Teaching News

01 Apr 2019

[Call for application] Advanced Imaging: Deep Learning in Imaging and Cell Biology

Applications are open for the Croucher Summer Course on Advanced Imaging: Deep Learning in Imaging and Cell Biology organized by HKU-Pasteur from 25th to 30th of August, 2019. 

Date: August 25-30, 2019
Venue: LKS Faculty of Medicine, The University of Hong Kong
Imaging lies at the heart of the investigation of biological processes from the molecular level to entire organisms. While steady advances in microscopy technology are opening new windows into the inner workings of the biological systems, imaging has hard limits stemming from optics of the microscope, chemistry of fluorophores and the necessity to keep the imaged sample alive. Recently, deep learning has emerged as a powerful approach to making trade-offs between imaging speed, image quality and sample health, that make many previously inaccessible imaging scenarios possible. It has been shown that by incorporating deep learning driven image restoration into imaging pipelines, it is possible to image biological specimen with dramatically reduced laser power, achieve isotropic resolution from under-sampled 3D volumes and even resolve structures below the diffraction limit faster.
This course will focus on the application of leading deep learning framework for microscopy image restoration, the Content Aware Image Restoration (CARE), to various biological image restoration tasks. The power of deep learning in microscopy will be demonstrated using open source tools such as Fiji, KNIME and Jupyter notebooks that make the advanced technologies accessible to anyone.
Besides the in-depth practical experience with CARE, the participants will learn about alternative computational approaches to super-resolution microscopy and about handling of big microscopy image datasets. Finally, the impact of computational techniques on biological imaging will be demonstrated on frontier biological applications spanning across scales of biological complexity from molecular (Cryo-EM), to subcellular (nuclear organization) to organismal (tissue mechanics) levels.
During the practical part of the course the students will learn how to:
- Collect appropriate training data on the provided samples using diverse microscopy hardware.
- Train CARE networks on state-of-the-art as well as commodity computer hardware.
- Apply CARE networks to restore the data acquired during the course.
- Learn how to evaluate the CARE results and avoid potential artefacts.
Course directors:
Prof Roberto BRUZZONE, HKU-Pasteur Research Pole, The University of Hong Kong, HKSAR 
Dr Musa MHLANGA, University of Cape Town, South Africa
Prof George TSAO, School of Biomedical Sciences, The University of Hong Kong, HKSAR
Sian Culley, MRC Laboratory for Molecular Cell Biology, University College London, UK
Florian Jug, Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
Musa Mhlanga, University of Cape Town, South Africa
Gaia Pigino, Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG), Dresden, Germany
Pavel Tomancak, Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
Martin Weigert, Center for Systems Biology Dresden, Dresden, Germany
Marino Zerial, Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG), Dresden, Germany
Christophe Zimmer, Institut Pasteur, France

Registration Fee: HK$ 3000, non refundable

Registration Deadline: May 31, 2019

Participants’ profile: Postgraduate Students, Post-docs and Junior Group Leaders.

Travel fellowship: Up to 5 fellowships will be awarded to the best applicants.
Please contact course secretary if you have enquiries at corefac@hku.hk.