Advanced Imaging - Deep learning in Imaging & Cell Biology

You are about to enter the application round for Croucher Summer Course: Advanced Imaging - Deep learning in Imaging & Cell Biology

Sunday 25 August

Li Ka Shing Faculty of Medicine 21 Sassoon Road

09:30

Welcome & introduction of the Course

Roberto Bruzzone, Musa Mhlanga, George Tsao

10:00

Students’ self-introduction

12:30
Lunch
13:30

Lecture 1: Introduction to deep learning

15:00

Tutorial

Microscope Operation Training & Hands-on Practice

17:00

Introduction of Fiji

18:00
Wrap up session
18:30
Welcome reception

Monday 26 August

Li Ka Shing Faculty of Medicine 21 Sassoon Road

09:00

Lecture 2: Deep Learning in Systems Biology: High Content Screening

10:30
Break
11:00

Lecture 3: Content-Aware Image Restoration for Light and Electron Microscopy Facilitates Quantitative Data Analysis

  • Florian Jug Max Planck Institute of Molecular Cell Biology and Genetics
12:30
Lunch
13:30

Practical session

Acquiring image data and training set data on microscopes from provided samples

CARE - Denoising, Isotropic; NoiseToVoid

18:00
Wrap up session

Tuesday 27 August

Li Ka Shing Faculty of Medicine 21 Sassoon Road

09:00

Lecture 4: Towards a mechanistic understanding of cellular processes by cryo-EM

  • Gaia Pigino Max Planck Institute of Molecular Cell Biology and Genetics, Germany
10:30
Break
11:00

Lecture 5: A new force awakens: comparative approach to tissue morphogenesis in insects

  • Pavel Tomancak Max Planck Institute of Molecular Cell Biology and Genetics
12:30
Lunch
13:30

Practical session

Processing of the data acquired the previous day on provided virtual Paperspace computers in the cloud

CARE - Denoising, Isotropic; NoiseToVoid

18:00
Wrap up session

Wednesday 28 August

Li Ka Shing Faculty of Medicine 21 Sassoon Road

09:00

Lecture 6: Multi-scale analysis of cell and tissue organization

  • Marino Zerial Max Planck Institute of Molecular Cell Biology and Genetics
10:30
Break
11:00

Lecture 7: Image restoration and segmentation with machine learning

  • Martin Weigert Max Planck Institute of Molecular Cell Biology and Genetics
12:30
Lunch
13:30

Practical session

Second round of microscopy and processing to demonstrate CARE and NoiseToVoid

Practical session on StarDist 

18:00
Wrap up session
18:30

Lecture 8: DataViz with 3DScript in Fiji

  • Florian Jug Max Planck Institute of Molecular Cell Biology and Genetics

Thursday 29 August

Li Ka Shing Faculty of Medicine 21 Sassoon Road

09:00

Lecture 9: Deep learning for massive imaging in microscopy and pathology, deep learning for the masses

10:30
Break
11:00

Lecture 10: Open source analytics for super-resolution microscopy

  • Sian Culley University College London

    MRC Laboratory for Molecular Cell Biology, University College London, UK


12:30
Lunch
13:30

Practical session

SRRF, SQUIRREL/UNICORN and ANA-PALM

18:00
Wrap up session

Friday 30 August

Li Ka Shing Faculty of Medicine 21 Sassoon Road

09:00

Data analysis

10:30
Break
11:00

Data analysis

12:30
Lunch
13:30

Presentation of the results of the practical workshops and general discussion

18:30
Celebration Dinner

Speakers

  • Data Sian Culley University College London MRC Laboratory for Molecular Cell Biology, University College London, UK
  • Data Florian Jug Max Planck Institute of Molecular Cell Biology and Genetics
  • Data Musa Mhlanga University of Cape Town
  • Data Gaia Pigino Max Planck Institute of Molecular Cell Biology and Genetics, Germany
  • Data Pavel Tomancak Max Planck Institute of Molecular Cell Biology and Genetics
  • Data Martin Weigert Max Planck Institute of Molecular Cell Biology and Genetics
  • Data Marino Zerial Max Planck Institute of Molecular Cell Biology and Genetics
  • Data Christophe Zimmer Institut Pasteur, France

Information

Directors:


Roberto Bruzzone

HKU-Pasteur Research Pole, The University of Hong Kong, HKSAR

Musa Mhlanga

University of Cape Town, South Africa


George Tsao

School of Biomedical Sciences, The University of Hong Kong, HKSAR