geomcell design of cell geometry július parulek 1,2, miloš Šrámek 2,3 and ivan zahradník 1 (1)...
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GeomCellDesign of Cell Geometry
Július Parulek1,2, Miloš Šrámek2,3 and Ivan Zahradník1
(1) Institute of Molecular Physiology and Genetics, Slovak Academy of Sciences, Slovakia(2) Faculty of Mathematics, Physics and Informatics, Comenius University, Bratislava, Slovakia(3) Austrian Academy of Sciences, Austria
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Overview
Introduction to GeomCell Previous work on geometrical
modeling of muscle cells Representation of mitochondrial
shape GeomCell Implementation Conclusions and future work
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GeomCell - Intro An environment for virtual cell modeling
based on a precise geometric background possibilities of modern computer graphics
and computer hardware to represent a virtual micro-world of cells
first building blocks for representation of a static cell geometry
models of skeletal muscle tissues idealized models rather than exact
reconstruction
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Muscle Cell Organelles
(Courtesy of Dr. Novotová)
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Muscle Cell Organelles
Laon
git
ud
inal axis
Transversal axis
(Courtesy of Dr. Novotová)
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Input Data - EM images
(Courtesy of Dr. Novotová)
Volume and surface density (stereology)
Volume and surface density (stereology)
Sizes(morphometry)
Sizes(morphometry)
Shape(morphology)
Shape(morphology)
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Cell Model Organelles
Desired subset of cell organelles:1) Myofibrils2) Sarcolemma3) Sarcoplasmic reticulum4) Mitochondria5) T-tubules
1
3
2
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XISL Implicit Objects
XISL – Implicit modeling environment XML based modeling language C++ library, tools (conversion,
rendering, ...)
f(x) > 0
f(x) < 0
f(x) = 0
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Cross-sectional Graphs Produce carrier
skeletons for all virtual organelles
Directly used in modeling of myofibrils Thin and long cylindrical
objects cross-sectional graphs
(c-graph) in a system of parallel planes
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Cross-sectional Graphs (cont.)
Real EM images c-graph2D implicit shapes
Quadratic interpolation of the 2D shapes
Minimal distance specification
Minimal distance specification
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Extended Interpolation Spatial warp metamorphosis utilized in
sarcoplasmic reticulum (SR) modeling two compartments: terminal cisterns of the
SR (A) and Longitudinal SR (B) skeleton: a set of seed (C) points distributed
in a system of cross-sectional planes
A
B C
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Mitochondrial Shape
Elliptically shaped and prolonged organelles of irregular smooth forms and variable sizes implicit sweep objects
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Components of Sweep Objects
A 2D sweep primitive (template) and a 3D sweep trajectory
2D template2D template 3D trajectory3D trajectory
Sweep objectSweep object
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Template defined as 2D implicit ellipsoid with variable dimensions
Trajectory as quadratic B-spline
Sweep Components for Mitchondria
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Method Overview
Transformation (MS) maps the 2D template along the curve using so-called reference frames (RF)
Rotation of RF around C’(t)
fe
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Method Overview (cont.)
Estimate all curve points NP(x) (parameters si), for which x lies in the template planes
Resultant function
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Problem of Parameter Estimation
Analytical solution (a, param t) of a general curve trajectory is rarely possible
for instance: cubic spline (C(t) is degree 3) - the polynomial (a) is degree 5
Solution in using quadratic curves analytical solution
(a)(a)
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End Caps
Union with two implicit semi-ellipsoids at both ends
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Model Generation
Fully automatic, guided by Model Description Language (MDL) basic cell dimensions c-graph distribution organelle’s geometric parameters
specified in a probabilistic sense Quantification, visualization, …
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GeomCell Implementation Computationally intensive tasks
generation of large number of models evaluation of volume and surface areas of
organelles model visualization
High throughput computing required Utilization of a grid environment
retrieval of cell models using metadata (morphological and stereological data, images, MDL spec.,…)
eased with a GUI portal
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Conclusions and Future Work System for cell model generation,
quantification, visualization and conversion implemented in Grid environment - GeomCell
Organelle’s behavior add physical layer to all objects growth, deformations, cell
contraction, … Pathological cells
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Thank You for Your Attention
Homepage: www.sccg.sk/~parulekCell modeling project: www.sccg.sk/~parulek/cellGrid implementation:http://cvs.ui.sav.sk/twiki/bin/view/EGEE//GeomCellInEGEE-MuscleCellModelingOnTheGrid
Visualization of a volumetric format of a cell model