1. science
2. mathematics
3. geometry

Fakultät Informatik
Zoomable Cell
Matthias Reimann, Anne Tuukannen, Michael Schroeder
Marcel Spehr, Dimitrij Schlesinger, Stefan Gumhold
Vision
Microscopy images
10.000nm
1.000 nm
A
B
Data
Protein interactions and 3D structures
100 nm
C
D
10 nm
E
Natural coordinate system
F
Abstract cell
G
1 nm
H
I
Zoomable cell
>200.000 images from
scientific literature
>48.000 3D protein
structures from PDB
?
2
Achievements

Protein interactions and 3D structures



Natural Coordinate System


Algorithm for constraint-based construction of large complexes with use case in
histone methyltransferase SET1
(In Proteomics 2010)
Novelty: constrain combinatorial explosion with protein interaction data
Network visualisation with power graphs with disease applications
Novelty: exploiting modules in graphs for visualisation
(In Experimental Cell Research 2010, Neurological Research 2010, 2 submitted)
DOG4DAG: Semi-automated generation of term, definitions, and hierarchies
Novelty: First system to integrate all steps of ontology generation + Evaluation
(In Bioinformatics 2010)
Microscopy images

Image search and classification with natural coordinate system
Novelty: Image library with 1.3Mio images, Implementation of image similarity
measures and filters, GoImage system with 745000 images
(manuscript in preparation)
3
Contents

Constraint-based modelling of complexes

Image search and classification with natural coordinate system

Limits and Perspectives
4
Histones and histone methyltransferases

DNA is a long string wound around histones
Molecular Cell Biology, Lodish et al.

Histones are modified by histone methyltransferases
Met
Histone H3
Dim-5 protein
Suv39-type histone K9 methyltransferase
Interactions of SET1 subunits
Positive
Interactions
Set1
Set1
Set1
Set1
Set1
Set1
Bre2
Swd1
Swd2
Bre2
-
Bre2
Shg1
Ssp1
Swd1
Swd2
Swd3
Bre2
Swd3
Swd2
Sdc1
Negative
Interactions
AP/MS and Y2H Roguev et al. 2004 , Dehe et al. JBC (2006)
Set1 - Sdc1
Bre2 – Sdc1 – Bre2
6
Workflow
7
Constraints
8
Model
9
Contents

Constraint-based modelling of complexes

Image search and classification with natural coordinate system

Limits and Perspectives
10
Image search and classification

Current engines:




Yale Image finder, (FigSearch), BioText Search Engine
No web
No filtering of graphs, tables, formulas, photos, etc.
Zoomable Cell image search




90% of images not suitable
Yahoo Boss API to retrieve several millions of images
Bottom up approach:

Manual selection of 2.000 from 20.000 images

Expansion of seed images to 745.000 images by image similarity
Image similarity

Gist scene descriptor (960 image features)

Approximate nearest neighbour clustering
11
266 images for
Endoplasmic reticulum
2 out of 266 for rodents
Similar images
12
Navigation in Large Information Spaces

Similarity based vector representation of images transforms
problem into search scenario in high dimensions

Image features constitute space

Images are instances of space points

Usage of Kernel PCA permits consistent handling of similarities
from different feature domains
Similarity
Measures di
Kernel PCA
Combined
Feature Space ϕ
(dimensionality
adjustable)
Image features
Name
Runtime /
image
Quality
Reference
Gist
0.15 sec
++
[Oliva and Torralba;
2006]
Image details
CEDD
0.01 sec
+++
[Chatzichristofis and
Boutalis; 2008]
Specific content
Tanimoto
Coefficient
FCTH
0.01 sec
++
[Chatzichristofis and
Boutalis; 2008]
Specific content
Tanimoto
Coefficient
CLD; SCD;
EHD;
0.01 sec
+
[Manjunath et al;
2002]
Specific content;
intuitiveness
1 sec
++
Unpublished; Inhouse development
Model complexity;
computation time
SIFT Bag-ofFeatures
0.3 sec
++
[Csurka et al; 2004]
Perspective
transformations;
image clutter
Annotation
0.001 sec
+++
[Joachims, 1999]
Existence and
quality of labels
Low Res
0.004 sec
+
Segmentation
Limits
Affine image
transformations;
illumination changes
Similarity
e  L2
e  L2
Dot Product
e  L2
String kernel (word
frequencies)
e  L1
Directed Search Strategies in ϕ
ϕ2

Idea from Optimization

Taxi-Cab Method:
reduce to 1D minimization along ϕ axes

User performs search interactively:

Problem: sparsely sampled space
x0
ϕ1
ϕ2
ϕ1
Directed Search Strategies in ϕ
Sample along each ϕ axis:

as close as possible to axis

reachability of all images
Solution

use Voronoi Regions of ϕ axes to assign
all images

filter out all images that can be reached
indirectly over remaining images
Results
Star view and user feedback
18
Continuous zoom at different time steps and resolutions

Problem: Transforming one image into another by
generating a sequence of intermediate images to
achieve a seamless transition
I

2
As automatic as possible
and user adjustable

Thin plate spline + optical flow
Contributions, Limits, and Perspectives

Contributions:





Limits:




Small scale, semi-automated, constraint-based modelling of complexes possible
Compact visualisation of protein interaction networks with power graphs
Image search (library, textual and image similarity, navigation, learning)
Zooming
Large-scale, automated modelling of complexes not possible
Additional data needed on structures, interactions, EM maps, localisation
Integration of coherent image data
Perspective:


Concrete application in fruitfly development
Integrating video microscopy data, manual annotation, protein and protein
interaction data
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