Gideon Jägenstedt joins as PhD student the Soft Matter Lab

(Photo by A. Argun.)
Gideon Jägenstedt started his PhD at the Physics Department of the University of Gothenburg on the 1st of September 2023.

Gideon has a master degree in Complex Adaptive Systems from Chalmers University of Technology.

In his PhD, Gideon will focus his research on deep learning.

Gideon Jägenstedt defended his Master Thesis on 8 June 2023. Congrats!

Tracking of two simulated particles over 20 frames using an object-focused variational autoencoder. (Image by G. Jägenstedt.)
Gideon Jägenstedt defended his Master Thesis on 8 June 2023 at 11:00. Congrats!

Title: End-to-End Object Tracking on Simulated Microscopy Video

Object tracking in microscopy time-lapse videos is currently mostly done in two steps often using two neural network models, first the images are segmented in order to detect each object within each time frame and extract their centroids using one neural network model. A selected set of properties on the centroids are then used as an input to a second neural network that creates the temporal trajectories by linking the centroids over a sequence of frames.

This work proposes a novel method to combine the object detection step and the
linking step which should, in theory, create better linking in time since the combined model has access to not only a set of properties but the complete image of the centroids. Two different architectures of a combined model were tested, one supervised model based on graph neural networks (GNN) and one unsupervised model based on a variational autoencoder (VAE).

The supervised GNN-based model did not succeed in predicting the position of the centroids, but it showed promise in linking the centroids between frames. Therefore, the VAE-based model was developed that uses the same approach for linking. The VAE-based model resulted in a mean absolute error of under 0.002 on its detection placement, a detection miss-rate of 2.69 %, and an F1-score of 81.2 % when linking trajectories on simulated data.

Supervisor: Jesus Pineda Castro
Examiner: Giovanni Volpe
Opponent: Mirja Granfors

Place: PJ
Time: 8 June, 2023, 11:00

Gideon Jägenstedt joins the Soft Matter Lab

(Photo by A. Argun.)
Gideon Jägenstedt joined the Soft Matter Lab on 29 August 2022.

Gideon is a Master student in the Complex Adaptive Systems at Chalmers University of Technology.

During his time at the Soft Matter Lab, he will work on his Master thesis project on particle representation and graph neural networks.