Fraunhofer at Hopkins

After fifteen months of work, the big "D-Day" of final demos has finally come. Lots of Fraunhofer representatives came to Hopkins for two days of presentations, demos, and discussions about the future of the collaboration.



(As usual, bigger pictures after the click.)

Saftiges Nierchen

Hier ist ein Zwischenstand des Nierchenprojekts. Nicht das Ergebnis (3D-B-Mode-Ultraschall) ist entscheidend, sondern das Funktionieren der gesamten Modul-Pipeline bis dahin...

Breakthrough

Today was one of those rare breakthrough days.

After many months of work, about 90% of the modules on our side of our Hopkins/Fraunhofer cooperation project that I am working on started working together.
The system consists of lots of separate reusable executables that "run anywhere" (meaning on any of our four or five project machines) and communicate with each other using mostly TCP/IP or shared memory. And over the course of the last two or three days, I figured out (with some help) the last remaining stumbling block to get the data constructed that the Fraunhofer people need.

It's about 8:20pm, so that means I can go home early.

Thanksgiving Lab Turkey

What happened around the Thanksgiving turkey that Ioana and Brian invited us for.



As usual, click through for full picture glory.

Week before Thanksgiving

Impressions from the week before Thanksgiving when Matthias came to Baltimore for the project integration testing.



As usual, click through for the slideshow.

Abstract Space Mouse

Is this worth a conference submission?

More Billions

Today, no new absurdities. Instead, some news.

The Johns Hopkins University has again topped the NSF Research Funding ranking (for the n-th year straight). In fiscal year 2008, it spent almost 1.7 billion USD. Almost half of it went for the Applied Physics Lab APL, for DARPA- and NASA-sponsored research.
That's up 8% from last year, while inflation in the U.S. over the last year hovered at around zero.

SPIE Symposium on Medical Imaging 2010

"SPIE Paper Number 7625-53 Acceptance and Manuscript Information

Dear Philipp J. Stolka,

On behalf of the chairs for the upcoming "Visualization, Image-Guided Procedures, and Modeling" conference, it is my pleasure to confirm the acceptance of your submission, "A 3D-elastography-guided system for laparoscopic partial nephrectomies." This conference is part of the SPIE Symposium on Medical Imaging which will be held February 13-18, 2010 in San Diego, California USA.

PRESENTATION DETAILS
Paper Number: 7625-53
Presentation Type: oral
Presentation Date: 16 Feb 2010
Presentation Duration: 20 minutes [...]"

This is in addition to the three other papers that got into this conference that also have my name on it... somehow.

Probably the longest double in the world

Everybody knows doubles can become pretty large. How large, exactly, was a mystery to me until I ran into a voxelspace allocation issue today. I had to copy the mm-value out of the debugger to properly assess its size. Now I am pretty confident that doubles can grow at least up to 17 inches and a bit. That's slightly more than one-point-four foot, I think. Or square root of two feet. Or foot. Not to confuse with two square foot. Big foot.


Click the image for full-foot glory.

Hopkins, One Year Later

Last week, my little boss extended my contract here at Hopkins for another year. (End of newsflash, opinion piece follows.)

(I just looked up the term "op-ed", which I had presumed to mean "opinion-editorial" or sth. like that. However, it means, "opposite of the editorial page". How good I didn't embarrass myself.)

So, I've spent almost eleven months at Hopkins by now, working in Little Boss' ultrasound lab. I learned a lot about the use of ultrasound in interventional settings, about ultrasound physics, about elastography, registration, about hardware, about compilers, code optimization, and linkers, and also about students, student life, guiding students, running a lab, acquiring projects, running collaborations, and politics. Life at a private research university is stressful (luckily, I am blissfully shielded from funding acquisition almost completely).

In fact, X told me long ago that a) I would love the country for its gadgets (true), and b) I would learn how to work properly at Hopkins (also true). Unless one makes a very conscious decision to get out of lab in the evenings, one gets absorbed.

Now I am looking down the barrel of another year at Hopkins, in Taylor's LCSR, in Emad's MUSiiC lab, where by now I have seen people come and go, have seen students grow and students break, with reasonable researchers and crazy scientists, with personal quarrels and project vendettas.
It's a big place, it's got lots of people, and every day brings about a new piece of wisdom, knowledge, or at least some insight.

Mt. Washington is a quiet, green suburb. Sitting at my breakfast table on the rear deck, there is one other house that can be seen peeking through the forest. Squirrels, raccoons, and deer abound, with foxes here and there. Admittedly, one can hear the expressway in the valley when the wind is coming the wrong way, and the police helicopters' din is a staple of Baltimore life. Luckily, East Baltimore and "Death Valley" (north of JHMI) are far away.

Overall, it's a good experience. You get to work with great people, have captivating projects, get to work on your own ideas, push some publications, and have an agreeable life. In my private life, I am no smarter than I was before. Still, I'm looking forward to the beginning of year two.

Homewood, Medical School, and Mt. Washington

A few random pics from when my Mom was here for a visit.



As usual, hit the link and view the original post.

Baltimore Artscape, and Lab space

Two completely unrelated picture sets, one from the annual Baltimore Artscape festival that regularly draws crowds to music, art sales, movies, and food, and one from our lab, deserted at night.



As usual, click on the slide show to see bigger pics.

2010 JHFCU Calendar

"Congratulations on having your photo(s) selected for JHFCU’s 2010 calendar photo contest. We received many entries and had only a limited number of slots, so we picked the photos that we felt best represented the Hopkins community and Baltimore area. [...]"

Since I sent them three and got only limited information, I guess that the one below got chosen! The value of the R1 got proved again!



(Yes, I know the pic is full of artifacts. However, I only accept criticism from somebody who has ever tried to take pictures of dark objects against the sun in snow conditions.)

Saturday's "First Annual DMIP Beach Retreat" - Radiology organized this year's 2nd retreat, this time with no science at all!

2009 IEEE International Ultrasonics Symposium (IUS)

Re: Abstract ID: 1044
Abstract Title: 5DOF Trajectory Reconstruction for Handheld Ultrasound with Local Sensors

Dear Philipp Stolka:

We are pleased to inform you that the above referenced abstract has been accepted for Poster presentation during the 2009 IEEE International Ultrasonics Symposium (IUS). The symposium will be held from September 20-23, 2009 at the Ergife Palace Hotel, Roma, Italy.

[...]

Luckily I didn't hand in the abstract under its working title "Bastard SpaceMouse".

LEGO Heaven

I cannot complain too much.

Today, our mechanical engineering maven agreed with me that my LEGO-based approach seems feasible.
Later, I went searching for LEGO in our lab and found a whole room full of LEGO... up to the ceiling.
Now, I got a few boxes (only a selection of them is shown below), an iced tea, and found myself a quiet secluded spot with a great view over the campus greens... it feels like being a kid all over again :-)

Hobby, Work, and the Value of Colleagues

It is important to have your work be your hobby... and maybe your hobby be your work.
This is the case with my task here. I enjoy it.

And although programming is just a small part of it, it is very enjoyable, too. Even though I have to admit that I learned more about programming and learned more from my (ex-)colleagues while I was at UBT. Honestly, my programming skills (no matter how limited) have grown tremendously while working with some of my old labmates.

First and foremost Techno and Dabbelju, I really appreciate all the little and also the bigger things that I learned from you. They still help me every day in programming, debugging, and profiling.

(As I have said a long time ago, I brought my T_Matrix<T,homo> class with me, and I use it proudly ;-). Over the last week, I spent way too much time working with it, and I learned a lot about programming, C++, and my own old faults during that time. And while I whittled away at some old bugs and shortcomings, its performance just today increased from 2fps through 4fps and 6fps all the way to 23fps.
When this happened I called it a day.)

How the 2nd Battery was Lost and Found

The improbable story of the disappeared battery, with particular focus on its incomprehensible reappearance after it was already given up for good and considered lost forever.

VM Size Overload

At some point, even a well-maintained Mac OS X machine will give up.
Here, the MATLAB instance with its outrageous VM request made it stop completely (click the pic to embiggen).

Early Morning (Another Early Morning)

Experiments are looming tomorrow and the day after tomorrow... well, since it is already 3:07am in the morning, they are scheduled today and tomorrow. I am still in lab, writing programs like a busy squirrel.

In any case, this is an instant message I just got from a student:

"I am in [the Hopkins] lib.. and its very difficult to find [a good] place to sit... even at this time"

Hopkins people are crazy.

Intel, we are rock stars

Feels like our lab...
... every morning, the Researchers are coming in.

JHU Robofest 2009

Saturday, the robotics people at Hopkins organized a "Robofest" - lots of young kids from neighboring highschools came in and competed in several different robotics tasks... like finding dark spots or navigating a slalom course.



As usual, larger pictures after the click (on the slideshow above).

DMIP Retreat 2009

Last Monday, the JHMI DMIP (the department where my little boss has his primary affiliation) had its annual retreat at Oregon Ridge Park north of Baltimore. Kind of Watschenfeld, only with 3x as many people and 1/3rd the available time.

PJS presented an awesome project proposal idea. However, it is still just an idea. And, PJS got an award - not for technical or scientific excellence, but for being the first on location (no, really).

da Vinci S

Today, the LCSR got a new robot - a da Vinci S from Intuitive.

From Da Vinci S

Teraflop

This post's title is not a reference to anything around me (for the record).

Instead, it refers to a performance measure, for the non-computing scientists among the readers. More specifically, a teraflop (or Teraflop, or teraFLOP, or TeraFLOPS, or whatever) means one trillion (that is, 10^12) floating point operations per second. In any case, it is almost a lulz number.

The important part is how fast we got there. In 1999, Apple released the G4 PowerMac, which was touted as "the world's fastest desktop computer ever" and which broke the gigaflop barrier for home computers, at 1-4 Gflops. Less than a decade later, I am sitting in my lab here at Hopkins and am poring over hardware specifications.

The task is to order a single workstation PC for some ultrasound projects in our group. Many of those projects involve lots and lots of correlation computations - elastography or strain imaging is full of them; for 128x2000 ultrasound RF arrays and "small enough" windows, this amounts to a huge number of correlations. So we moved beyond quad-cores, dual-processors, hyperthreading, clustering, and so on - instead the focus is on GPGPU programming (effectively CUDA), or programming a high-performance supercomputation device. Nvidia's Tesla cards are one example of this species, one of which will probably end up in the workstation-class PC, completely dwarfing the computation power of the CPUs inside. A single Tesla C1060, for example, has a performance of nearly one Teraflop, at a price point for a complete system not much higher than $5000. Even a fully-specced 4-card system with almost four Teraflops under your desk clocks in at well below $10k, including dual-Xeons, 16GB of RAM, and friggin' huge monitors.

This is a speedup factor of 1000 within one decade. In this light, that older post sounds very nostalgic.

Ohne Worte (Calendar)

Here's to another crazy day

Recently, Balto is covered under a closed layer of ice. Snow has fallen, melted, and coalesced into a cracking, slippery, hard cake-icing-like blanket.


Another crazy day.

After lunch, I had to do a presentation of half a dozen project ideas for students' course projects in Taylor's "Computer-Integrated Surgery 2" in my PI's absence. The students kept their pokerfaces under a barrage of prime ideas from a couple of researchers here... they must be tough vis-a-vis the incessant displays of brillance around them. Or maybe they were just tired.

Late lunch, then another event - "FACEBOOK 101: Demo Day - The New 'Face' of the Web". In an intersession course, students had developed a bunch of Facebook applications all revolving around video and photos, and today was demo day. They dispersed around a bunch of laptops in the lounge area upstairs and showed off what they had invented and implemented during those three weeks.


Afterwards, another PhD student approached me with yet another project idea we could co-mentor in the afore-mentioned CIS2 course - so back to PowerPoint to whip up another inspiring slide, after discussing how much is too much for a semester project. At Hopkins, students regularly have to sign NDAs about their engineering projects.

Just when I believed the day would be over, my desk neighbor approached me and reminded me of today's dinner outing. So a bunch of colleagues started moving, avalanche-like, towards a nearby dinner bar. Astonishingly enough, a few of them are smokers, as it turned out afterwards.


And, I got myself into the vortex of classes here... or seminars. Finally, after so many years, medical computing science (after high school, initially I contemplated studying that) and I finally meet in terms of actual courses.

Impressions

Homewood.


Gefräßiger Plapperkäfer von Traal:
"Ein zum Verrücktwerden dämliches Vieh, es nimmt an, wenn du es nicht siehst, kann es dich auch nicht sehen - bescheuert wie eine Bürste, aber sehr, sehr gefräßig."



From Eadweard Muybridge's time-lapse photographs of a man riding a galloping horse.



From Homewood.

The Week

This Friday, an absolute crazy week came to a close.

Starting last Thursday, when our Fraunhofer project partner Matthias from Darmstadt arrived here for a week of work, all available time was filled with projects, presentations, and food.



On Monday, the ERC-CISST lab where I am working was celebrating its 10 Year Graduation - meaning that the NSF had funded the Sonderforschungsbereich-like structure for a decade with copious amounts of money, which now ran out. However, over the course of the lab's existence, this "seeding money" had been relegated to the status of peanuts, supplemented by proportionately larger other sources of funding. Still, this anniversary was a momentous day. Everybody had their demos, presentations, and posters prepared, and lots of big people had come for a day full of talks and (free) food. My (big) boss even changed from fishing into evening attire for the occasion. The whole lab was buzzing with discussion, plenary talks, and excitement. Here at the LCSR (the name that the ERC-CISST is migrating to) it is imperative to carry a lab notebook with you all the time to jot down the sparks of inspiration and the wealth of information that you keep getting any given day.
The day ended with a dinner reception full of laudatios for Taylor, some outrageously long speeches, and a truly prime dinner.











On Wednesday, Matthias and I went to JHMI to attend a laparoscopic partial nephrectomy (removing part of the kidney due to tumor invasion). For me, it was the first operation to have witnessed from beginning to end, and definitely an experience I won't forget anytime soon. The excitement and stress level during the time-critical parts of the operation were nerve-wrecking. The whole thing took much longer than expected - over five instead of less than three hours (including preparations over ten hours) - and was conducted by one very experienced and extremely professional young doctor. Eventually the local anatomy turned out worse than expected, and so the intervention unfortunately had to be converted to a radical nephrectomy. So it came that on Wednesday evening, between 10 and 11pm, I was able to put my hands on a freshly excised, still warm human kidney for the first time.






It was much bigger than expected, redder, and softer. The cancerous lesion was clearly palpable, and the whole kidney looked very disorganized. Anatomically it looked very similar to the pig kidneys I had dissected and prepared the weeks before, so it was absolutely awesome to compare all the features I already knew to this unexpected new specimen of a very different kind.



Afterwards, we trashed our scrubs, got our clothing back, and left the hospital excited and unbelievably hungry, tired, and freezing. Until well past midnight we stayed out in a small diner near Homewood which is famous for its trashy and very scary horror-movie-like ambience which draws its power exclusively from harmless children's toys and dolls arranged in frightening compositions.

On Thursday, Emad, Matthias, and I got the chance to present our respective ultrasound-related work to an international audience of students and faculty that had assembled at the LCSR for a week-long winter school on surgical robotics. As ours is a small world, I could recognize some of the faces from my visit to the summer school in Montpellier in 2003.

After his presentation, Matthias left for Germany, the winter school frenzy wound down, no more operations, so on Friday I was able to collect my thoughts for the first time in a week. I rummaged through some old data we collected earlier that needs some post-processing, received some overdue CT data information, got some calls from the JHMI regarding still other CT scans, continued working on a publication draft, and finally got to sneak into the final-day buffet dinner reception of the crazy week's winter school. Almost no students or faculty were left, so only a hard core of JHU members and some foreign students and professors were attending.

At my table, two senior research scientist staff from my office, a Japanese professor from Tokyo University, and myself got to sit right next to each other. We shared our experiences with Japan (the Romanian one of the two researchers had worked at this professor's lab some years earlier and considers returning, the Korean one would like to go there to work, and I would, too) and then continued ruminating on the power of China, the fall of the U.S., and where to go to sit through the economic downturn. The general consensus was that hightech medical engineering might always be in high demand (or so we hope), and that Australia is a good place to go. Sure, the consensus also said that for us, it is absolutely necessary to go to Japan for work once, too - but Australia is trying hard to attract top-notch science to edge itself into the first league of research and technology nations. At first we were surprised at this finding, but then we convinced ourselves that Australian universities command a prime set of researchers, have lots of money, pay generously, search top-tier faculty, and are in general an attractive offer. It is at the end of the world, but maybe the world might come to there.

In all probability, I have forgotten a fair amount of what happened this week, but hopefully the notes above will serve (me) well enough to retain some vague scaffolding of memory.

Life and Death of a Kidney

The kidneys ended their lives in this place - a slaughterhouse in Mt. Airy, some 35 miles out of Baltimore. It seems that when it comes to food and health, America acknowledges there might be drawbacks to individualism, and restricts slaughtering to only a few places.


The warm kidney were put on ice and later went on to be soaked with physiological sodium chloride solution (I learned that's the name of plain NaCl solution) to rinse them.


I specifically ordered kidneys for research, not for food. This means they came with all their plumbing still attached.


However, their plumbing was not useful for our research. We need to circulate contrast agent through them, so I worked for most of the day to graft some valves onto them. During this comparatively menial task I learned that kidneys have only three tubes connecting them to the outside world - renal artery, renal vein, and urethra.


Once set up, they were ready to undergo internal rinsing. There is an astounding capability to hold water in those kidneys. I could flush four or five of those syringes into them with nary any visible change. However, it became apparent to the touch that something is accumulating inside.


There are still more to work with.


Each of the kidneys has a different personality, which you learn to appreciate after groping them for the better part of a day.


One of them even conveniently sports some kind of lesion, maybe even a tumor. Which is great for us.
Although not visible on these pictures, they are by now filled to the brim with contrast agent (a suspension of titanium oxide in slightly gelly agar-agar). This is very white, pretty fluid while still in liquid phase, and very prone to find its way out of a pressurized environment, which I learned the hard way. When injecting it into one of the kidneys, the tubing became loose and the pressurized syringe-kidney system exploded in the lab, sending white goo everywhere up the walls and over the table.


This is kind of midway for the kidney phantoms: the CT room at JHMI. They are scanned here so we have something to compare with the later ultrasound images. This comes in a later installment.

Presentation Rot, Statistics, and Other Impressions

Several disconnected impressions. Life is sometimes hectic, sometimes slow.

A company's stab at being funny. Rather desperate.



Here, people are fleeing from what was probably the worst presentation in conscious memory of mankind. It was like bad conference presentations, only release didn't come after 15min. Embarassment all around. We suspected everything from a psychological experiment to a bad case of brain rot.


"You are a statistic" (sure, this is Baltimore) and, strangely enough, "Starbucks - hijo de puta".


"Sue 'em".

K&R's K

The other day, when I went to the restrooms, I noticed a big bunch of people crowding in the LCSR's main lecture/seminar hall. This happens frequently, the seminars are usually held by interesting people about interesting things, coffee and cookies are usually free, so naturally they draw a crowd. This time, something was different. There were people lining up the rear wall; it is rare to have the whole place filled. On my way back, I stumbled across a guy from the lab who asked me, "did you hear of the seminar now?"

It seems the news weren't spreading the official way, instead being handed down personally... It turned out that this lecture was held by Brian Kernighan himself (the 'K' in Kernighan&Ritchie, the inventors of C at Bell Labs). He talked for nearly an hour about 'The Changing Face of Programming', with his experience of probably forty years and his stature as one of the fixtures of our trade behind his words.

This is the kind of things happening to you here.

Sandwiched even more in JHMI

Always look on the bright side, and cherish what you have.
A very neat administrative aide just peeked in, and informed me that for the next six weeks, a new "resident" (short for what? resident MD? resident evil?) will be lodged into this lab. Which then, by definition, probably becomes a mixed lab-office space. Although "space" is not really the proper description.



Luckily this is not to be my regular workplace. The above really shows most (maybe 75%) of the lab.

Sandwich in JHMI

Finally, the car search has terminated.
After making a full circle, I have come back to my landlords' car. They wanted to sell it, I needed a car, and with all the regulatory hoops one has to jump through to get a car registered and on the street here, it was much simpler to simply borrow an existing, registered one.
Let's call this one Sandwich. It's an sufficiently Anglosaxon name, and it is a sandwich solution between me having been in Germany and me going somewhere else later.





Today, I have packed up the 3DOF robot stage and moved it from the JHU Homewood campus to the Johns Hopkins Hospital lab. Actually, "lab" is a euphemism. Emad himself told me so. He's trying to convince himself that the small, windowless basement room he was assigned is a lab.



Along the hallway walls outside the lab's door, there are little windowless holes in the walls. In each one, there is one researcher (or more) huddled over a keyboard, busy researching.