor images of embryonic and postnatal brains.
Somewhat different format, and outside group, how do we share these?
High resolution slice volumes
o We can’t seem to read these at the moment
o Data offered for sharing:
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High resolution cell volumes
o MBAT needs to improve the visualization of this sort of data, there are resolution
issues, and it needs to be able to find maximum intensity projection.
o Data offered for sharing:
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Gene expression data
o How do we wish to proceed with different types of information?
o Data offered for sharing:
 Data from Desmond Smith
 Zapala/Bloom/Barlow Affymetrix data
III. USABILITY:
General use issues that need to be addressed or made better
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Way to proceed with interoperability between atlasing efforts
Improve zooming capabilities
Make easier volume management, examine issue of “bundling” files, or other file format
o Label files, brain graphs
Would it be better if the different workspaces be different applications?
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