# Konversatorium on Friday, November 10, 2017 - 10:30

## Multiscale Modeling and Visualization of Cells and their Membranes

Multiscale modeling and visualization of cellular environments is an important topic from a scientific as well as educational perspective. It plays an important role in analyzing and understanding metabolic processes, structural molecular complexes or the targeting of drugs.

The CELLmicrocosmos project combines different information layers for multiple purposes:

At the molecular level, the MembraneEditor is used by many projects to model heterogeneous membranes as a base for molecular simulations and analyses [SDGS11]. Showing small parallels to cellVIEW [LAPV15], the CellExplorer is a software tool which can be used to visualize and explore cell environments at the mesoscopic level. Combined with the PathwayIntegration, cytological networks can be localized and integrated into these cell environments [KoGS16, SKSH10]. In the recent years we developed a number of new cytological visualization approaches which can be explored on multiple scales: from the local computer, to web browsers, to mobile phones and Head-‐mounted displays, and to large-‐scale virtual environments like the CAVE2 [FNTT13, KoGS16, SBHG14, SHKC16, SWXC15]. In this context we are currently working with the CeBiTec Bielefeld on the visualization of a Chlamydomas rheinhardtii cell.

[FNTT13] FEBRETTI, Alessandro; NISHIMOTO, Arthur; THIGPEN, Terrance; TALANDIS, Jonas; LONG, Lance; PIRTLE, J. D.; PETERKA, Tom; VERLO, Alan; et al.:

CAVE2: a hybrid reality environment for immersive simulation and information analysis. In: IS&T/SPIE lectronic Imaging : International Society for Optics and Photonics, 2013, pp. 864903-‐864903–12

[KoGS16] KOVANCI, Gökhan; GHAFFAR, Mehmood; SOMMER, Björn: Web-‐based hybrid-‐ dimensional Visualization and Exploration of Cytological Localization Scenarios. In: Journal of Integrative Bioinformatics 13 (2016), no. 4, p. 298

[LAPV15] LE MUZIC, Mathieu; AUTIN, Ludovic; PARULEK, Julius; VIOLA, Ivan: cellVIEW: a tool for illustrative and multi-‐scale rendering of large biomolecular datasets. In: Proceedings of the Eurographics Workshop on Visual Computing for Biology and Medicine : Eurographics Association, 2015, pp. 61–70

[SBHG14] SOMMER, Björn; BENDER, Christian; HOPPE, Tobias; GAMROTH, Christian; JELONEK, Lukas: Stereoscopic cell visualization: from mesoscopic to molecular scale. In: Electronic Imaging, Proceedings of Stereoscopic Displays and Applications XXVIII 23 (2014), no. 1, pp. 011007-‐1-‐011007-‐10

[SDGS11] SOMMER, B.; DINGERSEN, T.; GAMROTH, C.;SCHNEIDER, S. E.; RUBERT, S.; KRÜGER, J.; DIETZ, K. J.: CELLmicrocosmos 2.2 MembraneEditor: a modular interactive

shape-‐based software approach to solve heterogeneous Membrane Packing Problems. In: Journal of Chemical Information and Modeling 5 (2011), no. 51, pp. 1165–1182

[SHKC16] SOMMER, Björn; HAMACHER, Andreas; KALUZA, Owen; CZAUDERNA, Tobias;

KLAPPERSTÜCK, Matthias; BIERE, Niklas; CIVICO, Marco; THOMAS, Bruce; et al.: Stereoscopic Space Map – Semi-‐immersive Configuration of 3D-‐stereoscopic Tours

in Multi-‐display Environments. In: Electronic Imaging, Proceedings of Stereoscopic Displays and Applications XXVII 2016 (2016), no. 5, pp. 1–9

[SKSH10] SOMMER, Björn; KÜNSEMÖLLER, Jörn; SAND, Norbert; HUSEMANN, Arne; RUMMING, Madis; KORMEIER, Benjamin: CELLmicrocosmos 4.1: an interactive approach to integrating spatially localized metabolic networks into a virtual 3D cell environment. In: FRED, Ana; FILIPE, Joaquim; GAMBOA, Hugo (eds.): BIOSTEC 2010, 2010,pp. 90–95

[SWXC15] SOMMER, Björn; WANG, Stephen Jia; XU, Lifeng; CHEN, Ming; SCHREIBER, Falk: Hybrid-‐Dimensional Visualization and Interaction -‐ Integrating 2D and 3D Visualization with Semi-‐Immersive Navigation Techniques. In: Big Data Visual Analytics (BDVA), 2015 : IEEE, 2015, pp. 1–8

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Guest talk Bjoern Sommer | 4.56 MB |

## Quantifying the Convergence of Light-Transport Algorithms (DAEV)

This work aims at improving methods for measuring the error of unbiased, physically

based light-transport algorithms. State-of-the-art papers show algorithmic improvements

via error measures like Mean Square Error (MSE) or visual comparison of equal-time

renderings. These methods are unreliable since outliers can cause MSE variance and

visual comparison is inherently subjective.

We introduce a simple proxy algorithm: pure algorithms produce one image corresponding

to the computation budget N . The proxy, on the other hand, averages N independent

images with a computation budget of 1. The proxy algorithm fulfils the preconditions

for the Central Limit Theorem (CLT), and hence, we know that its convergence rate is

Θ(1/N ). Since this same convergence rate applies for all methods executed using the

proxy algorithm, comparisons using variance- or standard-deviation-per-pixel images are

possible. These per-pixel error images can be routinely computed and allow comparing

the render quality of different lighting effects. Additionally, the average of pixel variances

is more robust against outliers compared to the traditional MSE or comparable metrics

computed for the pure algorithm.

We further propose the Error Spectrum Ensemble (ESE) as a new tool for evaluating light-

transport algorithms. It summarizes expected error and outliers over spatial frequencies.

ESE is generated using the data from the proxy algorithm: N error images are computed

using a reference, transformed into Fourier power spectra and compressed using radial

averages. The descriptor is a summary of those radial averages.

In the results, we show that standard-deviation images, short equal-time renderings, ESE

and expected MSE are valuable tools for assessing light-transport algorithms.