The following list contains different types of publications related to the work of the SURFsara visualization group. It contains both publications that were (co-)authored by us, as well as publications by other parties describing work and projects we were involved in.

Visualization applied to 2D/3D scientific datasets
Paul Melis, SURFsara • 15-02-2019 • Presentation (video) • English

An overview of uses for and types of visualization, tooling choices and much more. A case study of applying visualization to a simulation of red blood cells by the UvA. Remote visualization overview. The CompBioMed "Virtual Humans" animation. And some more advanced methods of visualization, such as AR, VR or the Looking Glass.

3d printingaugmented realitycompbiomedinformation visualizationlooking glassmicrosoft hololensremote visualizationscientific visualizationvirtual reality

VARR Out seminar - 5 november 2018
University of Amsterdam, SURF • 30-11-2018 • Video • Dutch

A retrospective on the first VARR Out seminar on Virtual and Augmented Reality for Research, held November 5th, 2018. This event was co-organized by SURF and the University of Amsterdam and brought together Dutch researchers working with/on AR and VR and technology providers. The program included presentations by researchers and a demonstration market.

Slides for the presentations, plus a video recording of a selection of them, can be found here.

augmented realityuniversity of amsterdamvirtual reality

50 days of play: first-time development for the Hololens, a retrospective and comparison with VR
Paul Melis, SURFsara • 30-11-2018 • Presentation (slides) • English

Experiences doing first-time development for the Microsoft HoloLens, on a project involving scientific visualization with Unity and VTK.

Presented at the VARR Out seminar 2018.

augmented realitymicrosoft hololensunityvarr out seminarvtk

Gegevens gevangen in een tastbaar model
Marleen Hoebe • 25-08-2018 • Newspaper article • Dutch

An interview in Parool with Paul Melis (SURFsara) on the use of 3D printing for scientific visualization.

3d printing3dataprint

3DATAPRINT: On the use of 3D printing for scientific visualisation
P.E.C. Melis, S.J. Marrink, S. Thallmair, A. Blass, V. Spandan Arza, J. Nijkamp, N. Janssen, G. Z├ívodszky • 15-06-2018 • Report • English

We present the results of a case-based study in using 3D printing for applications in scientific visualization. The goal was to get insight into the practical sides of producing 3D prints from 3D scientific data and make a (qualitative) evaluation of the added values of using 3D printing for visualization purposes. A set of different use cases, from varying scientific domains, is presented. The 3D prints produced for these cases were deemed a success, with more detail in the 3D prints possible than expected, while providing alternative interpretation and communication options compared to on-screen 2D/3D visualizations. For example, in providing more natural interaction with the 3D model and easier communication by physically pointing out elements of interest, or just handing over a 3D print. For the cases involving complex 3D surfaces the advantages appeared to be in a better sense and understanding of spatial structures compared to onscreen 3D visualization and more natural interaction.

3d printing3dataprintblendernetherlands cancer institutepythonscientific visualizationsimulationuniversity of amsterdamuniversity of groningenuniversity of twente

GeneVis - An interactive visualization tool for combining cross-discipline datasets within genetics
Casper van Leeuwen • 7-05-2018 • Article • English

GeneVis is a web-based tool to visualize complementary data sets of different disciplines within the field of genetics. It overlays gene-cluster information, gene-interaction data and gene-disease association data by means of web-based interactive graph visualizations. This allows an intuitive and quick assessment of possible relations between the different datasets. By starting from a high-level graph abstraction based on gene clusters, which can be selected for detailed inspection at the gene-interaction level in a separate window, GeneVis circumvents the common visual clutter problem when using gene datasets with a high number of gene entries.

d3.jsinformation visualizationvumcweb-based visualization

Automation and orchestration
Migiel de Vos (SURFnet), Tijs de Kler (SURFsara) • 14-03-2018 • blog post and animation • English

SURF conducts research on the opportunities of automation and orchestration. We work on our own automation and orchestration framework that offers provisioning across multiple technology domains in a uniform way. By implementing automation and orchestration, we are able to respond to users' current and future network needs.

At SuperComputing 2017 in Denver, USA a demonstration was shown of automated network provisioning. Visitors could direct the data flow in a network setup in Denver. They would wear a Microsoft HoloLens that showed instructions and data overlays in an augmented reality interface.

augmented realitydemonstrationmicrosoft hololenssupercomputing 2017surfnetunity

Visualizing large cell-based simulations: a bloody mess?
Paul Melis • 12-12-2017 • Presentation (slides) • English

A case study of different visualization approaches applied to data from cell-based simulations of blood by the University of Amsterdam. From classical scientific visualization, through information visualization using a custom tool to interactively visualizing millions of cells. Plus what it takes to turn the simulation of data into beautiful animations worthy of an IMAX theater.

Presented at the Super D event 2017, Amsterdam.

blendercompbiomedhpcscientific visualizationsimulationuniversity of amsterdam

Virtual Humans
Fernando Cucchietti (BSC), Guillermo Marin (BSC), Paul Melis (SURFsara), Casper van Leeuwen (SURFsara) and many others • 12-10-2017 • Animation • English

A 6-minute animation describing the achievements and goals of researchers working on recreating the human body inside a computer. Through accurate scientific data visualizations, Virtual Humans gives us a glimpse of this truly personalised medicine of the near future, and its long term implications for our healthcare and our lifestyle.

Presented at the London Science Museum Lates.

blendercompbiomedhpcscientific visualizationsimulationuniversity of amsterdam

Visualizing large-scale simulations of blood
Paul Melis • 27-10-2017 • Presentation (video) • English

A use case of applying Blender to visualizing simulations of blood on the cellular level, using simulation data by the University of Amsterdam. These simulations are produced on high-performance compute clusters and can contain thousands of cells. As these are scientific simulations there are some differences and challenges compared to the usual use of Blender for VFX and animations.

Presented at the Blender Conference 2017, Amsterdam.

blendercompbiomedhpcscientific visualizationsimulationuniversity of amsterdam

Animatie Netwerkfunctievirtualisatie in een virtual-realityomgeving
Gerben van Malestein (SURFnet) • 26-01-2017 • Blog post with animation • Dutch

A really cool animation showing the workings of our shared SC16 demonstration with SURFnet, involving network function virtualization, virtual reality and remote data processing.

The associated blog post is in Dutch, but the animation is narrated in English.

demonstrationhtc viveleap motionmicrosoft kinectsupercomputing 2016surfnetunreal enginevirtual reality

Demonstrating network functions with virtual reality
Migiel de Vos (SURFnet) • 16-12-2016 • SURF Innovation Blog article • English
demonstrationhtc viveleap motionmicrosoft kinectsupercomputing 2016surfnetunreal enginevirtual reality

Interactive volume rendering using the Oculus Rift and the Visualization Toolkit
Jordy Perlee (UvA) • 17-06-2015 • Bachelor thesis • English

Bachelor thesis on the use of OculusVTK (developed by SURFsara) for interactive volume rendering in Virtual Reality.

university of amsterdamvirtual realityvtk

Edubloggers verkennen virtual reality
Marjolein van Trigt (Computable) • 20-05-2016 • Article • English
virtual reality

Case: Shopping in the virtual supermarket
Wilma Waterlander (VU), Tijs de Kler (SURFsara) • 18-05-2016 • SURF knowledge base article • English
serious gamingunityvirtual supermarketvu university

Using a 3D virtual supermarket to measure food purchase behavior: a validation study
W.E. Waterlander (University of Auckland), Y. Jiang, I.H.M. Steenhuis, C. Ni Mhurchu • 28-04-2015 • Scientific publication • English
serious gamingunityvirtual supermarketvu university

A Milky Way Galaxy simulation using 1 billion particles
Jeroen Bedorf, Evghenii Gaburov (SURFsara), M.S. Fuji, K. Nitadori, T. Ishiyama, S. Portegies Zwart • 20-11-2014 • Animation • English

In this short video a large-scale galaxy simulation performed on the GPU is shown. 3D visualization was performed using the Bonsai software, mostly by Jeroen Bedorf (CWI) and Evghenii Gaburov (SURFsara), with some small contributions by the Visualization group. Easter egg: try to spot the USS Enterprise zipping by ;-)

cwigpuleiden universityscientific visualizationsupercomputing 2014

The New Zealand Virtual Supermarket
Wilma Waterlander (University of Auckland) • 21-05-2014 • Article • English
serious gamingunityuniversity of aucklandvirtual supermarket

Criminele Netwerken
VPRO Labyrint & prof. dr. Peter Sloot (UvA) • 20-11-2013 • Short documentary • Dutch

A short documentary on the use of data analysis and simulation for the disruption of criminal networks. The interactive netwerk visualizations were done using software co-developed by UvA and SURFsara and were filmed in the Collaboratorium.

graph visualizationinformation visualizationuniversity of amsterdam

Real-time long-distance pre-visualisation with live keying using commodity hardware: compositing in the cloud
Paul Melis (SARA), Meindert Kok (NFTA), et al. • 08-10-2013 • Technical report • English

A in-depth technical description of the demonstration with NFTA at the Cinegrid Workshop 2012

c++cinegridclouddemonstrationnetherlands film academypythonremote visualizationstreaming

Live Actors in Virtual Sets Compositing in the Cloud
SARA, NFTA • 01-02-2013 • Video registration • English

Performed at the 2012 CineGrid International Workshop this technology demonstration showed the combination of a live movie set with actors in Amsterdam, real-time green-screen compositing and direction from San Diego. The camera images recorded in Amsterdam were processed in real-time and streamed over a dedicated optical connection to the CineGrid workshop in San Diego.

The movie linked was produced by CalIT2 and records the demonstration.

cinegridclouddemonstrationnetherlands film academyremote visualizationstreaming

Cyberdorpspomp voor onderzoekers
Richard Keizer (AG Innovation) • 15-06-2012 • Article • Dutch

A short article on the Collaboratorium, published not long after it was opened.


The virtual supermarket: an innovative research tool to study consumer food purchasing behaviour
W.E. Waterlander (VU), M. Scarpa (SARA), D. Lentz (VU), I.H.M. Steenhuis (VU) • 25-07-2011 • Scientific publication • English

A report on the first Virtual Supermarket project, a collaboration between VU University and SARA.

serious gamingunityvirtual supermarketvu university

Disk to Network Streaming at 42 Gbit/s
R. van der Pol (SARA) • 11-02-2011 • Presentation • English

An in-depth technical overview of our 42 Gbit/s high-resolution visualization streaming demo, as shown at SC10.

remote visualizationscientific visualizationstreamingsupercomputing 2010