Weekly Status Update #2

It’s time for another Weekly Status Update. This time featuring project meetings, half-way points, Scrum and a webcam feed for a coffee bar featuring great tits ;)

  • This week I had a user-committee meeting with the STW (where my project funding comes from). These meetings happen every six months, but this time it was extra special, because at this halfway-point, a decision is made on the continuation of the project. Unfortunately the decision had to be postponed, because several members of our user-committee couldn’t attend the meeting. I’ll have to delay my ‘Champagne for everyone!’-moment just a little while longer.
  • Speaking of halfway-points, this month I started the third year of my PhD. Time sure flies when you’re a PhD candidate… I am not too happy about this, because I feel there is still a lot of work to do and precious little time to get it done in. But now is not the time to get overwhelmed of course, if anything it is time to start stepping up my game ;)
  • In the interest of games being stepped up, my cool office roomies and I started a Scrum board for our PhD projects. I will write a full blog post on the basics of Scrum and how to apply Scrum in your PhD after I try it out for a little while longer. It is a definite upgrade though, because earlier I went from this:
    Desktop Scrum

    Desktop Scrum

    to this:

    Whiteboard Scrum

    Whiteboard Scrum

  •  And now for something completely different. If you have a dual (or triple) monitor set-up, I have a suggestion for a nice webcamfeed to display on your second screen. Go forth and check out the Piip-Show. It’s a live show about  life inside a bird feeder decorated as a coffee bar. It features sound too, so it is also great if you enjoy listening to some relaxing nature sounds while you work. It’s really cool to see all the different creatures enjoying some snacks in the bar. I’ve seen magpies, nuthatches, great tits, blue tits, bullfinches, squirrels, woodpeckers and sparrows so far. That’s right, nuthatches, peckers and great tits that are SFW ;) I hope I can convince you of the awesomeness of the whole thing with these action screencaps I took:

That about sums up my week, have a great Easter weekend!

Search Term Gems: Your Questions Answered #1

It’s time for some search term gems! I thought it might be beneficial to look through the search terms people used to get to my website and respond to any questions you might have. Depending on the amount of search terms I get usable for this, I hope to make this into a regular thing :) Let’s get started with the first 5 questions after the jump: Continue reading

Weekly Status Update #1

I’ve noticed I am having a really hard time maintaining a regular blog posting frequency here. So, inspired by Charl Botha’s always awesome ‘Weekly Head Voices’, I present you: the Weekly Status Update #1. The general idea and rules for these status updates:

  1. They will be bite-sized short updates.
  2. They will contain assorted musings, cool finds and perhaps some highlights from my lab journal.
  3. These may or may not contain useful/helpful information and will probably be completely incoherent.
  4. I have a thing for bullet point lists, so expect those in there too.

Right, so let’s get started!

  • As you may or may not know, I had the privilege of being the daily supervisor for two students for their nine month Master of Science thesis projects. Last month, both students successfully obtained their MSc titles. If these theses were like their babies, I would be like a very proud grandmother. Seriously though, I don’t really know how to describe how proud I am of them and their awesome projects, but I can describe their projects instead:
    • Berend Klein-Haneveld presented “RegistrationShop – an interactive 3D medical volume registration tool”. In his work he developed RegistrationShop as a tool that aims to make the complex process of 3D volume registration easier by providing simple interaction techniques and real-time visual feedback of the current registration results. Users are able to place landmarks in 3D either by surface picking or by tracing a ray through the volume until the desired location is reached. During the registration process they are provided with visualizations of both the moving and fixed volumes as well as the current registration result in a combined view.


      Main interface of Berend Klein-Haneveld’s RegistrationShop with two CT lung datasets.

    • Cees-Willem Hofstede presented “The Online Anatomical Human – an online browser and annotation system for real human anatomy”. He worked on bringing anatomical education to a web browser, by creating an online environment in which a 3D anatomical model of the pelvis is linked to 2D medical imaging data. Users are able to annotate structures directly on the 3D mesh using landmark, brush and line tools and can enrich the model with their annotations.


      The Online Anatomical Human with a 3D model of the pelvis and linked orthogonal planes containing cryosectional data and label information.

  • You don’t need to tell me how awesome anatomical research is, but I read this cool article on how anatomical science is undergoing a revival. If there is anything I have learnt in working with anatomical researchers during my PhD project, it is that human anatomy is not a fully explored known thing. There are still many exciting new discoveries to be made in the field. Also, the consequences of lacking anatomical knowledge can be disastrous for surgical outcome. This combined with medical imaging and visualization techniques makes for a very exciting area of scientific research.
  • Do you know what sounds baby sloths make? Neither did I, but wow, am I glad I found out! Meh! Eh!

That’s about all I wanted to share for this week! Please reprimand me if I do not manage to post weekly status updates and enjoy your week :)

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:

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The Delft Data Science New Year Event

Yesterday the Delft Data Science New Year Event took place in, you guessed it, Delft! It was a fun afternoon filled with interesting talks, posters and demos. The head of our Computer Graphics and Visualization group, Elmar Eisemann, gave a talk on ‘Visualization and Big Data’ including live demos of remote rendering using Exposure Render, the webviewer of my project made by MSc student Cees-Willem Hofstede, and also his Leap Motion powered controls. 

The Delft Data Science crowd

The Delft Data Science crowd. I was there too! ;) Picture courtesy of the CUbRIK Project

Check out my first attempt at Storifying it after the jump:

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The new MedVis book is available! I’ve already seen a copy and wow, it is glorious! Filled with beautiful imagery and all the latest and greatest medvis developments in many interesting research areas. My name is even in it somewhere ;) Check the companion website for details on where to order and exclusive online content!

The new MedVis book

The new MedVis book cover


My all time favorite task management system has a 24 hour sale (over 50% off) on their premium year  subscription. If you are already a premium user they’ll extend your subscription for a year ^^

Three tasks a day keeps the procrastination away

These last few months I have adopted an amazingly low-tech morning routine to start my workday consisting of selecting the three tasks I want to get done today. Sometimes our task managers can get flooded with an overload of tasks and this overload can make it hard to focus. This feeling of being overwhelmed can quickly turn into procrastination if you let it. For me it helps to pick three things that I at least want to get done that day as the first thing I do when I get to work. I am of course not the first person to think of something like this, but I just want to share this as a simple tip.

My desk setup

My desk setup with the three tasks system in the upper left (and lots of cable clutter I’m not too proud of)

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New publication: Lymphatic drainage pathways from the cervix uteri

In a previous post, I mentioned I made a 3D interactive pdf for a medical publication. This paper was recently accepted at the Gynecologic Oncology journal and it is now available online: Lymphatic drainage pathways from the cervix uteri; implications for radical hysterectomy? I’ll try and do a little ‘Science in plain English’, for those interested but not all that familiar with the medical jargon.

A hysterectomy is a surgical treatment for early-stage cervical cancer where the womb is taken out. Typically also part of the lymphatic system in the region is removed to prevent the cancer from spreading. There are different types of hysterectomies that vary by how much tissue is taken out: Continue reading