Updated my Publications Page

In a small attempt at blowing away the cobwebs in this website, I have updated my Publications page. I switched from manual updates (*shudder*) to the Papercite plug-in, which updates from a bibtex file stored in my Dropbox. I am in the process of adding PDF files for every single publication, and experiencing the joys of wading through publisher regulations to check what their conditions are for sharing post-prints.

In this regard, SHERPA/RoMEO has been very helpful. You simply look for a specific journal and see what they allow. For example, the Computers & Graphics journal published by Elsevier places a 24-month embargo on putting your post-print on open access repositories and institutional pages, but does allow author’s to put the accepted manuscript on their personal website or blog immediately. Yay for having a blog!

So here is a blog-exclusive, the PDF of our accepted paper ‘Real-time Field Aligned Stripe Patterns'[1] is now hosted on this very website! Another recent publication that I may have failed to mention here so far is our Survey on Multimodal Medical Visualization[2].

[1] [doi] N. Lichtenberg, N. Smit, C. Hansen, and K. Lawonn, “Real-time field aligned stripe patterns,” Computers & Graphics, vol. 74, p. 137–149, 2018.
[Bibtex]
@article{lichtenberg_real-time_2018,
title = {Real-time field aligned stripe patterns},
volume = {74},
issn = {0097-8493},
url = {http://noeskasmit.com/wp-content/uploads/2018/08/lichtenberg_2018.pdf},
doi = {10.1016/j.cag.2018.04.008},
abstract = {In this paper, we present a parameterization technique that can be applied to surface meshes in real-time without time-consuming preprocessing steps. The parameterization is suitable for the display of (un-)oriented patterns and texture patches, and to sample a surface in a periodic fashion. The method is inspired by existing work that solves a global optimization problem to generate a continuous stripe pattern on the surface, from which texture coordinates can be derived. We propose a local optimization approach that is suitable for parallel execution on the GPU, which drastically reduces computation time. With this, we achieve on-the-fly texturing of 3D, medium-sized (up to 70 k vertices) surface meshes. The algorithm takes a tangent vector field as input and aligns the texture coordinates to it. Our technique achieves real-time parameterization of the surface meshes by employing a parallelizable local search algorithm that converges to a local minimum in a few iterations. The calculation in real-time allows for live parameter updates and determination of varying texture coordinates. Furthermore, the method can handle non-manifold meshes. The technique is useful in various applications, e.g., biomedical visualization and flow visualization. We highlight our method{\textquoteright}s potential by providing usage scenarios for several applications.},
urldate = {2018-07-29},
journal = {{Computers \& Graphics}},
author = {Lichtenberg, Nils and Smit, Noeska and Hansen, Christian and Lawonn, Kai},
month = aug,
year = {2018},
keywords = {Computational geometry,, Computer graphics, Parameterization, Visualization},
pages = {137--149},
}
[2] [doi] K. Lawonn, N. Smit, K. Bühler, and B. Preim, “A Survey on Multimodal Medical Data Visualization,” Computer Graphics Forum, 2017.
[Bibtex]
@article{lawonn_survey_2017,
title = {A {Survey} on {Multimodal} {Medical} {Data} {Visualization}},
doi = {10.1111/cgf.13306},
journal = {{Computer Graphics Forum}},
author = {Lawonn, Kai and Smit, Noeska and B{\"u}hler, Katja and Preim, Bernhard},
abstract = {Multimodal data of the complex human anatomy contain a wealth of information. To visualize and explore such data, techniques
for emphasizing important structures and controlling visibility are essential. Such fused overview visualizations guide
physicians to suspicious regions to be analyzed in detail, e.g. with slice-based viewing. We give an overview of state of the art
in multimodal medical data visualization techniques. Multimodal medical data consists of multiple scans of the same subject
using various acquisition methods, often combining multiple complimentary types of information. Three-dimensional visualization
techniques for multimodal medical data can be used in diagnosis, treatment planning, doctor-patient communication
as well as interdisciplinary communication. Over the years, multiple techniques have been developed in order to cope with
the various associated challenges and present the relevant information from multiple sources in an insightful way. We present
an overview of these techniques and analyze the specific challenges that arise in multimodal data visualization and how recent
works aimed to solve these, often using smart visibility techniques. We provide a taxonomy of these multimodal visualization applications
based on the modalities used and the visualization techniques employed. Additionally, we identify unsolved problems
as potential future research directions.
},
month = oct,
year = {2017},
url = {https://vis.uib.no/wp-content/papercite-data/pdfs/LawonnSmit-2017-MULTI.pdf}
}

New video interview

Another day, another video interview 😉 This time about medical visualization and computer science in general for the University of Bergen, department of Informatics. Medical visualization is also an active research topic here in the recently established Mohn Medical Imaging and Visualization (MMIV) centre.

The video was produced by Joakim Birkelund, who did an absolutely amazing job with editing and camera-work.

IEEE VIS 2017 Conference Report

My first conference report not on medvis.org, and not only that, a part of it is on eagereyes.org, and a part of it is right here! I’ll write conference reports on this blog as well, that may not contain 100% medvis content. There’s a first time for everything 🙂 Why not the IEEE VIS 2017 conference report?

Continue reading IEEE VIS 2017 Conference Report

Interview by the Department of Informatics at the University of Bergen

I’m going to go ahead and resist the urge to write about how I did not write for a while. Does this mean I just did? Anyway, I was recently interviewed by Pina Kingman and Eli Ertresvaag for the webpage of the Department of Informatics at the University of Bergen. I think I look super-tense, which is quite amazing considering this is my third video interview already 🙂 Also, it is quite noticeable in the written text that I don’t speak to 10-year-olds on the regular!

Noeska Smit

You can find the new interview here. Soon the written part will be available in Norwegian too! My very first video interview by Tweakers is still available here as well (in Dutch). The more recent second interview by the TU Delft Graduate School is still available too.

Almost 2017 – about time for a 2016 review

The last day of the year is upon us, so it’s just about time for a review of 2016 and to look forward to 2017! I really enjoyed writing a similar post last year, looking back at last year and looking forward to next year, so this means you get to suffer through another one of them :). Again, first of all, my best wishes to all of you for 2017! I hope you have an amazing year with lot of awesomeness all around.

Let’s get down to review business, starting with the looking back part:

  • Again, I didn’t blog so much, and I really hope to do more next year. I have a long to-do list especially for medvis.org, so I really want to get back into it soon. For personal reasons (still the same ones as last year), I am making this personal blog a bit less personal, and a bit more work-related. I am especially inspired currently by Veronika’s awesome (and frequent) blogposts to start writing more again myself 🙂
  • I guess one of the major events last year for me personally was my PhD defense. I wrote about it before, so won’t go into too much detail here. I am looking back still on a really cool day with a lot of cool people, and still very thankful to all those people that made this possible for me.
  • The other major event was moving to a new job and a new country. While last year, at the time of writing my review post, I had no idea this would actually be happening, I accepted a position as a researcher here in the Bergen, Norway, at the visualization group in the department of informatics from the 1st of August. A nice contrast from last year’s review: “I could definitely see that becoming sort of just a thing to do on the weekends while living there” vs. now: “Walking up mountains in the weekend, waddup!”:

    View from Fløyen on a nice Søndagstur
    View from Fløyen on a nice Søndagstur
  • I really enjoyed last year ‘academically’, as I got to enjoy a lot of my favorite activties: cool collaborations, paper writing, and attending conferences. I presented papers at Eurographics, EuroVis, VIS, and attended VCBM, co-authoring a paper there too and winning a MedViz image award. I still also have two journal papers under revision, and I find I enjoy these less than conference papers, mainly because they have been dragging on over longer periods of time. Besides, the papers in our field in top conferences end up in journals anyway, and then you get to meet cool people at conferences as an added bonus. This could lead to new collaborations, which in turn could lead to new conference papers, and more conference attending 🙂 Yea, more of my favorite things!

As for looking forward, all three wishes I made last year for this year (more collaborations, wrapping up papers, getting doctorified + starting something new) came true, so fingers crossed for 2017’s plans as well:

  • First some news: from the 1st of January 2017, I’ll be working as an associate professor (tenure-track) in medical visualization at the Bergen visualization group. I am far beyond excited about this: the research environment and opportunities for true interdisciplinairy medvis collaborations here are incredible, so I am thankful for this amazing opportunity. Therefore, in 2017 and the coming years, I hope to further develop and establish my research agenda, perhaps moving away a bit from the pelvic area, and into new and exciting challenges.
  • In March, I am visiting Magdeburg again for the VCBM fachgruppe meeting. I visited Magdeburg last year to finalize a STAR, and look forward to returning next year.
  • In May, I am giving an invited talk together with Annelot Kraima at the annual national symposium for surgical assistants. Really excited to present our joint work including PelVis there for a new audience.
  • In 2017, I’ll also be co-chairing the EuroRV³ workshop, which is co-located with EuroVis 2017 in Barcelona (so much co- going on there! I also hope it will be co-ol ;)). The theme of this international EuroVis Workshop on Reproducibility, Verification, and Validation in Visualization will be “Perception in Visualization”, and we will be releasing a call for contributions soon :).
  • Finally, for 2017 besides continuing the things I’m already enjoying, I’m looking forward to new experiences and learning new skills. For instance, I am working on a project proposal currently, and will be teaching as well. I am also learning the Norwegian language, both via Duolingo as via a ‘real course’. Exciting times ahead!

That about wraps it up! I noticed compared to last year’s plans for next year, I now have more concrete plans lined up for next year already, and I consider this a good thing :). I hope this will help with focus and productivity in 2017. Again, all the best to all my (lol) dear blog readers: gott nytt år!

Defended my PhD thesis ‘The Virtual Surgical Pelvis: Anatomy Visualization for Education and Surgical Planning’

On the 31st of October, yes that’s Halloween, I successfully defended my PhD thesis/got doctorified. After presenting PelVis at IEEE VIS in Baltimore, I flew straight back to the Netherlands for this special occassion. Jetlag notwithstanding, I did manage to answer one hour’s worth of questions and can now officially call myself doctor (not that I would ^^). I’ve got some pictures for you, my faithful blog readers, of course, taken by my brother and official event photographer Joeri Smit:

I made a special page for my thesis, with some more details and a download link to the pdf version here. I had an amazing day, and would like to thank all those involved for this (read the Acknowledgments chapter in my thesis for a more wordy thank you ;)).

Photo by Marieke Roggeveen for the TU Delft
Photo by Marieke Roggeveen for the TU Delft

MedViz image contest 2016 winner!

noeska smitI know, it’s been a while since I last posted, and it’s also been a while since this happened, but… I was one of the winners of the MedViz image contest 2016 which was given out during the joint MedViz conference and Eurographics Workshop on Visual Computing in Biology and Medicine (aka VCBM), right here in Bergen.

There were three winners in this image contest, and besides our pelvis, also Sergej Stoppel and Niels de Hoon received a prize, with their works entitled ‘Arteries in focus’ and ‘Turbulent flow in an aorta’, respectively:

medviz image contest 2016 winners
MedViz image contest 2016 winners

I sent in the following submission:

PelVis

PelVis
Authors
Noeska Smit, Kai Lawonn, Annelot Kraima, Marco de Ruiter, Hessam Sokooti, Stefan Bruckner, Elmar Eisemann, Anna Vilanova
Short Description
This image depicts PelVis [1], an interactive application for surgical planning for the Total Mesorectal Excision (TME) procedure. During this surgical procedure, undesired side-effects occur in up to 80% of the cases due to damage to the autonomic nerves. These nerves are damaged easily, since they are not visible in pre-operative MRI or even during the surgery. In order to visualize these nerves, we built an atlas model, the Virtual Surgical Pelvis (VSP) [1], that reveals zones in which the autonomic nerves reside based on cryosection and immunohistochemical studies. In the PelVis application, we register this atlas to patient-specific clinical MRI data and thus are able to make patient-specific virtual models of the individual patient, and to reveal the autonomic nerve zones pre-operatively, as displayed here in yellow. We highlight the distance of the mesorectal wall to these nerve zones using a colormap (red to white) combined with isolines. Furthermore, other surgically relevant anatomy is shown for spatial context, without occluding the view on the mesorectum, and the linked atlas-enriched MRI data can be explored interactively [3].
[1]: Smit, N., Lawonn, K., Kraima, A., DeRuiter, M., Sokooti, H., Bruckner, S., … & Vilanova, A. PelVis: Atlas-based Surgical Planning for Oncological Pelvic Surgery. (2017) IEEE Transactions on Visualization & Computer Graphics, (1), 1-1. Accepted, to appear.
[2]: Kraima, A., Smit, N. N., Jansma, D., West, N. P., Quirke, P., Rutten, H. J., … & DeRuiter, M. C. (2014). 62. The virtual surgical pelvis: A highly-detailed 3D pelvic model for anatomical education and surgical simulation. European Journal of Surgical Oncology, 40(11), S32.

That’s right, we now have an award-winning pelvis :). Pictures in this post were made by the multi-talented Veronika Šoltészová.

VCBM 2016 paper ‘Sline: Seamless Line Illustration for Interactive Biomedical Visualization’ accepted!

Our paper ‘ Sline: Seamless Line Illustration for Interactive Biomedical Visualization’ was accepted for presentation at VCBM 2016, the 6th Eurographics Workshop on Visual Computing for Biology and Medicine. I’ve attended all VCBM editions since 2012, and am happy I can attend this one as well in Bergen, Norway. Which is extra convenient, since it’s my new hometown! I accepted a position as a researcher in the amazing visualization group at the University of Bergen and just started this week ^^

Back to Sline though, it’s a cool technique where you can pick an illustrative rendering style per structure using a single parameter slider. Behold:

Our Virtual Surgical Pelvis illustrated using Sline
Our Virtual Surgical Pelvis illustrated using Sline. So the organs and bones are hatched to draw attention here, while the nerves and vessels are de-emphasized by rendering only the silhouettes.

authors:  Nils Lichtenberg, Noeska Smit, Christian Hansen, and Kai Lawonn

abstract: In medical visualization of surface information, problems often arise when visualizing several overlapping structures simultaneously. There is a trade-off between visualizing multiple structures in a detailed way and limiting visual clutter, in order to allow users to focus on the main structures. Illustrative visualization techniques can help alleviate these problems by defining a level of abstraction per structure. However, clinical uptake of these advanced visualization techniques so far has been limited due to the complex parameter settings required.

To bring advanced medical visualization closer to clinical application, we propose a novel illustrative technique that offers a seamless transition between various levels of abstraction and detail. Using a single comprehensive parameter, users are able to quickly define a visual representation per structure that fits the visualization requirements for focus and context structures. This technique can be applied to any biomedical context in which multiple surfaces are routinely visualized, such as neurosurgery, radiotherapy planning or drug design. Additionally, we introduce a novel hatching technique, that runs in real-time and does not require texture coordinates. An informal evaluation with experts from different biomedical domains reveals that our technique allows users to design focus-and-context visualizations in a fast and intuitive manner.

VIS – SciVis paper ‘PelVis: Atlas-based Surgical Planning for Oncological Pelvic Surgery’ accepted!

Our paper ‘PelVis: Atlas-based Surgical Planning for Oncological Pelvic Surgery’ was accepted for presentation at our largest conference, VIS (and publication in IEEE Transactions on Visualization and Computer Graphics)!

Abstract: Due to the intricate relationship between the pelvic organs and vital structures, such as vessels and nerves, pelvic anatomy is often considered to be complex to comprehend. In oncological pelvic surgery, a trade-off has to be made between complete tumor resection and preserving function by preventing damage to the nerves. Damage to the autonomic nerves causes undesirable post-operative side-effects such as fecal and urinal incontinence, as well as sexual dysfunction in up to 80 percent of the cases. Since these autonomic nerves are not visible in pre-operative MRI scans or during surgery, avoiding nerve damage during such a surgical procedure becomes challenging.

In this work, we present visualization methods to represent context, target, and risk structures for surgical planning. We employ distance-based and occlusion management techniques in an atlas-based surgical planning tool for oncological pelvic surgery. Patient-specific pre-operative MRI scans are registered to an atlas model that includes nerve information. Through several interactive linked views, the spatial relationships and distances between the organs, tumor and risk zones are visualized to improve understanding, while avoiding occlusion. In this way, the surgeon can examine surgically relevant structures and plan the procedure before going into the operating theater, thus raising awareness of the autonomic nerve zone regions and potentially reducing post-operative complications. Furthermore, we present the results of a domain expert evaluation with surgical oncologists that demonstrates the advantages of our approach.