towards a zoomable cell abstract cell natural coordinate system data >48.000 3d protein...
TRANSCRIPT
![Page 1: Towards a zoomable cell abstract cell natural coordinate system Data >48.000 3D Protein Structures from PDB ? A IHGFBCDE >200.000 Images from scientific](https://reader035.vdocuments.mx/reader035/viewer/2022062713/56649cb75503460f9497d3da/html5/thumbnails/1.jpg)
towards a zoomable cell
QuickTime™ and aTIFF (LZW) decompressor
are needed to see this picture.
abstract cellnatural coordinate systemData
>48.000 3D ProteinStructures from PDB
QuickTime™
and a
TIFF (LZW) decom
pressor
are needed to see this picture.
QuickTime™
and a
TIFF (LZW) decom
pressor
are needed to see this picture.
?
A IHGFB C D E
>200.000 Images from scientific publications
1
![Page 2: Towards a zoomable cell abstract cell natural coordinate system Data >48.000 3D Protein Structures from PDB ? A IHGFBCDE >200.000 Images from scientific](https://reader035.vdocuments.mx/reader035/viewer/2022062713/56649cb75503460f9497d3da/html5/thumbnails/2.jpg)
Computer Graphicsand Visualization
TECHNISCHEUNIVERSITÄTDRESDEN
Zoomable Cell
Stefan Gumhold Michael Schröder
Norbert Blenn Anne Tuukkanen
Marcel Spehr Matthias Reimann
![Page 3: Towards a zoomable cell abstract cell natural coordinate system Data >48.000 3D Protein Structures from PDB ? A IHGFBCDE >200.000 Images from scientific](https://reader035.vdocuments.mx/reader035/viewer/2022062713/56649cb75503460f9497d3da/html5/thumbnails/3.jpg)
Computer Graphicsand Visualization
Zoomable Cell, SPP 1335, Kickoff Meeting, 9.12.08, Dagstuhl 3
Goals Data analysis
Natural coordinate system (NCS) Mapping of images from literature to NCS 3D models of complexes in NCS
Visualization aggregation of images, volumes and 3D models Rendering across scale from 10m to 1Å Natural adjustment of visualization parameters with
dynamic labeling
HCI support for Virtual Reality environments speech control and input device development flexible navigation community support through web integration
Impact Interface life scientists „from different scales“ data aggregation and analysis platform production of illustrative materials
![Page 4: Towards a zoomable cell abstract cell natural coordinate system Data >48.000 3D Protein Structures from PDB ? A IHGFBCDE >200.000 Images from scientific](https://reader035.vdocuments.mx/reader035/viewer/2022062713/56649cb75503460f9497d3da/html5/thumbnails/4.jpg)
Computer Graphicsand Visualization
Zoomable Cell, SPP 1335, Kickoff Meeting, 9.12.08, Dagstuhl 4
Human CellsNew Problems
Several different instances of the same type
each instance is flexible
cells are treated badly before imaging
very different imaging modalities are used
Deformation Framework
![Page 5: Towards a zoomable cell abstract cell natural coordinate system Data >48.000 3D Protein Structures from PDB ? A IHGFBCDE >200.000 Images from scientific](https://reader035.vdocuments.mx/reader035/viewer/2022062713/56649cb75503460f9497d3da/html5/thumbnails/5.jpg)
Computer Graphicsand Visualization
Zoomable Cell, SPP 1335, Kickoff Meeting, 9.12.08, Dagstuhl 5
Various Data Types
cell
nucleus
pore
complexes
proteins
primitives, smooth surfaces
implicit surfaces
height fields
images: 2D, 3D, perspective
images: 2D, 3D, perspective
![Page 6: Towards a zoomable cell abstract cell natural coordinate system Data >48.000 3D Protein Structures from PDB ? A IHGFBCDE >200.000 Images from scientific](https://reader035.vdocuments.mx/reader035/viewer/2022062713/56649cb75503460f9497d3da/html5/thumbnails/6.jpg)
Computer Graphicsand Visualization
Zoomable Cell, SPP 1335, Kickoff Meeting, 9.12.08, Dagstuhl 6
Data Augmentation define reference models
for each dataset scale imaging modality features
points curves regions
labeling of features
for pairs of datasets feature mapping additional alignment information
nucleolusenvelop
pore
![Page 7: Towards a zoomable cell abstract cell natural coordinate system Data >48.000 3D Protein Structures from PDB ? A IHGFBCDE >200.000 Images from scientific](https://reader035.vdocuments.mx/reader035/viewer/2022062713/56649cb75503460f9497d3da/html5/thumbnails/7.jpg)
Computer Graphicsand Visualization
Zoomable Cell, SPP 1335, Kickoff Meeting, 9.12.08, Dagstuhl 7
Integration of Datasets
Segmentation
FeatureDetection
Labeling
non-rigidRegistration
![Page 8: Towards a zoomable cell abstract cell natural coordinate system Data >48.000 3D Protein Structures from PDB ? A IHGFBCDE >200.000 Images from scientific](https://reader035.vdocuments.mx/reader035/viewer/2022062713/56649cb75503460f9497d3da/html5/thumbnails/8.jpg)
Computer Graphicsand Visualization
Zoomable Cell, SPP 1335, Kickoff Meeting, 9.12.08, Dagstuhl 8
Deformation
reference model
![Page 9: Towards a zoomable cell abstract cell natural coordinate system Data >48.000 3D Protein Structures from PDB ? A IHGFBCDE >200.000 Images from scientific](https://reader035.vdocuments.mx/reader035/viewer/2022062713/56649cb75503460f9497d3da/html5/thumbnails/9.jpg)
Computer Graphicsand Visualization
Zoomable Cell, SPP 1335, Kickoff Meeting, 9.12.08, Dagstuhl 9
Plan to a Solution
start with fully interactive tools
add automation step by step with full interactivity for corrections
find features that persist over different scales
develop learning based segmentation approaches
exploit mutual information to register datasets of different dimension and
modality
![Page 10: Towards a zoomable cell abstract cell natural coordinate system Data >48.000 3D Protein Structures from PDB ? A IHGFBCDE >200.000 Images from scientific](https://reader035.vdocuments.mx/reader035/viewer/2022062713/56649cb75503460f9497d3da/html5/thumbnails/10.jpg)
Computer Graphicsand Visualization
Zoomable Cell, SPP 1335, Kickoff Meeting, 9.12.08, Dagstuhl 10
Visualization Engine protein structures
primitive splatting tubes, surfaces deferred shading sorting based transparency
3d surface models LOD based rendering depth peeling based transparency
Images & Volumes volume rendering compression transfer functions
![Page 11: Towards a zoomable cell abstract cell natural coordinate system Data >48.000 3D Protein Structures from PDB ? A IHGFBCDE >200.000 Images from scientific](https://reader035.vdocuments.mx/reader035/viewer/2022062713/56649cb75503460f9497d3da/html5/thumbnails/11.jpg)
Computer Graphicsand Visualization
Example Images
![Page 12: Towards a zoomable cell abstract cell natural coordinate system Data >48.000 3D Protein Structures from PDB ? A IHGFBCDE >200.000 Images from scientific](https://reader035.vdocuments.mx/reader035/viewer/2022062713/56649cb75503460f9497d3da/html5/thumbnails/12.jpg)
Computer Graphicsand Visualization
Query Based Exploration of Images
![Page 13: Towards a zoomable cell abstract cell natural coordinate system Data >48.000 3D Protein Structures from PDB ? A IHGFBCDE >200.000 Images from scientific](https://reader035.vdocuments.mx/reader035/viewer/2022062713/56649cb75503460f9497d3da/html5/thumbnails/13.jpg)
Available image information
• Expert labeled text (categorical)
• Unstructured information of related text (textual)
• Inherent image features (abstract description of image appearance)
More reliable and structured
Less reliable and structured
![Page 14: Towards a zoomable cell abstract cell natural coordinate system Data >48.000 3D Protein Structures from PDB ? A IHGFBCDE >200.000 Images from scientific](https://reader035.vdocuments.mx/reader035/viewer/2022062713/56649cb75503460f9497d3da/html5/thumbnails/14.jpg)
Navigation/Exploration
• Around 100.000 images currently available to us• Even with automatic analysis one needs supporting browsing techniques• If we have features that measure appropriate image similarities:
– Hierarchical Browsing– Fish-Eye View
![Page 15: Towards a zoomable cell abstract cell natural coordinate system Data >48.000 3D Protein Structures from PDB ? A IHGFBCDE >200.000 Images from scientific](https://reader035.vdocuments.mx/reader035/viewer/2022062713/56649cb75503460f9497d3da/html5/thumbnails/15.jpg)
Hierarchical Browsing
![Page 16: Towards a zoomable cell abstract cell natural coordinate system Data >48.000 3D Protein Structures from PDB ? A IHGFBCDE >200.000 Images from scientific](https://reader035.vdocuments.mx/reader035/viewer/2022062713/56649cb75503460f9497d3da/html5/thumbnails/16.jpg)
Fish-Eye View
![Page 17: Towards a zoomable cell abstract cell natural coordinate system Data >48.000 3D Protein Structures from PDB ? A IHGFBCDE >200.000 Images from scientific](https://reader035.vdocuments.mx/reader035/viewer/2022062713/56649cb75503460f9497d3da/html5/thumbnails/17.jpg)
Methods to structure image data set
• By hand• Automatic analysis (off-the-shelf methods)
– Unsupervised (Clustering)– Supervised (Multiclass Support Vector machines)
• Need for appropriate problem oriented feature set
![Page 18: Towards a zoomable cell abstract cell natural coordinate system Data >48.000 3D Protein Structures from PDB ? A IHGFBCDE >200.000 Images from scientific](https://reader035.vdocuments.mx/reader035/viewer/2022062713/56649cb75503460f9497d3da/html5/thumbnails/18.jpg)
Image Feature Definition
• Vast numbers of image descriptors are available• Need for general purpose image descriptors because of wide variety of
image origins• Standardized Multimedia content description (MPEG-7)
![Page 19: Towards a zoomable cell abstract cell natural coordinate system Data >48.000 3D Protein Structures from PDB ? A IHGFBCDE >200.000 Images from scientific](https://reader035.vdocuments.mx/reader035/viewer/2022062713/56649cb75503460f9497d3da/html5/thumbnails/19.jpg)
![Page 20: Towards a zoomable cell abstract cell natural coordinate system Data >48.000 3D Protein Structures from PDB ? A IHGFBCDE >200.000 Images from scientific](https://reader035.vdocuments.mx/reader035/viewer/2022062713/56649cb75503460f9497d3da/html5/thumbnails/20.jpg)
![Page 21: Towards a zoomable cell abstract cell natural coordinate system Data >48.000 3D Protein Structures from PDB ? A IHGFBCDE >200.000 Images from scientific](https://reader035.vdocuments.mx/reader035/viewer/2022062713/56649cb75503460f9497d3da/html5/thumbnails/21.jpg)
![Page 22: Towards a zoomable cell abstract cell natural coordinate system Data >48.000 3D Protein Structures from PDB ? A IHGFBCDE >200.000 Images from scientific](https://reader035.vdocuments.mx/reader035/viewer/2022062713/56649cb75503460f9497d3da/html5/thumbnails/22.jpg)
![Page 23: Towards a zoomable cell abstract cell natural coordinate system Data >48.000 3D Protein Structures from PDB ? A IHGFBCDE >200.000 Images from scientific](https://reader035.vdocuments.mx/reader035/viewer/2022062713/56649cb75503460f9497d3da/html5/thumbnails/23.jpg)
![Page 24: Towards a zoomable cell abstract cell natural coordinate system Data >48.000 3D Protein Structures from PDB ? A IHGFBCDE >200.000 Images from scientific](https://reader035.vdocuments.mx/reader035/viewer/2022062713/56649cb75503460f9497d3da/html5/thumbnails/24.jpg)
![Page 25: Towards a zoomable cell abstract cell natural coordinate system Data >48.000 3D Protein Structures from PDB ? A IHGFBCDE >200.000 Images from scientific](https://reader035.vdocuments.mx/reader035/viewer/2022062713/56649cb75503460f9497d3da/html5/thumbnails/25.jpg)
![Page 26: Towards a zoomable cell abstract cell natural coordinate system Data >48.000 3D Protein Structures from PDB ? A IHGFBCDE >200.000 Images from scientific](https://reader035.vdocuments.mx/reader035/viewer/2022062713/56649cb75503460f9497d3da/html5/thumbnails/26.jpg)
![Page 27: Towards a zoomable cell abstract cell natural coordinate system Data >48.000 3D Protein Structures from PDB ? A IHGFBCDE >200.000 Images from scientific](https://reader035.vdocuments.mx/reader035/viewer/2022062713/56649cb75503460f9497d3da/html5/thumbnails/27.jpg)
Class information from Image Features
1. Definition of semantic classes (assisted and manually, Gene Ontology labels)
2. Relation of abstract image descriptors to semantic classes (training, learning)
3. Evaluation of generalization ability
![Page 28: Towards a zoomable cell abstract cell natural coordinate system Data >48.000 3D Protein Structures from PDB ? A IHGFBCDE >200.000 Images from scientific](https://reader035.vdocuments.mx/reader035/viewer/2022062713/56649cb75503460f9497d3da/html5/thumbnails/28.jpg)
GoImage – Semantic Image Search
Comprehensive protein-interaction mapping projects underway
What is the cost of completing an interactome map and what is the best strategy for minimizing the cost?
How can quality and coverage of interaction data be maximized?
![Page 29: Towards a zoomable cell abstract cell natural coordinate system Data >48.000 3D Protein Structures from PDB ? A IHGFBCDE >200.000 Images from scientific](https://reader035.vdocuments.mx/reader035/viewer/2022062713/56649cb75503460f9497d3da/html5/thumbnails/29.jpg)
GoImage – Semantic Image Search
![Page 30: Towards a zoomable cell abstract cell natural coordinate system Data >48.000 3D Protein Structures from PDB ? A IHGFBCDE >200.000 Images from scientific](https://reader035.vdocuments.mx/reader035/viewer/2022062713/56649cb75503460f9497d3da/html5/thumbnails/30.jpg)
GoImage – Semantic Image Search
![Page 31: Towards a zoomable cell abstract cell natural coordinate system Data >48.000 3D Protein Structures from PDB ? A IHGFBCDE >200.000 Images from scientific](https://reader035.vdocuments.mx/reader035/viewer/2022062713/56649cb75503460f9497d3da/html5/thumbnails/31.jpg)
Refinement of a search for membranes through selecting nuclear envelope p.a.
![Page 32: Towards a zoomable cell abstract cell natural coordinate system Data >48.000 3D Protein Structures from PDB ? A IHGFBCDE >200.000 Images from scientific](https://reader035.vdocuments.mx/reader035/viewer/2022062713/56649cb75503460f9497d3da/html5/thumbnails/32.jpg)