SDSC-AI4Science seminar: A graph matching approach to tracking neurons in freely-moving C. Elegans

We are happy to announce the second seminar of the SDSC - AI4Science monthly seminar series.

Place:  BCH 2103 (or via zoom https://epfl.zoom.us/j/63741505372)

Speaker: Corinne Jones, Sr. Data Scientist at SDSC

Title: A Graph Matching Approach to Tracking Neurons in Freely-Moving C. elegans

 

Abstract: Recent advances in 3D microscopy allow for recording the neurons in freely-moving C. elegans at high frame rates. In order to be able to study the calcium activity in the neurons, it is necessary to be able to track the individual neurons from frame to frame. However, doing this by hand for tens of neurons in a single ten-minute recording requires more than a hundred hours. Moreover, most methods proposed in the literature for tracking neurons focus on immobilized or partially-immobilized worms and fail to generalize to the freely-moving-worm setting. In this talk I will present an approach based on graph matching for tracking freely-moving C. elegans in the setting where a subset of neurons are marked with red fluorescence. The approach will be demonstrated on three recordings. We find that with two labeled frames we can typically track the neurons and pieces of neurites with over 70% accuracy, with more reliable annotations for the most distinctive neurons. This is joint work with the lab of Sahand Rahi and Guillaume Obozinski. 

The SDSC - AI4Science seminar is co-organized monthly by the EPFL AI4Science Initiative and the Swiss Data Science Center and focussing on projects in which data science, statistics, machine learning and AI are applied to the sciences. Each seminar will feature a presentation of one applied project, geared towards an audience with expertise in Data Science methods, from the initial formulation of a research question in science associated with sources of data, to the model, algorithms and analyses produced. The presentation will be highlighting the choices made, the challenges encountered, interesting technical questions and possible further developments. A number of the projects presented will be collaborative projects of the Swiss Data Science Center. One of the objectives of the seminar is to foster exchanges between researchers working in methods and applied data science research in the sciences, and to create new opportunities of collaborations.

Each session will feature a talk followed by a discussion with the audience, to be continued over fingerfood and drinks