Eggsperts

Source: MVO Pluimvee Award - Follow @in_ovo - Official website

Internship - Getting results

In the meantime, half of my internship has passed and we're finally getting some results. The first few weeks I've mainly done some reading and getting acquainted with the various software packages. AFter that, there were some long weeks of debugging and testing our template matching program, called Argos. Luckily, we're in good contact with FEI, so some bugs were fixed pretty fast and we exchanged several tips. It's a nice idea to be helping out with the development of a commercial software package.

The image you see above, is the 3D visualization of different bacteria. This is done with template matching and segmentation based on the resultating correlation files. The original data consists of cryo electron microscopy tomograms.

In the next few weeks, I'll be working on a protocol so the rest of the people in the lab can create images like this as well. Images belong to the department of Molecular Cell Biology, section Electron Microscopy of the LUMC. Please contact them if you want to use (one of) the images.

Scuba diving marketing

Scuba divers are weird folks. Not only do they love to get into water below 14° Celsius, get aroused by the encounter with a 4 mm nude snail or are the only people in the water loving to see a shark up and close, they also collect as much information about the people they dived with as possibly can. Names, dates of birth, addresses, shoe sizes but most of all: stickers and stamps.

Have a look at the log of an average diver and it's filled with stamps and stickers in all shapes and colours. Most people use standard stamps of cartoon characters or have the same stickers you used to get from your teacher when you were in kindergarten. It's like divers want to leave their mark on every buddy they had or sort of mark their territory.

But you could also see it as public relations or marketing. Some diver's sticker or stamp are real collectables to others. And of course it is a nice little memory of a special dive. So I must admit, I'm participating in this collection frenzy as well. Not as a collector, but I do have my own marketing material as you can see above. Cool, ain't it?

If you want to get one too, book a guided dive, introduction dive or diving course at Divecentre De Grevelingen.

Research internship

Automatic segmentation, rendering and visualization of cellular macromolecular complexes in (cryo) electron tomograms

For my master biomedical sciences I'm doing a research internship at the department of Molecular Cell Biology, section Electron Microscopy in the LUMC. During this 20 week project, I'm working on developing a protocol for the automatic segmentation and visualization of cellular structures in cryo electron tomograms.

In short, this means that I'm trying to automatically detect structures in 3D images of cells, in order to make nice 3D models out of these structures. Why? 3D models can help to clarify a theory and make results more easy to understand. Segmentation (the allocation of parts of an image to a structure) is currently done by hand. This is a very time-consuming and subjective method. I'm going to use small 3D-volumes to detect larger structures in the tomograms. This is called template matching.

During this project I'll be working with a programm called ARGOS, which is designed for template matching in tomograms by FEI (producer of electron microscopes), and with a software package called Amira.

My whisky cabinet

For a while I've been collecting interesting whiskies, as I'm really hooked on this refined drink. I won't call my self a connaisseur, but I have tasted a few and know what I like. If you're interested, please have a look at my collection on connosr.com.

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