Graph Neural Network for Cell Tracking in Microscopy Videos

Tal Ben-Haim, Tammy Riklin Raviv

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

1 Scopus citations


We present a novel graph neural network (GNN) approach for cell tracking in high-throughput microscopy videos. By modeling the entire time-lapse sequence as a direct graph where cell instances are represented by its nodes and their associations by its edges, we extract the entire set of cell trajectories by looking for the maximal paths in the graph. This is accomplished by several key contributions incorporated into an end-to-end deep learning framework. We exploit a deep metric learning algorithm to extract cell feature vectors that distinguish between instances of different biological cells and assemble same cell instances. We introduce a new GNN block type which enables a mutual update of node and edge feature vectors, thus facilitating the underlying message passing process. The message passing concept, whose extent is determined by the number of GNN blocks, is of fundamental importance as it enables the ‘flow’ of information between nodes and edges much behind their neighbors in consecutive frames. Finally, we solve an edge classification problem and use the identified active edges to construct the cells’ tracks and lineage trees. We demonstrate the strengths of the proposed cell tracking approach by applying it to 2D and 3D datasets of different cell types, imaging setups, and experimental conditions. We show that our framework outperforms current state-of-the-art methods on most of the evaluated datasets. The code is available at

Original languageEnglish
Title of host publicationComputer Vision – ECCV 2022 - 17th European Conference, Proceedings
EditorsShai Avidan, Gabriel Brostow, Moustapha Cissé, Giovanni Maria Farinella, Tal Hassner
PublisherSpringer Science and Business Media Deutschland GmbH
Number of pages17
ISBN (Print)9783031198021
StatePublished - 1 Jan 2022
Event17th European Conference on Computer Vision, ECCV 2022 - Tel Aviv, Israel
Duration: 23 Oct 202227 Oct 2022

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume13681 LNCS
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349


Conference17th European Conference on Computer Vision, ECCV 2022
CityTel Aviv


  • Cell tracking
  • Graph Neural Network
  • Microscopy videos

ASJC Scopus subject areas

  • Theoretical Computer Science
  • Computer Science (all)


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