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Falk, Martin, Dr.rer.nat.ORCID iD iconorcid.org/0000-0003-1511-5006
Biography [eng]

Martin Falk is an assistant lecturer in the Scientific Visualization Group at Linköping University. He received his Ph.D. degree (Dr.rer.nat.) from the University of Stuttgart in 2013. His research interests include large-scale volume rendering, visualizations in the context of pathology and systems biology, large spatio-temporal data, glyph-based rendering, and GPU-based simulations. 

Publications (10 of 20) Show all publications
Falk, M., Tobiasson, V., Bock, A., Hansen, C. & Ynnerman, A. (2023). A Visual Environment for Data Driven Protein Modeling and Validation. IEEE Transactions on Visualization and Computer Graphics
Open this publication in new window or tab >>A Visual Environment for Data Driven Protein Modeling and Validation
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2023 (English)In: IEEE Transactions on Visualization and Computer Graphics, ISSN 1077-2626, E-ISSN 1941-0506Article in journal (Refereed) Epub ahead of print
Abstract [en]

In structural biology, validation and verification of new atomic models are crucial and necessary steps which limit the production of reliable molecular models for publications and databases. An atomic model is the result of meticulous modeling and matching and is evaluated using a variety of metrics that provide clues to improve and refine the model so it fits our understanding of molecules and physical constraints. In cryo electron microscopy (cryo-EM) the validation is also part of an iterative modeling process in which there is a need to judge the quality of the model during the creation phase. A shortcoming is that the process and results of the validation are rarely communicated using visual metaphors.

This work presents a visual framework for molecular validation. The framework was developed in close collaboration with domain experts in a participatory design process. Its core is a novel visual representation based on 2D heatmaps that shows all available validation metrics in a linear fashion, presenting a global overview of the atomic model and provide domain experts with interactive analysis tools. Additional information stemming from the underlying data, such as a variety of local quality measures, is used to guide the user's attention toward regions of higher relevance. Linked with the heatmap is a three-dimensional molecular visualization providing the spatial context of the structures and chosen metrics. Additional views of statistical properties of the structure are included in the visual framework. We demonstrate the utility of the framework and its visual guidance with examples from cryo-EM.

Place, publisher, year, edition, pages
Institute of Electrical and Electronics Engineers (IEEE), 2023
Keywords
molecular visualization, cryo-EM, model validation, verification
National Category
Computer Sciences
Identifiers
urn:nbn:se:liu:diva-195458 (URN)10.1109/tvcg.2023.3286582 (DOI)37327104 (PubMedID)
Funder
ELLIIT - The Linköping‐Lund Initiative on IT and Mobile CommunicationsSwedish Research Council, 2015-05462Knut and Alice Wallenberg Foundation, KAW 2019.0024NIH (National Institutes of Health), R01EB023947NIH (National Institutes of Health), R01EB031872
Note

The supplemental material is available under https://osf.io/pqymt/ (DOI: 10.17605/OSF.IO/PQYMT).

Available from: 2023-06-20 Created: 2023-06-20 Last updated: 2024-03-28Bibliographically approved
Menges, A.-L., Nackenhorst, M., Müller, J. R., Engl, M.-L., Hegenloh, R., Pelisek, J., . . . Busch, A. (2023). Completing the view – histologic insights from circular AAA specimen including 3D imaging. Diagnostic Pathology, 18(1), Article ID 73.
Open this publication in new window or tab >>Completing the view – histologic insights from circular AAA specimen including 3D imaging
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2023 (English)In: Diagnostic Pathology, E-ISSN 1746-1596, Vol. 18, no 1, article id 73Article in journal (Refereed) Published
Abstract [en]

Abdominal aortic aneurysm (AAA) is a pathologic enlargement of the infrarenal aorta with an associated risk of rupture. However, the responsible mechanisms are only partially understood. Based on murine and human samples, a heterogeneous distribution of characteristic pathologic features across the aneurysm circumference is expected. Yet, complete histologic workup of the aneurysm sac is scarcely reported. Here, samples from five AAAs covering the complete circumference partially as aortic rings are investigated by histologic means (HE, EvG, immunohistochemistry) and a new method embedding the complete ring. Additionally, two different methods of serial histologic section alignment are applied to create a 3D view. The typical histopathologic features of AAA, elastic fiber degradation, matrix remodeling with collagen deposition, calcification, inflammatory cell infiltration and thrombus coverage were distributed without recognizable pattern across the aneurysm sac in all five patients. Analysis of digitally scanned entire aortic rings facilitates the visualization of these observations. Immunohistochemistry is feasible in such specimen, however, tricky due to tissue disintegration. 3D image stacks were created using open-source and non-generic software correcting for non-rigid warping between consecutive sections. Secondly, 3D image viewers allowed visualization of in-depth changes of the investigated pathologic hallmarks. In conclusion, this exploratory descriptive study demonstrates a heterogeneous histomorphology around the AAA circumference. Warranting an increased sample size, these results might need to be considered in future mechanistic research, especially in reference to intraluminal thrombus coverage. 3D histology of such circular specimen could be a valuable visualization tool for further analysis.

Place, publisher, year, edition, pages
BMC, 2023
Keywords
Abdominal Aortic Aneurysm; Aneurysm sac; 3D histology; Inflammation
National Category
Clinical Medicine
Identifiers
urn:nbn:se:liu:diva-195472 (URN)10.1186/s13000-023-01359-z (DOI)001003802000001 ()37308870 (PubMedID)
Funder
ELLIIT - The Linköping‐Lund Initiative on IT and Mobile Communications
Available from: 2023-06-20 Created: 2023-06-20 Last updated: 2024-03-07
Skånberg, R., Falk, M., Linares, M., Ynnerman, A. & Hotz, I. (2022). Tracking Internal Frames of Reference for Consistent Molecular Distribution Functions. IEEE Transactions on Visualization and Computer Graphics, 28(9), 3126-3137
Open this publication in new window or tab >>Tracking Internal Frames of Reference for Consistent Molecular Distribution Functions
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2022 (English)In: IEEE Transactions on Visualization and Computer Graphics, ISSN 1077-2626, E-ISSN 1941-0506, Vol. 28, no 9, p. 3126-3137Article in journal (Refereed) Published
Abstract [en]

In molecular analysis, Spatial Distribution Functions (SDF) are fundamental instruments in answering questions related to spatial occurrences and relations of atomic structures over time. Given a molecular trajectory, SDFs can, for example, reveal the occurrence of water in relation to particular structures and hence provide clues of hydrophobic and hydrophilic regions. For the computation of meaningful distribution functions, the definition of molecular reference structures is essential. Therefore we introduce the concept of an internal frame of reference (IFR) for labeled point sets that represent selected molecular structures, and we propose an algorithm for tracking the IFR over time and space using a variant of Kabschs algorithm. This approach lets us generate a consistent space for the aggregation of the SDF for molecular trajectories and molecular ensembles. We demonstrate the usefulness of the technique by applying it to temporal molecular trajectories as well as ensemble datasets. The examples include different docking scenarios with DNA, insulin, and aspirin.

Place, publisher, year, edition, pages
IEEE COMPUTER SOC, 2022
Keywords
Distribution functions, Trajectory, Visualization, Graphical models, Numerical models, Shape, Periodic structures
National Category
Chemical Sciences Mathematics Computer and Information Sciences
Identifiers
urn:nbn:se:liu:diva-174336 (URN)10.1109/TVCG.2021.3051632 (DOI)000833767700005 ()33444141 (PubMedID)
Note

Funding agencies: Excellence Center at Linkoping and Lund in Information Technology (ELLIIT); Swedish e-Science Research Centre (SeRC)

Available from: 2021-03-20 Created: 2021-03-20 Last updated: 2023-01-13
Friederici, A., Falk, M. & Hotz, I. (2021). A Winding Angle Framework for Tracking and Exploring Eddy Transport in Oceanic Ensemble Simulations. In: Workshop on Visualisation in Environmental Sciences (EnvirVis): . Paper presented at EnvirVis: Workshop on Visualisation in Environmental Sciences (EnvirVis2021). The Eurographics Association
Open this publication in new window or tab >>A Winding Angle Framework for Tracking and Exploring Eddy Transport in Oceanic Ensemble Simulations
2021 (English)In: Workshop on Visualisation in Environmental Sciences (EnvirVis), The Eurographics Association , 2021Conference paper, Published paper (Refereed)
Abstract [en]

Oceanic eddies, which are highly mass-coherent vortices traveling through the earth's waters, are of special interest for their mixing properties. Therefore, large-scale ensemble simulations are performed to approximate their possible evolution. Analyzing their development and transport behavior requires a stable extraction of both their shape and properties of water masses within. We present a framework for extracting the time series of full 3D eddy geometries based on an winding angle criterion. Our analysis tools enables users to explore the results in-depth by linking extracted volumes to extensive statistics collected across several ensemble members. The methods are showcased on an ensemble simulation of the Red Sea. We show that our extraction produces stable and coherent geometries even for highly irregular eddies in the Red Sea. These capabilities are utilized to evaluate the stability of our method with respect to variations of user-defined parameters. Feedback gathered from domain experts was very positive and indicates that our methods will be considered for newly simulated, even larger data sets.

Place, publisher, year, edition, pages
The Eurographics Association, 2021
Keywords
Eddy extraction, Tracking, Visual exploration, Oceanic ensemble simulation
National Category
Computer Sciences
Identifiers
urn:nbn:se:liu:diva-177625 (URN)10.2312/envirvis.20211079 (DOI)
Conference
EnvirVis: Workshop on Visualisation in Environmental Sciences (EnvirVis2021)
Funder
Swedish Foundation for Strategic Research, BD15-0082
Available from: 2021-06-30 Created: 2021-06-30 Last updated: 2024-01-02
Masood, T. B., Budin, J., Falk, M., Favelier, G., Garth, C., Gueunet, C., . . . Wozniak, M. (2021). An Overview of the Topology ToolKit. In: Ingrid Hotz, Talha Bin Masood, Filip Sadlo and Julien Tierny (Ed.), Ingrid Hotz, Talha Bin Masood, Filip Sadlo and Julien Tierny (Ed.), Topological Methods in Data Analysis and Visualization VI: Theory, Applications, and Software. Paper presented at TopoInVis 2019 (pp. 327-342). Paper presented at TopoInVis 2019. Springer
Open this publication in new window or tab >>An Overview of the Topology ToolKit
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2021 (English)In: Topological Methods in Data Analysis and Visualization VI: Theory, Applications, and Software / [ed] Ingrid Hotz, Talha Bin Masood, Filip Sadlo and Julien Tierny, Springer, 2021, p. 327-342Chapter in book (Refereed)
Abstract [en]

This software paper gives an overview of the features supported by the Topology ToolKitTopology ToolKit (TTK), which is an  Open-sourceopen-source library for  Topological data analysistopological data analysis (TDA). TTK implements, in a generic and efficient way, a substantial collection of reference algorithms in TDA. Since its initial public release in 2017, both its user and developer bases have grown, resulting in a significant increase in the number of supported features. In contrast to the original paper introducing TTK [40] (which detailed the core algorithms and data structures of TTK), the purpose of this Softwaresoftware paper is to describe the list of features currently supported by TTK, ranging from image segmentation tools to advanced topological analysis of high-dimensional data, with concrete usage examples available on the TTK website [42].

Place, publisher, year, edition, pages
Springer, 2021
Series
Mathematics and Visualization, ISSN 1612-3786, E-ISSN 2197-666X
National Category
Computer Sciences Human Computer Interaction
Identifiers
urn:nbn:se:liu:diva-182267 (URN)10.1007/978-3-030-83500-2_16 (DOI)2-s2.0-85116769555 (Scopus ID)9783030835002 (ISBN)9783030834999 (ISBN)
Conference
TopoInVis 2019
Available from: 2022-01-11 Created: 2022-01-11 Last updated: 2022-09-01Bibliographically approved
Lukasczyk, J., Beran, J., Engelke, W., Falk, M., Friederici, A., Garth, C., . . . Tierny, J. (2021). Report of the TopoInVis TTK Hackathon: Experiences, Lessons Learned, and Perspectives. In: Ingrid Hotz, Talha Bin Masood, Filip Sadlo and Julien Tierny (Ed.), Topological Methods in Data Analysis and Visualization VI: Theory, Applications, and Software (pp. 359-373). Springer
Open this publication in new window or tab >>Report of the TopoInVis TTK Hackathon: Experiences, Lessons Learned, and Perspectives
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2021 (English)In: Topological Methods in Data Analysis and Visualization VI: Theory, Applications, and Software / [ed] Ingrid Hotz, Talha Bin Masood, Filip Sadlo and Julien Tierny, Springer, 2021, p. 359-373Chapter in book (Refereed)
Abstract [en]

This paper documents the organization, the execution, and the results of the Topology ToolKit (TTK) hackathon that took place at the TopoInVis 2019 conference. The primary goal of the hackathon was to promote TTK in our research community as a unified software development platform for topology-based data analysis algorithms. To this end, participants were first introduced to the structure and capabilities of TTK, and then worked on their own TTK-related projects while being mentored by senior TTK developers. Notable outcomes of the hackathon were first steps towards Python and Docker packages, further integration of TTK in Inviwo, the extension of TTK with new algorithms, and the discovery of current limitations of TTK as well as future development directions.

Place, publisher, year, edition, pages
Springer, 2021
Series
Mathematics and Visualization, ISSN 1612-3786, E-ISSN 2197-666X
National Category
Computer Sciences Human Computer Interaction
Identifiers
urn:nbn:se:liu:diva-182266 (URN)10.1007/978-3-030-83500-2_18 (DOI)2-s2.0-85116762856 (Scopus ID)9783030834999 (ISBN)9783030835002 (ISBN)
Available from: 2022-01-11 Created: 2022-01-11 Last updated: 2022-09-01Bibliographically approved
Abrikosov, A. I., Masood, T. B., Falk, M. & Hotz, I. (2021). Topological analysis of density fields: An evaluation of segmentation methods. Computers & graphics, 98, 231-241
Open this publication in new window or tab >>Topological analysis of density fields: An evaluation of segmentation methods
2021 (English)In: Computers & graphics, ISSN 0097-8493, E-ISSN 1873-7684, Vol. 98, p. 231-241Article in journal (Refereed) Published
Abstract [en]

Topological and geometric segmentation methods provide powerful concepts for detailed field analysis and visualization. However, when it comes to a quantitative analysis that requires highly accurate geometric segmentation, there is a large discrepancy between the promising theory and the available computational approaches. In this paper, we compare and evaluate various segmentation methods with the aim to identify and quantify the extent of these discrepancies. Thereby, we focus on an application from quantum chemistry: the analysis of electron density fields. It is a scalar quantity that can be experimentally measured or theoretically computed. In the evaluation we consider methods originating from the domain of quantum chemistry and computational topology. We apply the methods to the charge density of a set of crystals and molecules. Therefore, we segment the volumes into atomic regions and derive and compare quantitative measures such as total charge and dipole moments from these regions. As a result, we conclude that an accurate geometry determination can be crucial for correctly segmenting and analyzing a scalar field, here demonstrated on the electron density field.

Place, publisher, year, edition, pages
Elsevier, 2021
Keywords
Topological data analysis, Scalar fields, Morse–Smale complex, Voronoi diagram, Numerical methods, Visualization
National Category
Computer and Information Sciences
Identifiers
urn:nbn:se:liu:diva-177624 (URN)10.1016/j.cag.2021.05.015 (DOI)000684519700007 ()
Funder
Swedish Research Council, 2018-07085Swedish Research Council, 2019-05487
Note

Funding: Excellence Center at Linkoping and Lund in Information Technology (ELLIIT); Swedish e-Science Research Centre (SeRC); Swedish Research Council (VR)Swedish Research Council [2018-07085, 2019-05487]; Swedish Research CouncilSwedish Research CouncilEuropean Commission [2018-05973]

Available from: 2021-06-30 Created: 2021-06-30 Last updated: 2021-09-01Bibliographically approved
Dieckmann, M. E., Falk, M., Folini, D., Walder, R., Steneteg, P., Hotz, I. & Ynnerman, A. (2020). Collisionless Rayleigh–Taylor-like instability of the boundary between a hot pair plasma and an electron–proton plasma: The undular mode. Physics of Plasmas, 27(11), 1-14, Article ID 112106.
Open this publication in new window or tab >>Collisionless Rayleigh–Taylor-like instability of the boundary between a hot pair plasma and an electron–proton plasma: The undular mode
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2020 (English)In: Physics of Plasmas, ISSN 1070-664X, E-ISSN 1089-7674, Vol. 27, no 11, p. 1-14, article id 112106Article in journal (Refereed) Published
Abstract [en]

We study with a two-dimensional particle-in-cell simulation the stability of a discontinuity or piston, which separates an electron–positron cloud from a cooler electron–proton plasma. Such a piston might be present in the relativistic jets of accreting black holes separating the jet material from the surrounding ambient plasma and when pair clouds form during an x-ray flare and expand into the plasma of the accretion disk corona. We inject a pair plasma at a simulation boundary with a mildly relativistic temperature and mean speed. It flows across a spatially uniform electron–proton plasma, which is permeated by a background magnetic field. The magnetic field is aligned with one simulation direction and oriented orthogonally to the mean velocity vector of the pair cloud. The expanding pair cloud expels the magnetic field and piles it up at its front. It is amplified to a value large enough to trap ambient electrons. The current of the trapped electrons, which is carried with the expanding cloud front, drives an electric field that accelerates protons. A solitary wave grows and changes into a piston after it saturated. Our simulations show that this piston undergoes a collisionless instability similar to a Rayleigh–Taylor instability. The undular mode grows and we observe fingers in the proton density distribution. The effect of the instability is to deform the piston but it cannot destroy it.

Place, publisher, year, edition, pages
American Institute of Physics (AIP), 2020
Keywords
PIC simulation, collisionless plasma, shock
National Category
Fusion, Plasma and Space Physics
Identifiers
urn:nbn:se:liu:diva-171119 (URN)10.1063/5.0018321 (DOI)000591344800002 ()
Note

Funding agencies:Ecole Nationale Superieure de Lyon, Universite de Lyon; French National Program of High Energy (PNHE); EPOCH [EP/P02212X/1]; French supercomputing facilities GENCI [A0070406960]

Available from: 2020-11-05 Created: 2020-11-05 Last updated: 2020-12-16Bibliographically approved
Falk, M., Ljung, P., Lundström, C., Ynnerman, A. & Hotz, I. (2020). Feature Exploration in Medical Volume Data using Local Frequency Distributions. In: B. Kozlíková, M. Krone, and N. N. Smit (Ed.), : . Paper presented at Eurographics Workshop on Visual Computing for Biology and Medicine (VCBM), Tübingen, Germany, September 28 – October 1, 1010.
Open this publication in new window or tab >>Feature Exploration in Medical Volume Data using Local Frequency Distributions
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2020 (English)In: / [ed] B. Kozlíková, M. Krone, and N. N. Smit, 2020Conference paper, Published paper (Refereed)
Abstract [en]

Frequency distributions (FD) are an important instrument when analyzing and investigating scientific data. In volumetric visualization, for example, frequency distributions visualized as histograms, often assist the user in the process of designing transfer function (TF) primitives. Yet a single point in the distribution can correspond to multiple features in the data, particularly in low-dimensional TFs that dominate time-critical domains such as health care. In this paper, we propose contributions to the area of medical volume data exploration, in particular Computed Tomography (CT) data, based on the decomposition of local frequency distributions (LFD). By considering the local neighborhood utilizing LFDs we can incorporate a measure for neighborhood similarity to differentiate features thereby enhancing the classification abilities of existing methods. This also allows us to link the attribute space of the histogram with the spatial properties of the data to improve the user experience and simplify the exploration step. We propose three approaches for data exploration which we illustrate with several visualization cases highlighting distinct features that are not identifiable when considering only the global frequency distribution. We demonstrate the power of the method on selected datasets.

Keywords
Scientific Visualization, Frequency Distributions, Volume Rendering
National Category
Media and Communication Technology
Identifiers
urn:nbn:se:liu:diva-170755 (URN)10.2312/vcbm.20201166 (DOI)
Conference
Eurographics Workshop on Visual Computing for Biology and Medicine (VCBM), Tübingen, Germany, September 28 – October 1, 1010
Funder
Swedish e‐Science Research CenterELLIIT - The Linköping‐Lund Initiative on IT and Mobile Communications
Available from: 2020-10-20 Created: 2020-10-20 Last updated: 2021-09-23Bibliographically approved
Jönsson, D., Steneteg, P., Sundén, E., Englund, R., Kottravel, S., Falk, M., . . . Ropinski, T. (2020). Inviwo - A Visualization System with Usage Abstraction Levels. IEEE Transactions on Visualization and Computer Graphics, 26(11), 3241-3254
Open this publication in new window or tab >>Inviwo - A Visualization System with Usage Abstraction Levels
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2020 (English)In: IEEE Transactions on Visualization and Computer Graphics, ISSN 1077-2626, Vol. 26, no 11, p. 3241-3254Article in journal (Refereed) Published
Abstract [en]

The complexity of todays visualization applications demands specific visualization systems tailored for the development of these applications. Frequently, such systems utilize levels of abstraction to improve the application development process, for insta

Place, publisher, year, edition, pages
IEEE, 2020
Keywords
Data visualization; Visualization; Pipelines; Debugging; Interoperability; Documentation; Games; Visualization systems; data visualization; visual analytics; data analysis; computer graphics; image processing
National Category
Media and Communication Technology
Identifiers
urn:nbn:se:liu:diva-160860 (URN)10.1109/TVCG.2019.2920639 (DOI)000574745100009 ()31180858 (PubMedID)
Funder
Swedish e‐Science Research CenterELLIIT - The Linköping‐Lund Initiative on IT and Mobile CommunicationsSwedish Research Council, 2015-05462Knut and Alice Wallenberg Foundation, 2013- 0076
Note

Funding agencies:  Swedish e-Science Research Centre (SeRC); Deutsche Forschungsgemeinschaft (DFG)German Research Foundation (DFG) [RO3408/3-1]; ExcellenceCenter at Linkoping and Lund in Information Technology (ELLIIT); Knut and Alice Wallenberg Foundation (KAW)Knut & Alice

Available from: 2019-10-10 Created: 2019-10-10 Last updated: 2022-06-03
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ORCID iD: ORCID iD iconorcid.org/0000-0003-1511-5006

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