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Overview
This workgroup has been formed to tackle creating a neuroinformatics framework using multimodal digital atlases to coordinate access to disparate forms of data and present them in a clear and concise manner. These atlases can be built to encompass many different kinds of data, enabling visualization, data analyses, and information retrieval in a relatively intuitive setting.
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Other important information and links
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- Download beta version of the Mouse BIRN Atlasing Toolkit (MBAT) (11/18/05)
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- This program can be found on the BIRN Portal at /home/Public/MouseBIRN_Publicdata/MBAT. It is offered as a .zip package, a .tgz package, or simply download the whole MBAT program folder.
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- This program can be found on the BIRN Portal on the MBAT download page. It is offered as a .zip package, a .tgz package, or simply download the whole MBAT program folder.
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Overview
This workgroup has been formed to tackle creating a neuroinformatics framework using multimodal digital atlases to coordinate access to disparate forms of data and present them in a clear and concise manner. These atlases can be built to encompass many different kinds of data, enabling visualization, data analyses, and information retrieval in a relatively intuitive setting.
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| META FILEATTACHMENT | atlas_workplan_6_1_05.doc | attr="" comment="Atlasing Plan and Action items. Word doc" date="1119652103" path="atlas_workplan_6_1_05.doc" size="49664" user="jboline" version="1.1" |
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| META FILEATTACHMENT | atlas_workplan_6_1_05.pdf | attr="" comment="Atlasing Plan and Action items. pdf" date="1119652217" path="atlas_workplan_6_1_05.pdf" size="26166" user="jboline" version="1.1" |
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| META FILEATTACHMENT | AtlasIntegrationScenarios?.doc | attr="" comment="Expanded version of Atlas Integration Scenarios" date="1121128250" path="AtlasIntegrationScenarios.doc" size="45056" user="MaryannEMartone" version="1.2" |
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| META FILEATTACHMENT | MouseBrainEnvironment?.html | attr="" comment="A mouse brain study environment" date="1121371701" path="MouseBrainEnvironment.html" size="9626" user="AlexandraBadea" version="1.1" |
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| META FILEATTACHMENT | Atlasstatus11_05.doc | attr="" comment="Status of atlasing project and related issues" date="1132610853" moveby="jboline" movedto="MouseBIRN.MouseBIRNAtlasing" movedwhen="1146010749" movefrom="MouseBIRN.MouseBIRNProgress" path="Atlas status 11_05.doc" size="63488" user="jboline" version="1.1" |
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Atlas Related Working Pages
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Overview
This workgroup has been formed to tackle creating a neuroinformatics framework using multimodal digital atlases to coordinate access to disparate forms of data and present them in a clear and concise manner. These atlases can be built to encompass many different kinds of data, enabling visualization, data analyses, and information retrieval in a relatively intuitive setting.
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Atlas Planning and Action Items
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Goals
- Exchange of:
- Atlas state
- Metadata
- Data (images, segmentations, etc)
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Atlasing workshop day at the BIRN AHM (10/26/05)
Click here for notes from the meeting
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- Locations referenced via:
- Spatial coordinates
- Ontology
- Verbal descriptions
- Rat atlas as proxy (images and segmentation-scalable into mouse atlas)
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- Mechanisms of integration across atlas clients
- Specification of state of atlas client
- API for initializing exchange service and submitting and retrieving states
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Atlas Plan and Action Items generated at June 2005 mouse AHM:
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Planning
Plans and Action Items
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Atlas workgroup meetings dealing with biological aspects of atlasing
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Working Areas
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Link to Temporary Mouse BIRN Portal
http://gis.sdsc.edu/birn/
Download beta version of the Mouse BIRN Atlasing Toolkit (MBAT) (11/18/05)
This program can be found on the BIRN Portal at /home/Public/MouseBIRN_Publicdata/MBAT. It is offered as a .zip package, a .tgz package, or simply download the whole MBAT program folder.
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Other important information and links
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Use Cases
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Updates/Progress
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Atlas integration notes and task list:
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| META FILEATTACHMENT | atlas_workplan_6_1_05.pdf | attr="" comment="Atlasing Plan and Action items. pdf" date="1119652217" path="atlas_workplan_6_1_05.pdf" size="26166" user="jboline" version="1.1" |
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| META FILEATTACHMENT | AtlasIntegrationScenarios?.doc | attr="" comment="Expanded version of Atlas Integration Scenarios" date="1121128250" path="AtlasIntegrationScenarios.doc" size="45056" user="MaryannEMartone" version="1.2" |
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| META FILEATTACHMENT | MouseBrainEnvironment?.html | attr="" comment="A mouse brain study environment" date="1121371701" path="MouseBrainEnvironment.html" size="9626" user="AlexandraBadea" version="1.1" |
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| META FILEATTACHMENT | 2006_3_08_atlasingissues.doc | attr="" comment="Atlasing WG meet to discuss structure hierarchy and online collaborative atlas building" date="1141859237" path="2006_3_08_atlasing issues.doc" size="38400" user="jboline" version="1.2" |
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| META FILEATTACHMENT | Atlasstatus11_05.doc | attr="" comment="Status of atlasing project and related issues" date="1132610853" moveby="jboline" movedto="MouseBIRN.MouseBIRNAtlasing" movedwhen="1146010749" movefrom="MouseBIRN.MouseBIRNProgress" path="Atlas status 11_05.doc" size="63488" user="jboline" version="1.1" |
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Atlas workgroup meetings dealing with biological aspects of atlasing
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Link to Temporary Mouse BIRN Portal
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Atlas integration notes and task list:
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1. Exchange of state between atlases:
Things to do here:
- a) we will send the API and demos around
- b) review the API and demo communications, to see if it will fit your atlas (Willy and Joshua will help with this)
- c) review the current representation of "atlas state", to see if it is general enough
- d) formally describe spatial reference systems we use: e.g. Stereotaxic1 (used at UCLA), Stereotaxic2 (used in UCSD atlas), image1 (used at Drexel)
- e) define transformations between all coordinate systems, and some canonical stareotaxic system (either Stereotaxic1 or 2)
- f) create services for converting between the coordinate systems (though for a limited number of coordinate systems just sharing conversion code fragments would be more robust). It is straightforward for some conversions; may be pretty involved when converting from image to stereotaxic. For the latter, we need to have a couple test cases
- g) create services for format conversion: i.e. between polygons specified as coordinate pairs or triplets, and collections of pixels/voxels (Bill mentioned that they may have appropriate code at Drexel).
Now with respect to ontology - the "semantic reference system" may be handled in a similar way: i.e. when giving a name of a feature must also
specify the ontology in which it lives.
2. Ability to search registered images/volumes/segmentations available in other atlases.
- a) UCSD will send the schema of our spatial registry source
- b) we need to see how to register 3D volumes and 2D images to such or similar source (using Drexel's alignment/warping tools?), so that the metadata sources can be searched in uniform way.
3. Ability to load images / slices / segmentations into any atlas.
- a) UCSD will provide sample code for retrieving image fragments from ArcIMS
- b) UCSD will develop a web service to return feature coordinates (as polygon boundary, as well as label point) given the feature name and set of slices
- c) let's go first through a manual process of loading each other's images.
Syntax for Atlas Interoperation
http://imhotep.ucsd.edu:7873/trantj/mouse_birn/newXMLFormat.htm
Examples of Syntax and XML schemas for atlas state exchange (as of 6/28/2005)
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Defining "atlas"
- Where can you access your atlas/program?
- What coordinate system does your atlas use?
- What terminology do you use to map your data?
- What types and formats of data does your program read?
- What language is it written in and for which platforms?
- Does your program have a formal API?
UCSD
1. You can launch the SmartAtlas by Java WebStart (Java compiler
required , 1.4 or above preferred) at
http://imhotep.ucsd.edu:7873/smart_atlas_annotation/Testing.htm
2. Stereotaxic coordinate system (as in Paxinos, Franklin):
in front of/behind bregma -- ventral/dorsal to bregma -- lateral to midline
On coronal slices: the first coordinate is constant; the second coordinate increases downward, the third coordinate changes from -5 to +5, from left to right.
3. Paxinos labels, mapped where possible to UMLS concept ids and Neuronames
4. Currently reads image files(jpg, tiff,...etc) served by ArcIMS
image server and SRB. Also reads vector data (shapefiles), either from files or as binary streams served by ArcIMS feature service.
5. Java 1.4.2 for Unix and Windows
6. No formal API yet, though many elements are accessible: e.g. there is a standard language to query ArcIMS data services; access data in SRB; start the Atlas from a pre-defined state, etc.
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Drexel
Please see our entry on the MouseBIRN Tools page.
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UCLA
1) It can be downloaded from the LONI site at http://www.loni.ucla.edu/Software/Software_Detail.jsp?software_id=12., it is a stand alone application.
2) SHIVA doesn't automatically put the files into a coordinate system per se., we're working on defining the start points and such so that it will display coordinates. We are working on using the Paxinos bregma coordinate frame as a reference.
3) Theoretically it can be multiple ones but we'll focus on Paxinos and Swanson from BAMS.
4) Primarily Analyze Image, Minc, TIFF (simple), with a couple proprietary data formats (i.e. CIT, Duke). Plus there are some specific files for the atlas, including .keg (coordination file) and .lbl (label lookup table) files.
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5) Java 1.4.2 and 1.5 as well on Unix and windows.
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6) No API.
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| META FILEATTACHMENT | atlas_workplan_6_1_05.doc | attr="" comment="Atlasing Plan and Action items. Word doc" date="1119652103" path="atlas_workplan_6_1_05.doc" size="49664" user="jboline" version="1.1" |
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| META FILEATTACHMENT | atlas_workplan_6_1_05.pdf | attr="" comment="Atlasing Plan and Action items. pdf" date="1119652217" path="atlas_workplan_6_1_05.pdf" size="26166" user="jboline" version="1.1" |
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| META FILEATTACHMENT | state_init.xsd | attr="" comment="initilize" date="1119979650" path="state_init.xsd" size="808" user="jboline" version="1.1" |
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| META FILEATTACHMENT | state_submit.xsd | attr="" comment="Submit" date="1119979672" path="state_submit.xsd" size="3533" user="jboline" version="1.1" |
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| META FILEATTACHMENT | state_retrieve.xsd | attr="" comment="Retrieve" date="1119979689" path="state_retrieve.xsd" size="1055" user="jboline" version="1.1" |
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| META FILEATTACHMENT | state_end.xsd | attr="" comment="End" date="1119979703" path="state_end.xsd" size="615" user="jboline" version="1.1" |
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| META FILEATTACHMENT | AtlasIntegrationScenarios?.doc | attr="" comment="Expanded version of Atlas Integration Scenarios" date="1121128250" path="AtlasIntegrationScenarios.doc" size="45056" user="MaryannEMartone" version="1.2" |
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| META FILEATTACHMENT | state_init.xml | attr="" comment="Example atlas_state init message, version of 6/28" date="1120710217" path="C:\PROJECTS\ATLASES\Interface_integration\6_28_schemas\state_init.xml" size="292" user="IlyaZaslavsky" version="1.1" |
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| META FILEATTACHMENT | state_submit.xml | attr="" comment="Example atlas_state submit message, version of 6/28" date="1120710310" path="C:\PROJECTS\ATLASES\Interface_integration\6_28_schemas\state_submit.xml" size="3234" user="IlyaZaslavsky" version="1.1" |
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| META FILEATTACHMENT | state_retrieve.xml | attr="" comment="Example atlas_state retrieve message, version of 6/28" date="1120710356" path="C:\PROJECTS\ATLASES\Interface_integration\6_28_schemas\state_retrieve.xml" size="424" user="IlyaZaslavsky" version="1.1" |
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| META FILEATTACHMENT | state_end.xml | attr="" comment="Example atlas_state end message, version of 6/28" date="1120710390" path="C:\PROJECTS\ATLASES\Interface_integration\6_28_schemas\state_end.xml" size="266" user="IlyaZaslavsky" version="1.1" |
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| META FILEATTACHMENT | MouseBrainEnvironment?.html | attr="" comment="A mouse brain study environment" date="1121371701" path="MouseBrainEnvironment.html" size="9626" user="AlexandraBadea" version="1.1" |
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| META FILEATTACHMENT | 2006_3_08_atlasingissues.doc | attr="" comment="Atlasing WG meet to discuss structure hierarchy and online collaborative atlas building" date="1141859237" path="2006_3_08_atlasing issues.doc" size="38400" user="jboline" version="1.2" |
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Atlas Plan and Action Items generated at June 2005 mouse AHM:
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- b) we need to see how to register 3D volumes and 2D images to such or similar source (using Drexel's alignment/warping tools?), so that the metadata sources can be searched in uniform way.
3. Ability to load images / slices / segmentations into any atlas.
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- a) UCSD will provide sample code for retrieving image fragments from ArcIMS?
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- a) UCSD will provide sample code for retrieving image fragments from ArcIMS
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- b) UCSD will develop a web service to return feature coordinates (as polygon boundary, as well as label point) given the feature name and set of slices
- c) let's go first through a manual process of loading each other's images.
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UCSD
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1. You can launch the SmartAtlas? by Java WebStart? (Java compiler
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1. You can launch the SmartAtlas by Java WebStart (Java compiler
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required , 1.4 or above preferred) at
http://imhotep.ucsd.edu:7873/smart_atlas_annotation/Testing.htm
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3. Paxinos labels, mapped where possible to UMLS concept ids and Neuronames
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4. Currently reads image files(jpg, tiff,...etc) served by ArcIMS?
image server and SRB. Also reads vector data (shapefiles), either from files or as binary streams served by ArcIMS? feature service.
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4. Currently reads image files(jpg, tiff,...etc) served by ArcIMS
image server and SRB. Also reads vector data (shapefiles), either from files or as binary streams served by ArcIMS feature service.
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5. Java 1.4.2 for Unix and Windows
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6. No formal API yet, though many elements are accessible: e.g. there is a standard language to query ArcIMS? data services; access data in SRB; start the Atlas from a pre-defined state, etc.
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6. No formal API yet, though many elements are accessible: e.g. there is a standard language to query ArcIMS data services; access data in SRB; start the Atlas from a pre-defined state, etc.
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Drexel
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Please see our entry on the MouseBIRN Tools page.
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Atlas Plan and Action Items generated at June 2005 mouse AHM:
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UCLA
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1) It can be downloaded from the LONI site at http://www.loni.ucla.edu/Software/Software_Detail.jsp?software_id=12., it is a stand alone application.
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2) SHIVA doesn't automatically put the files into a coordinate system per se., we're working on defining the start points and such so that it will display coordinates. We are working on using the Paxinos bregma coordinate frame as a reference.
3) Theoretically it can be multiple ones but we'll focus on Paxinos and Swanson from BAMS.
4) Primarily Analyze Image, Minc, TIFF (simple), with a couple proprietary data formats (i.e. CIT, Duke). Plus there are some specific files for the atlas, including .keg (coordination file) and .lbl (label lookup table) files.
5) Java 1.4.2 and 1.5 as well on Unix and windows.
6) No API.
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| META FILEATTACHMENT | atlas_workplan_6_1_05.doc | attr="" comment="Atlasing Plan and Action items. Word doc" date="1119652103" path="atlas_workplan_6_1_05.doc" size="49664" user="jboline" version="1.1" |
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| META FILEATTACHMENT | atlas_workplan_6_1_05.pdf | attr="" comment="Atlasing Plan and Action items. pdf" date="1119652217" path="atlas_workplan_6_1_05.pdf" size="26166" user="jboline" version="1.1" |
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Atlas Plan and Action Items generated at June 2005 mouse AHM:
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UCLA
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| META FILEATTACHMENT | atlas_workplan_6_1_05.doc | attr="" comment="Atlasing Plan and Action items. Word doc" date="1119652103" path="atlas_workplan_6_1_05.doc" size="49664" user="jboline" version="1.1" |
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| META FILEATTACHMENT | atlas_workplan_6_1_05.pdf | attr="" comment="Atlasing Plan and Action items. pdf" date="1119652217" path="atlas_workplan_6_1_05.pdf" size="26166" user="jboline" version="1.1" |
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| META FILEATTACHMENT | state_init.xsd | attr="" comment="initilize" date="1119979650" path="state_init.xsd" size="808" user="jboline" version="1.1" |
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| META FILEATTACHMENT | state_submit.xml | attr="" comment="Example atlas_state submit message, version of 6/28" date="1120710310" path="C:\PROJECTS\ATLASES\Interface_integration\6_28_schemas\state_submit.xml" size="3234" user="IlyaZaslavsky" version="1.1" |
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| META FILEATTACHMENT | state_retrieve.xml | attr="" comment="Example atlas_state retrieve message, version of 6/28" date="1120710356" path="C:\PROJECTS\ATLASES\Interface_integration\6_28_schemas\state_retrieve.xml" size="424" user="IlyaZaslavsky" version="1.1" |
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| META FILEATTACHMENT | state_end.xml | attr="" comment="Example atlas_state end message, version of 6/28" date="1120710390" path="C:\PROJECTS\ATLASES\Interface_integration\6_28_schemas\state_end.xml" size="266" user="IlyaZaslavsky" version="1.1" |
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| META FILEATTACHMENT | MouseBrainEnvironment?.html | attr="" comment="A mouse brain study environment" date="1121371701" path="MouseBrainEnvironment.html" size="9626" user="AlexandraBadea" version="1.1" |
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Atlas Plan and Action Items generated at June 2005 mouse AHM:
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Use Cases
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| META FILEATTACHMENT | atlas_workplan_6_1_05.doc | attr="" comment="Atlasing Plan and Action items. Word doc" date="1119652103" path="atlas_workplan_6_1_05.doc" size="49664" user="jboline" version="1.1" |
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| META FILEATTACHMENT | state_submit.xsd | attr="" comment="Submit" date="1119979672" path="state_submit.xsd" size="3533" user="jboline" version="1.1" |
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| META FILEATTACHMENT | state_retrieve.xsd | attr="" comment="Retrieve" date="1119979689" path="state_retrieve.xsd" size="1055" user="jboline" version="1.1" |
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| META FILEATTACHMENT | state_end.xsd | attr="" comment="End" date="1119979703" path="state_end.xsd" size="615" user="jboline" version="1.1" |
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| META FILEATTACHMENT | AtlasIntegrationScenarios?.doc | attr="" comment="Some brief notes and thoughts on possible use cases, with heavy emphasis on gene expression data" date="1120108241" path="Atlas Integration Scenarios.doc" size="26112" user="MaryannEMartone" version="1.1" |
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| META FILEATTACHMENT | AtlasIntegrationScenarios?.doc | attr="" comment="Expanded version of Atlas Integration Scenarios" date="1121128250" path="AtlasIntegrationScenarios.doc" size="45056" user="MaryannEMartone" version="1.2" |
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| META FILEATTACHMENT | state_init.xml | attr="" comment="Example atlas_state init message, version of 6/28" date="1120710217" path="C:\PROJECTS\ATLASES\Interface_integration\6_28_schemas\state_init.xml" size="292" user="IlyaZaslavsky" version="1.1" |
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| META FILEATTACHMENT | state_submit.xml | attr="" comment="Example atlas_state submit message, version of 6/28" date="1120710310" path="C:\PROJECTS\ATLASES\Interface_integration\6_28_schemas\state_submit.xml" size="3234" user="IlyaZaslavsky" version="1.1" |
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| META FILEATTACHMENT | state_retrieve.xml | attr="" comment="Example atlas_state retrieve message, version of 6/28" date="1120710356" path="C:\PROJECTS\ATLASES\Interface_integration\6_28_schemas\state_retrieve.xml" size="424" user="IlyaZaslavsky" version="1.1" |
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Atlas Plan and Action Items generated at June 2005 mouse AHM:
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Syntax for Atlas Interoperation
http://imhotep.ucsd.edu:7873/trantj/mouse_birn/newXMLFormat.htm
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Examples of Syntax and XML schemas for atlas state exchange
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Examples of Syntax and XML schemas for atlas state exchange (as of 6/28/2005)
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| META FILEATTACHMENT | state_retrieve.xsd | attr="" comment="Retrieve" date="1119979689" path="state_retrieve.xsd" size="1055" user="jboline" version="1.1" |
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| META FILEATTACHMENT | state_end.xsd | attr="" comment="End" date="1119979703" path="state_end.xsd" size="615" user="jboline" version="1.1" |
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| META FILEATTACHMENT | AtlasIntegrationScenarios?.doc | attr="" comment="Some brief notes and thoughts on possible use cases, with heavy emphasis on gene expression data" date="1120108241" path="Atlas Integration Scenarios.doc" size="26112" user="MaryannEMartone" version="1.1" |
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| META FILEATTACHMENT | state_init.xml | attr="" comment="Example atlas_state init message, version of 6/28" date="1120710217" path="C:\PROJECTS\ATLASES\Interface_integration\6_28_schemas\state_init.xml" size="292" user="IlyaZaslavsky" version="1.1" |
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| META FILEATTACHMENT | state_submit.xml | attr="" comment="Example atlas_state submit message, version of 6/28" date="1120710310" path="C:\PROJECTS\ATLASES\Interface_integration\6_28_schemas\state_submit.xml" size="3234" user="IlyaZaslavsky" version="1.1" |
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| META FILEATTACHMENT | state_retrieve.xml | attr="" comment="Example atlas_state retrieve message, version of 6/28" date="1120710356" path="C:\PROJECTS\ATLASES\Interface_integration\6_28_schemas\state_retrieve.xml" size="424" user="IlyaZaslavsky" version="1.1" |
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| META FILEATTACHMENT | state_end.xml | attr="" comment="Example atlas_state end message, version of 6/28" date="1120710390" path="C:\PROJECTS\ATLASES\Interface_integration\6_28_schemas\state_end.xml" size="266" user="IlyaZaslavsky" version="1.1" |
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Atlas Plan and Action Items generated at June 2005 mouse AHM:
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Use Cases
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| META FILEATTACHMENT | atlas_workplan_6_1_05.doc | attr="" comment="Atlasing Plan and Action items. Word doc" date="1119652103" path="atlas_workplan_6_1_05.doc" size="49664" user="jboline" version="1.1" |
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| META FILEATTACHMENT | atlas_workplan_6_1_05.pdf | attr="" comment="Atlasing Plan and Action items. pdf" date="1119652217" path="atlas_workplan_6_1_05.pdf" size="26166" user="jboline" version="1.1" |
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| META FILEATTACHMENT | state_submit.xsd | attr="" comment="Submit" date="1119979672" path="state_submit.xsd" size="3533" user="jboline" version="1.1" |
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| META FILEATTACHMENT | state_retrieve.xsd | attr="" comment="Retrieve" date="1119979689" path="state_retrieve.xsd" size="1055" user="jboline" version="1.1" |
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| META FILEATTACHMENT | state_end.xsd | attr="" comment="End" date="1119979703" path="state_end.xsd" size="615" user="jboline" version="1.1" |
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| META FILEATTACHMENT | AtlasIntegrationScenarios?.doc | attr="" comment="Some brief notes and thoughts on possible use cases, with heavy emphasis on gene expression data" date="1120108241" path="Atlas Integration Scenarios.doc" size="26112" user="MaryannEMartone" version="1.1" |
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Worksite for Atlasing groups to interact.
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Atlas integration notes and task list:
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Technical Notes
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1. Exchange of state between atlases:
Things to do here:
- a) we will send the API and demos around
- b) review the API and demo communications, to see if it will fit your atlas (Willy and Joshua will help with this)
- c) review the current representation of "atlas state", to see if it is general enough
- d) formally describe spatial reference systems we use: e.g. Stereotaxic1 (used at UCLA), Stereotaxic2 (used in UCSD atlas), image1 (used at Drexel)
- e) define transformations between all coordinate systems, and some canonical stareotaxic system (either Stereotaxic1 or 2)
- f) create services for converting between the coordinate systems (though for a limited number of coordinate systems just sharing conversion code fragments would be more robust). It is straightforward for some conversions; may be pretty involved when converting from image to stereotaxic. For the latter, we need to have a couple test cases
- g) create services for format conversion: i.e. between polygons specified as coordinate pairs or triplets, and collections of pixels/voxels (Bill mentioned that they may have appropriate code at Drexel).
Now with respect to ontology - the "semantic reference system" may be handled in a similar way: i.e. when giving a name of a feature must also
specify the ontology in which it lives.
2. Ability to search registered images/volumes/segmentations available in other atlases.
- a) UCSD will send the schema of our spatial registry source
- b) we need to see how to register 3D volumes and 2D images to such or similar source (using Drexel's alignment/warping tools?), so that the metadata sources can be searched in uniform way.
3. Ability to load images / slices / segmentations into any atlas.
- a) UCSD will provide sample code for retrieving image fragments from ArcIMS?
- b) UCSD will develop a web service to return feature coordinates (as polygon boundary, as well as label point) given the feature name and set of slices
- c) let's go first through a manual process of loading each other's images.
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