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Machine Learning and Bioimage Analysis

Short Academic Bio

Qin Yu obtained his PhD in Machine Learning for Bioimage Analysis from the European Molecular Biology Laboratory (EMBL) and Ruprecht-Karls-Universität Heidelberg, supervised by Dr Anna Kreshuk. His thesis focused on robust and accessible segmentation of cells and nuclei in 3D microscopy.

Before joining EMBL, he trained at the Centre for Integrative Systems Biology and Bioinformatics at Imperial College London and the MRC Laboratory of Medical Sciences, where he completed his MSc thesis under the supervision of Professor Aubrey Cunnington.

He received his first degree from University College London (UCL), where he read computer science, mathematics, and statistics. His early research included work on the formal verification of concurrent separation logic soundness, supervised by Professor James Brotherstone, followed by an MEng thesis on GPU computing and machine learning, supervised by Professor John Shawe-Taylor.

Invited Talks

  • 2025 - Potsdam, Germany 🇩🇪
    • The International Conference on Phenotypic Plasticity in Plants
  • 2025 - Changchun, China 🇨🇳
    • The Young Scholars Forum, The First Hospital of Jilin University

Peer Review

  • 2025 - PLoS Computational Biology

Teaching

Practical courses on deep learning for bioimage analysis with focus on segmentation:

  • 🇬🇧 UCL Mentor - University College London (2025)
  • 🇮🇹 From Images to Knowledge Workshop - Human Technopole (2024)
  • 🇩🇪 Theory@EMBL PhD Course - EMBL Heidelberg (2022, 2023)
  • 🇩🇪 Lautenschläger Summer School - EMBL Heidelberg (2022, 2023, 2024)
  • 🇩🇪 EMBL Course: Deep Learning - EMBL Heidelberg (2022)
  • 🇬🇧 EIPP Bioinformatics PhD Course - EMBL-EBI (2022)
  • 🇩🇪 Morphodynamics Workshop - Centre for Organismal Studies Heidelberg (2021)
  • 🇺🇸 Deep Learning for Microscopy Image Analysis - Marine Biological Laboratory (2021)

Publications

Deep Learning Algorithms

Bioimage Analysis Methods

Applied Bioimage Analysis