A seminar in shape theory

I had a tip from Ozan Öktem about an upcoming seminar which deals with recent developments for mathematical methods applicable to shape recognition and classification.

Here is the detailed description:

Time: Wed 2010-09-29 kl 13.15 - 15.00
Place: Room 3733 Lindstedtsvägen 25
Contact: Ozan Öktem (790 6606) or Sandra Di Rocco (790 7168)
Weblink: http://www.kth.se/sci/institutioner/math/kalender/2.21854/seminars/an-overview-of-computational-anatomy-1.65738

An overview of Computational Anatomy
Joint CIAM/Algebra and Geometry Seminar by Stéphanie Allassonnière from Centre de Mathematiques Appliquees, Ecole Polytechnique.

The seminar will provide an overview of Computational Anatomy which is an emerging discipline at the interface of geometry, statistics and image analysis, that aims to analyse and model biological shape variability at the population scale. The goal is not only to model the normal mean anatomy and its normal variations among a population, but also to discover morphological differences between normal and pathological populations, and possibly to detect, model and classify pathologies from structural abnormalities. Another goal is to correlate this variability information with other functional, genetic or structural information.

First, the goals and mathematical tools which are needed for such methods are presented. In particular, the focus will be on the deformable template framework, which assumes that the shapes that come from a given group (in term of age, sex, disease) are close to each other up to a class of deformations.

Next, the registration issue is introduced which is the central tool in this context. Its goal is to find the 'optimal' deformation that maps one shape onto another one. Some techniques which have been proposed to solve it will be presented bringing us to the Large Deformation Diffeomorphic Metric Mapping (LDDMM). This mathematically well-grounded method allows one to consider the registration of landmarks, curves, surfaces and images within the same framework.

The last part of the presentation will focus on the probabilistic and statistical questions that arise when we are provided with a population of images or shapes. The main issue is how to compute a "mean" and a "deviation" from this set. The main tools and results will be introduced whereas a more specific tutorial given the day after will discuss further issues.

Stéphanie Allassonnière received her PhD in 2007 from the Université of Paris 13 (France) in Applied Mathematics . The thesis was supervised by Alain Trouvé (ENS- Cachan) and Laurent Younes (CIS - Johns Hopkins University, Baltimore) and dealt with statistical estimation of template images using generative models. She then spent one year as a postdoctoral fellow in the CIS working with Laurent Younes and Michael Miller on statistics for medical imaging. Since 2008, she have been Assistant Professor in Ecole Polytechnique in the Applied Mathematics Department where she has continued her research on statistical analysis of images and deformations. In particular, she is studying the mathematical properties of the statistical estimators and stochastic estimation algorithms. She was recently awarded the "Prix Excellencia 2010" for her research work.

New seminar on the seminar list

I've added one more seminar to the academic meeting series list. Make room also for

Thursday 11th of November:
Love Nordin (PhD student at Department of Clinical Sciences, Danderyd Hospital): Detection of drug related cortical responses and pathophysiological mechanisms by using arterial spin labelling MRI techniques

ARC lecture

Anna Rieckmann invites you all to the lecture on Thursday, the 30th September, 10.00 - 12.00 by Dr. Marco Catani entitled "Defining the anatomical complexity of human networks" at the Aging Research Center (Gävlegatan 16). She thinks that this lecture may be of interest to many SMILE members!

neuGRID user test meeting, Brescia

Four of the lab's users (+ our previous guest Julia Miralbell) helped out with the second round of grid testing in Brescia during September 6-8. More functionalities had been implemented, and our users contributed with valuable feedback on the look and feel of the neuGRID user interface.

User meetings

The remaining user meetings during the autumn will take place on:

Tuesday 12/10
Tuesday 16/11
Tuesday 7/12

Autumn academic seminars

Here is the list of the seminars planned (so far!) in the autumn's academic meeting series.

Thursday 7th of October:
Eric Westman (PhD at Department of Neurobiology, Care Sciences and Society, Division of Clinical geriatrics, Karolinska Institute): A report from ICAD 2010

Thursday 14th of October:
Daniel Ferreira Padilla (PhD student at Psychobiology and Methodology Department, Faculty of Psychology, University of La Laguna, Tenerife, Spain): Image analysis under FreeSurfer: NGF dataset as test images

Thursday 28th of October:
Gabriela Spulber (PhD student at Institute of Clinical Medicine/neurology at University of Eastern Finland, Kuopio and Department of Neurobiology, Care Sciences and Society, Division of Clinical geriatrics, Karolinska Institute): TBD

Thursday 18th of November:
Tracing students (Linnea Engström, CH Ehrenkrona, Nathalie Thomé, Jenny Åström, all undergraduate students at Karolinska Institute): Manual tracing of the hippocampus, the anterior cingulate cortex and the entorhinal cortex

Thursday 25th of November:
Michael Schöll (PhD student at Department of Neurobiology, Care Sciences and Society, Division of Alzheimer Neurobiology, Karolinska Institute): Application of PET in Alzheimer's disease

Thursday 16th of December:
Martin Uppman (PhD student at Department of Clinical Science, Intervention and technology at Karolinska Institute, Stockholm): Integrating EEG and MRI

Starter Kit

I have produced a SMILE Starter Kit for all new users and anyone who feel they would like to brush up on how the lab works. It details among other things the various computer systems and softwares we have available here, our meeting series, the data policy, how to gain access to the emailing list and much more. Please ask the manager for your own personal copy!

Call for exam work projects

If you have a suitable project for a master student's thesis work, please contact me as there have been requests for exam works coming in (and no doubt more will come in the coming months). I will add your project to the SMILE web page listing exam work projects -- http://www.smile.ki.se/education/exam_en.html -- and also put you in contact with students asking for projects.

Posters

If you have produced expensive posters with no other place to put them after the event than rolled-up in a corner -- remember that you are always welcome to bring them to SMILE, where we will be happy to display them on our walls!

Visitors and a new co-worker

We have at the moment two visitors at the lab:

• Daniel Ferreira Padilla, PhD student at Psychobiology and Methodology Department, Faculty of Psychology, University of La Laguna, Tenerife, Spain, from August 2nd to November 1st. He is working together with Gabriela Spulber in Lars-Olof Wahlund's group.
• Stefania Geraci from Department of electronics, informatics and system science at University of Bologna, Italy, from August to January 2011. She is performing her master's thesis work (Reduction of pulse artefact in EEG data recordings at 3T) with Tie Qiang Li as supervisor.

We also welcome Carlos Aguilar Palomeque who will be working part-time in the lab for six months, mainly helping out with the computers.

Long hiatus

There has been a long break in the blog entries, due to large workload. Hopefully I will have time to update a little more often during the autumn! To compensate, I will now make several entries at once about recent and upcoming events.