Kidney Segmentation and other Adventures

 The past few weeks have come to a head. I previously spoke about what disease my project focused on, but not how the disease is addressed. Kidney volume is a pretty important in determining polycystic kidney disease (PKD) outcomes in patients. Unfortunately, total kidney volume (TKV) measurements come from manually contouring kidney. It can be time consuming to contour an unremarkable kidney, but the complicated geoemetries and partial voluming effects found in advanced cases makes the process even more difficult.

So this is where we set off: why not try to automate the segmentation? Luckily, a research fellow developed and trained the model, and we set off to evaluating inferences and further debugging the code. For many cases, the inference performed very well, but we found that we need to train it with some harder stuff. In other words, a harder case was more of a coin toss with the algorithm, but after much thought we are pretty optimistic that re-training with a more diverse dataset will go a long way.

(Left) A representative PKD Patient. The kidneys are much larger than would be expected and the presence of cysts can make parenchymal identification challenging. (Right) Model inference of the kidneys.

 In other news, I found myself in an impromptu shadowing experience. I wanted to watch some CT guided ablations for my upcoming research project, and I had to head over to the hospital to talk over the details with one of the interventional radiologists. I got there and after talking with him for 10 minutes, he realized "We have one going on right now. Let's watch!" The flexibility was amazing, and I got a small taste of the procedure before I get the full introduction next week!

Comments

Post a Comment

Popular posts from this blog

Week 1

For my first week of immersion I attended the OR's of a few different physicians as my clinical mentor Dr. Jason Spector of plastic surgery and reconstruction was on vacation this week. I was able to see three different hernia repairs, and one double mastectomy and bilateral DIEP flap.  I think my favorite thing I saw was the double mastectomy and bilateral DIEP flap. From what I understand, this is a procedure in which both breasts were removed and fat from the stomach is used to reconstruct the breasts. The novelty of the DIEP flap is that it does not require the removal of muscle which allows patients to recover quicker. Additionally, blood vessels from the fat in the stomach are left in tact and "hooked up" to corresponding vessels in the breast. All in all, the procedure essentially amounted to a breast reconstruction and tummy tuck. It was a 10 hour surgery that required multiple doctors and departments, as this was not just a purely cosmetic procedure- the patient ...
Read more

Week 1 - Samantha Bratcher

Image
Hi, everyone! My name is Samantha Bratcher. My clinical immersion is with Dr. Adam Talenfeld and Dr. Kyungmouk Steve Lee in the Interventional Radiology (IR) department. Although it's not very related to my field at the university (biomechanics/mechanobiology), the clinical experience has still been very interesting. The IR department is super friendly and all the clinicians have been very available to letting me shadow them. It's only been one week, but I've already learned a lot! Every day has been watching something new, from angioplasty to biopsy to embolization. I find it so crazy that they're able to thread a wire through someone's veins to practically any area of the body. It's always a bit crazy to watch. I got a video of a balloon angioplasty using this method. The balloon is inflated inside a person's veins to expand them and increase blood flow. The second video shows the veins and their quality. The rate at which the contrast dye flows through is...
Read more

Week One - Shenghao Tan

I am working with Dr. Mirella Salvatore from the infectious disease division. My research project will revolve around associations of COVID 19 patient clinical characteristics with their hostresponses throughout their hospitalization and recovery.   On the patient care side I have been following Dr. Ole Vielemeyer in ID consultation. A large part of the round is to discuss the choice of antibiotics, itsdosage and duration from lab results and examination reports. Some of the cases this week have been quite complicated and chronic; therefore, joint effort were required to provide adequate treatments. One patient had to battle both Crohn's disease and histoplasmosis, where the immunosuppressant and antibiotics used must be carefully considered to treat the histoplasma and maintain some immune system function, while not severing the GI tract. A part of medical care I learned that I haven't considered much of is the inpatient - outpatient transition: how is the treatments adjusted ...
Read more