This is my diary about my period abroad to develop my master’s thesis work on Vascular Biomechanics at the KTH Solid Mechanics department. I will tell the whole period in several articles, let’s start with September.
I had the opportunity to go abroad to prepare my master’s thesis project. The project started from a deep interest in the mechano-chemo-biological behavior of human soft tissues. They show a variety of complex behaviors with a lot of non-linearity, time dependence, and variability. They act as a living entity, changing their properties over time also based on the chemical and mechanical environment. All of this makes it really interesting to be modeled from a computational point of view. For this project, I had the opportunity to work together Christian Gasser at the KTH Solid Mechanics department focusing on vascular tissues.
I want to describe my experience from a technical point of view but also describe life abroad. The following aims to tell the difficulties and joys found during this journey, and narrate both living in Stockholm and working in a higher education institution.
Week 0
It’s time to pack!
Ready for the departure on 1st of September. I was just packing the last stuff when Airbnb decided to send a surprising postcard. Only a few hours after the classic 48h in advance mail, that remember about your travel plan, another email has arrived. Well, my reservation has been deleted less than 48 hours before the departure. This might sound scary but the real problems show up in the following hours, it was impossible to book an apartment in Stockholm with Airbnb, and each booking was resulting canceled in a few hours. It was really shocking. I tried to book ten different apartments in less than 12 hours and each booking was canceled or refused.
Without breaking down I found another accommodation through Booking.com. Obviously, it was more expensive due to the short notice but I could not postpone the departure. An important conference was planned for the following week and one of the most advanced Schools of Engineering in Europe is waiting for me. The KTH Royal Institute of Technology, located in Stockholm, is one of the best universities in Europe in its field and is ranked in the top 100 worldwide. KTH conducts research and education in engineering and technology and is Sweden’s largest technical university.
Now, all is packed, booked, and checked, and it is time to say bye to Italy.
Arrived in Stockholm
September 1st at 10 am, I’m in Sweden, I’m in Stockholm. With only a few hours of flight, I passed from sunny 35°C to rainy 15°C. It is a little shocking. Now, I know what to do, it is simple: open the SL App, of Stockholm public transport, and buy a ticket. I need to reach the KTH to complete the last bureaucratic stuff and after lunch, I can check in to my apartment.
In less than one hour I’m at the KTH Entrè office, and after signing the last document I’m officially part of the KTH staff! I can go to the Solid Mechanics Department to know Christian and Marta but first is better to go to the apartment for the check-in and to leave the luggage. I’m traveling with two bags and one backpack and they aren’t that light, plus it is also raining and cold.
Kista Gallery
The first day was a little busy but it is the weekend now and I have free time to visit the center of Stockholm and discover the area around the apartment. This apartment is located in Kista, in the upper part of Stockholm. Only after a few weeks, I discovered that most Swedish people in Stockholm didn’t like Kista. Several people online (see Reddit or Quora community) write that is related to muggings and drug-related crimes however Stockholm is one of the most secure cities (19th) worldwide. Pretty different from Rome. Furthermore, Kista is the largest Information and Communications Technology cluster in Europe, and second in the world only after Silicon Valley.
Maybe, it is not the best area in Stockholm but I can walk for less than 10 minutes from my apartment to arrive at the Kista Gallery, in September the weather is really good. It is a medium size mall but there is also the metro station for line 11. However, to reach my office at KTH Solid Mechanics department I need more than 1 hour of traveling with the change of two metro lines. Fortunately, these metros are among the most efficient ever seen.
Stockholm public transport is very well organized, and a little complex but you can easily use the SL app or Google Maps to plan your trip. They work very well and allow you to plan precise paths, also with timetables e suggestions.
Week 1
It’s Monday, the 5th of September, and today the Biomechanics Summer School starts. During this week I was able to deepen in computational biomechanics with experts in this field. There have been both general and specific lessons about the state of art of modeling vascular and cerebral tissue, bone, cartilage, and tendon, skin. Furthermore, I met a lot of Ph.D. students and professors from all over Europe, and each of them is working on some aspect of biomechanics modeling.
It is the weekend and why not take a run and find out what’s around the apartment? Well, around my apartment it is full of offices and big buildings with a lot of apartments. But, just behind the highway, there are a lot of cottages very characteristic.
Groceries shop
Groceries shops are not so different from the Italian ones. However, there are a lot of funny imitations of Italian food with doubt about quality and taste. Surely I won’t try this deceptively packaged food.
In the meantime, I also restart my workout routine in the gym of the flat complex. It is a small gym but there is a multifunction lat machine with also a pec-deck for the chest. Unfortunately, there is no barbell for either squat or bench press, but there are some dumbbells. It should be good to restart training.
Week 2
Monday, September 12th, It’s time to start! Finally, I can completely be focusing on my master’s thesis. My project is now defined. It involves the study of atherosclerotic plaque in the carotid artery from a computational point of view.
Atherosclerosis
Atherosclerosis is related to the development of abnormalities on the artery wall. These developed lesions may lead to narrowing with the buildup of an atheromatous plaque. When severe, it can result in coronary artery disease, stroke, peripheral artery disease, or kidney problems.
The atheroma is an accumulation of material in the inner layer of the arterial wall. The material consists of macrophage cells and contains lipids, calcium, and fibrous connective tissue. These different tissues distribution gives us different material properties and they turn into a complex mechanical description to evaluate stress and strain distribution.
Biomechanical analysis
This branch of computational studies focused on atherosclerotic plaque aims to identify a sort of biomechanical index that could help the physician to decide if surgery is needed. What is desired to be avoided is the plaque rupture that could lead to an ischemic stroke and death. This rupture is linked with the fibrous cap morpho-chemo-mechanical properties and the computation studied could help to better understand these mechanisms.
Furthermore, current clinical guidelines for stroke prevention in patients with carotid stenosis caused by atherosclerotic plaques remain reliant on general patient characteristics (and lifestyle) and static measures of the degree of stenosis. These guidelines are a problem both for patients with asymptomatic stenosis and mild-moderate stenosis.
Now I need to read a lot of literature both on computational and physiopathological topics about plaque in the carotid artery.
In the meantime, I also received some news from my supervisor and I can start discovering, using, and improving the algorithm for the conversion of medical images to a volumetric mesh.
Mesh generation
I am currently receiving medical images from the physicians obtained with CTA scanner. CTA, named Compute tomography angiography, uses an injection of contrast liquid into the circulation to fully evaluate blood vessel structure. It gives us a volumetric image constituted of several slices. Each slice contains a monochromatic image where the grayscale is related to tissue density through the Hounsfield scale:
\operatorname {HU}=1000{\mu-\mu_{\text{water} }\over \mu_{\text{water} }- \mu_{\text{air} }}The first extraordinary step is made with Elucid software that allows us to segment different tissue inside the plaque. So, what I’m currently receiving is a volumetric segmented image that I have to transform into a volumetric mesh with related tissue properties.
Now, essentially the algorithm works in two steps. First, it extracts triangular isosurfaces with a specified density from the volumetric images and then fills tetrahedral elements for the bounded subvolumes. It exploits a constrained Delaunay tethraedrailization to generate the mesh. This toolbox is easy to use but requires a lot of work to optimize several parameters so as to obtain the optimal mesh quality.
flowchart TB id1(Read medical images with `nrrd_test.m`) id2(Volumetric image) id2.1(Volume2Mesh) id2.2(Mesh repair) id2.3(Mesh figure) subgraph Mesh direction LR id2-->id2.1-->id2.2-->id2.3 end id3(Metrics section) id3.1(Save .png) id3.1.1(Show mesh limited) id3.1.2(Delete axis) subgraph Image id3-->id3.1-->id3.1.1 id3.1-->id3.1.2 id3.2(Reading image) id3.2.1(Binarization and filling) id3.2-->id3.2.1 id3-->id3.2 end id4(Numerical indexes) id1-->Mesh-->Image-->id4
Furthermore, this image processing obliged me also to review some image processing algorithms such as 3D filtration, smoothing, and closure algorithms. With this image processing elaboration, I am also able to extract features like diameter, area, and roundness of the vessel.
Facilities
Today September 14th there will be the “Research work follow-up”. It is a meeting where everyone in the Christian research group can show their progress. So I met the whole group. There are Christopher and Marta, PhD students, Willy and Shaima, postdoc, and another trainee, Joey.
Joey and I work in the Master’s student room where we can have a desk with a good computer. This room is prepared for master’s students doing their thesis but it is actually empty, it is all for us. Obviously, I can’t use only a monitor and I need to find as soon as possible an HDMI cable to connect my laptop to their monitor. Larger screen, faster work.
This week is not finished and the best part is yet to come.
Tourist in September
It is September 16th and my girlfriend is coming from Rome. We will use the weekend to visit Stockholm better.
We spent several days as tourists. We visit the central part of the city. Furthermore, we ate meatballs and elk in Gamla Stan, the city’s old town, and drink local beers. We also visit the Museum of Modern Art, the National Museum, and the Vasa. We also tried to switch from the Italian after-work to the Swedish Fika, but sweet snacks can’t beat puff pastry mini pizzas. Ahahahaha, and no! We didn´t visit the Abba museum.
I don’t want to include photos for every described place, you can easily search for better images on google. However, I included an interactive map where you can pick my highlighted visited site and see the info and also my photos. Be careful, some images may have captured unexpected situations.
Week 3
My girlfriend left Stockholm and it isn’t time to feel alone but it is time to be focused on the thesis. With the last news and updates from my supervisor, I can start using and improving an algorithm to transform medical images into mesh for FEA. But I have to wait for patient-specific medical images.
I’m training in the gym every two days and I also discovered the sauna. It is included in the apartment building and near the gym. Why not use it? I spent a lot of time sitting at the desk working on the computer and this is not so good for my posterior kinetic chain, the muscles shouldn’t stay so concracted for so long. Including training and long walks in my daily routine is a really good idea, maybe I might even start running.
In the meantime, in Italy, my little cat, the black one called “Puppolo“, is going to complete the vaccine cycle. Oh my god, in less than a month they have grown so much.
Nonlinear FEA
I’m waiting for patient-specific CTA images. Hoverer, I have one volumetric image model of a different vessel and I can use it to test both CFD and mechanical FEM models and better understanding this new nonlinear mechanical model. So I can do several analyses to test mesh quality and different hyperelastic mechanical models, such as the Yeoh or the Fung model to describe different tissutal behaviors. These first simulations look good and I can show them to my supervisor and talk about the following step.
It is the weekend, so why not visit the central area of Stockholm and the Museum of Technology with a long walk in Ladugårdsgärdet park? It is the end of September and it starts to be cold, but on sunny days there is a really good temperature.
Well, the journey is not finished yet but we will talk about the following weeks in the next articles.
