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.
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.
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}

How scientific conferences are like music festivals

Fresh out of the nightly brainfart department, a short look at the similarities between scientific conferences and music festivals as well as some tips and tricks that apply to both:

  • The bigger conferences often feature parallel sessions not unlike how music festivals can have multiple stages and concerts at the same time.

    Tip:  Take a look at the schedule beforehand and choose the talks/concerts you really must see beforehand, so you don’t miss out on anything important during the event.

  • The keynote speakers are like the headliners at a festival: big names in the field who are allowed more time to present their work.

    Tip: Keynotes and headline shows got that spot for a reason, while there are exceptions, in general you can expect high quality content and good delivery, so be sure to attend.

  • Big conferences and festivals can span multiple action-packed days and therefore be really exhausting.

    Tip: Eat and drink well to maintain your energy levels and just hang in there. Big conferences/festivals only come around once a year and you might not get the chance to go every year, so make the most of your time there!

Remote Desktop Tutorial – TU Delft edition

Earlier this week I discovered the magic of having access to my work pc from home by remote desktop wizardry. I’ve known for some time that it is possible, in a theoretical sense, but I always assumed there would be too much hassle involved. Now, thanks to the help my co-workers Francois and Ruud, I know better! And you can too 🙂

This is me doing a VMTK levelset segmentation at my TU Delft pc... On a Sunday morning from home!
This is me doing a VMTK levelset segmentation at my TU Delft pc… On a Sunday morning from home!

I will show you how to do this yourself (if you have a TU Delft desktop computer there too 😉 ) in a brief remote desktop tutorial after the jump:

Continue reading Remote Desktop Tutorial – TU Delft edition

Using Evernote to organize your PhD

Ideas, meeting minutes, lab journal notes, paper summaries, travel information, graduate school homework and project notes. During your life as a PhD you generate, process and receive so much information that organizing all of this can be a daunting task. Luckily there is great software that can help you get organized by making it easy to collect and find information across your devices. For me personally, Evernote is the best fit, so in this post I’ll show you how I use Evernote to organize my PhD.

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Preparing for a Scientific Meeting for PhD Students

The noble art of preparing for a scientific meeting is perhaps not the most exciting skill in your career, but fruitful meetings are definitely an important component of a successful PhD project. This week I flew to Leeds to visit the Virtual Pathology team with my medical project partners. So, an anatomist, a surgeon and a pathologist walk into a meeting room… This doesn’t sound like the start of a great joke, so I’ll stop myself right there. What I would like to discuss in this blog post however are some tips for having successful meetings. In your PhD there will be many meetings to be had, so you might as well make the most of them. Of course there are several types of meetings: the regular meetings with your supervisory team to discuss your progress and plans, meetings with your project partners to discuss project progress and then there are meetings with other scientists to discuss the possibilities for collaborations.

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Scientific Presentation Pro Tips Part 2: The Presentation

A while ago I wrote the first part of a series of posts on scientific presentation tips to present your research in a memorable and interesting way. In part 1, I described the preparation process, now it’s time for the actual presentation giving: what to do, what to wear and other convenient tips.

Continue reading Scientific Presentation Pro Tips Part 2: The Presentation

Inbox Zero Redux: reduce e-mail overload like a boss

I thought it would be nice to discuss one of the ‘golden oldies’ of e-mail overload countering here: Inbox Zero and my modifications to Inbox Zero Redux. It’s been a while since this approach was introduced by Merlin Mann (an e-mail wizard name if I’ve ever heard one), 7 years already, but I still try to get my inbox to zero e-mails daily. And actually succeed most of the times. It might be a different story if suddenly start receiving hundreds of e-mails every day, but for now, this is working well for me.

Continue reading Inbox Zero Redux: reduce e-mail overload like a boss

Scientific Presentation Pro Tips Part 1: The Preparation

In this post I’d like to give you some scientific presentation tips to present your research well. Over the years as a student and now PhD candidate I’ve given many a presentation and had many a course on giving good presentations. In my first couple of presentations I was a complete nervous wreck and could barely breathe, later on this ‘evolved’ into smiling during the entire presentation combined with (bad) improvisational jokes and now I can even state I actually look forward to preparing and giving presentations. I’d have to say the course I’ve learnt the most from was definitely ‘The Art of Presenting Science’ by the awesome Gijs Meeusen and his team, so some of the tips I’m writing about, I picked up there. I cannot recommend this course enough, so do try and take it somewhere if you’re able to. If you’re not, I believe Veronika will do a nice write up about this course at some point (edit: She did and it’s glorious! Check it out here!) . This post will describe phase one in the presentation giving process: the preparation. Whether you’re presenting for your research group, at a conference or elsewhere, always be prepared 🙂

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The Standing Desk Review

For the past five months I’ve been in the luxurious position(s) of having the option to do my work while standing when I feel like it. This is all thanks to the pleasant people at my work that arranged a special standing desk for me. I think it’s a good time for a review of my standing desk experiences. In this post I will describe the benefits I’ve personally experienced as well as the disadvantages and some tips and tricks.

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Gamification in your PhD? Gamify Your Life with HabitRPG!

Is gamification a suitable technique for maintaining motivation and momentum in your PhD? While I dislike buzzwords like these a lot, I think gamification has great potential in many applications. I guess most people are familiar with the success of Stack Overflow, a well-known example of gamification done right, but can techniques like these be successfully applied to everyday activities as well?

Continue reading Gamification in your PhD? Gamify Your Life with HabitRPG!