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 printing • augmented reality • compbiomed • information visualization • looking glass • microsoft hololens • remote visualization • scientific visualization • virtual 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.
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 reality • microsoft hololens • unity • varr out seminar • vtk
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 printing • 3dataprint
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. Závodszky • 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 printing • 3dataprint • blender • netherlands cancer institute • python • scientific visualization • simulation • university of amsterdam • university of groningen • university 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.js • information visualization • vumc • web-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.
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.blender • compbiomed • hpc • scientific visualization • simulation • university of amsterdam
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.
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.
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.
Demonstrating network functions with virtual reality
Migiel de Vos (SURFnet) • 16-12-2016 • SURF Innovation Blog article • English
demonstration • htc vive • leap motion • microsoft kinect • supercomputing 2016 • surfnet • unreal engine • virtual 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 amsterdam • virtual reality • vtk
Case: Shopping in the virtual supermarket
Wilma Waterlander (VU), Tijs de Kler (SURFsara) • 18-05-2016 • SURF knowledge base article • English
serious gaming • unity • virtual supermarket • vu 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 gaming • unity • virtual supermarket • vu 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 ;-)
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.
Real-time long-distance pre-visualisation with live
keying using commodity hardware: compositing in
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 2012c++ • cinegrid • cloud • demonstration • netherlands film academy • python • remote visualization • streaming
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.
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.collaboratorium
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 gaming • unity • virtual supermarket • vu 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 visualization • scientific visualization • streaming • supercomputing 2010