Monday physics colloquium

On Monday, November 14, Andrej Studen will give a lecture entitled PET imaging with silicon sensors. The lecture will be in the context of promotion to Assistant Professor. You are cordially invited at 16:15 to Faculty of Mathematics and Physics, Jadranska 19, lecture room F1.

Andrej Studen





ABSTRACT: Silicon seems an unlikely candidate for imaging in positron emission tomography. However, the ability to provide spatially accurate interaction positions of energetic photons can be exploited to yield significantly improved images. In the presentation, physics of PET imaging will be introduced, focusing on interplay of sensor spatial resolution and final image quality, concluded by potential application of silicon based PET imaging probes.

Journal Club #3

On Wednesday, October 26, Maruša Turk will present a paper entitled Mathematical Modeling of Therapy-induced Cancer Drug Resistance: Connecting Cancer Mechanisms to Population Survival Rates. The paper can be found here. We start at 11 AM in P.04.

Cordially invited!


Journal Club #2

On Thursday, October 6th, Damijan Valentinuzzi will present a paper entitled Mathematical Modeling of Cancer Immunotherapy and Its Synergy with Radiotherapy. The paper can be found here.

We start at 11 AM in lecture room F6. We hope you will join us!


Neurology meetings in Ljubljana

In the beginning of October (5-6 October and 6-8 October), Ljubljana Exhibition and Convention Center will host two neuroimaging meetings: 48th International Danube Neurology Symposium and 11th International Congress on Non-Motor Dysfunctions in Parkinson’s Disease and Related Disorders. Both meetings will also cover neuroimaging of neurodegenerative brain disorders with PET. More information about both meetings can be found in the following links:


Journal Club #1

On Monday, September 5th, Andrej Studen will open new journal club season with a paper entitledTheoretical analysis and simulation study of a high-resolution zoom-in PET system. The paper can be found here.

We start at 2 PM in lecture room F3. We hope you will join us!


Masters Thesis Defense

We invite you to Masters thesis defense of Nina Verdel and Jošt Stergar, the new members of Medical physics research group.

Nina Verdel: “Silicon photomultiplier as a Cherenkov radiation detector for positron emission tomography”, on Friday, September 2nd 2016, at 12.00 in Kuščer Lecture Room, Jadranska 19.


Jošt Stergar: “Optothermal manipulation of single submicron particles”, on Wednesday, September 7th 2016, at 9.00 in Kuščer Lecture Room, Jadranska 19.

IAEA Regional Training Course on Neuroimaging

Regional Training Course on Neuroimaging, organized by International Atomic Energy Agency (IAEA) will be held from September 6th – 9th 2016 in Ljubljana. The preliminary program can be found here. Domestic visitors can attend the course free of charge but the number of places is limited. You are all welcome!


Lecture: dr. ORLY ALTER (University of Utah, USA)

On Wednesday, June 29th, 2016 at 13:00, dr. ORLY ALTER (Scientific Computing and Imaging Institute and the Huntsman Cancer Institute, University of Utah) will give a lecture entitled Multi-Tensor Decompositions for Personalized Cancer Diagnostics and Prognostics. The lecture will be held in the main lecture hall of the Jožef Stefan Institute (JSI), Jamova 39, Ljubljana.


Multi-Tensor Decompositions for Personalized Cancer Diagnostics and Prognostics

We are developing new mathematical frameworks to do what no others currently can, that is, create a single coherent model from multiple high-dimensional datasets, known as tensors. The frameworks – comparative spectral decompositions – generalize those that underlie the theoretical description of the physical world. We are using the frameworks to compare and contrast datasets recording different aspects of a single disease, such as genomic profiles of multiple cell types from the same set of patients, measured more than once by several different methods. By using the complex structure of the datasets, rather than simplifying them as is commonly done, the frameworks enable the separation of patterns of DNA alterations – which occur only in the tumor genomes – from those that occur in the genomes of normal cells in the body, and from variations caused by experimental inconsistencies. The patterns that we uncover in the data are expected to offer answers to the open question of the relation between a tumor’s genome and a patient’s outcome. For example, recent comparisons of the genomes of tumor and normal cells from the same sets of ovarian and, separately, glioblastoma brain cancer patients uncovered patterns of DNA copy-number alterations that were found to be correlated with a patient’s survival and response to chemotherapy. For three decades prior, the best predictor of ovarian cancer survival was the tumor’s stage; more than a quarter of ovarian tumors are resistant to the platinum-based chemotherapy, the first-line treatment, yet no diagnostic existed to distinguish resistant from sensitive tumors before the treatment. For five decades prior, the best prognostic indicator of glioblastoma was the patient’s age at diagnosis. The ovarian and brain cancer data were published, but the patterns remained unknown until the team applied their comparative spectral decompositions. Pending experimental revalidation, we will bring the patterns that we uncover to the clinic, to be used in personalized diagnostic and prognostic pathology laboratory tests. The tests would predict a patient’s survival and response to therapy, and doctors could tailor treatment accordingly.

Dr. Orly Alter:

Dr. Alter is a USTAR associate professor of bioengineering and human genetics at the Scientific Computing and Imaging Institute and the Huntsman Cancer Institute at the University of Utah. Inventor of the “eigengene,” she pioneered the matrix and tensor modeling of large-scale molecular biological data, which, as she demonstrated, can be used to correctly predict previously unknown cellular mechanisms. Dr. Alter received her Ph.D. in applied physics at Stanford University, and her B.Sc. magna cum laude in physics at Tel Aviv University. Her Ph.D. thesis on “Quantum Measurement of a Single System,” which was published by Wiley-Interscience as a book, is recognized today as crucial to the field of gravitational wave detection.

Journal Club #17

On Wednesday, June 22th, Rok Dolenec will present a paper entitled Rebinning and reconstruction techniques for 3D TOF-PET. The paper can be found here.

As usual, we start at 2 PM in lecture room P.04. We hope you will join us!