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Undergraduates

EMBL welcomes undergraduate students of all disciplines in the natural sciences extending from biology, chemistry, physics and mathematics to medicine, informatics and engineering.

Visualising Life – Interdisciplinary Approaches to Biology

15-26 July 2019, EMBL Heidelberg, Germany

 

Programme

Week 1

TimeMonday 15 JulyTuesday 16 JulyWednesday 17 JulyThursday 18 JulyFriday 19 July
9.00-
10.00
Welcome by
Summer School Organisers
Seeing the unknown: What molecular labelling can do for developmental
biology

Mariana R.P. Alves
Basic concepts in developmental biology

Ulla-Maj Fiuza
Physics of early Embryo Morphogenesis

Chii Jou Chan
Lab Day
10.00-
11.00
Keynote lecture on Imaging

Jan Ellenberg
Superpowers of super-resolution microscopy and the hidden assembly
of disordered proteins in the NPC

Sofya Mikhaleva
Keynote lecture on Cell mechanics

Stefano De Renzis
Visualization of transcription in embryos

Timothy Jessen Fuqua
Lab Day
COFFEE BREAKCOFFEE BREAKCOFFEE BREAKCOFFEE BREAKLab Day
11.00-
12.00
Basics concepts of Microscopy

Carlo Bevilacqua
Looking deeper than microscopy: Imaging modalities beyond light for visualising
biology deep in tissues

Jakub Czuchnowski
Keynote lecture on Cell communication in developing systems

Alexander Aulehla
Keynote lecture on Morphogenesis in plants

Alexis Maizel
Lab Day
12.00-
13.00
LUNCHLUNCHLUNCHLUNCHLab Day
13.00-
18.00
Practicals: Microscopy Building

Robert Prevedel, Jakub Czuchnowski, Ling Wang
Practicals: Microscopy Building

Robert Prevedel, Jakub Czuchnowski, Ling Wang
Practicals: Imaging Biology

Aissam Ikmi, Anniek Stokkermans
13.00 Keynote lecture
Virginie Uhlmann

14:00 Keynote lecture
James Sharpe

Practicals: Imaging Biology
Lab Day
18.00Welcome eventDinnerMeet the EMBL PhD StudentsDinnerLab Day

There’s no programme activites during the weekend


Week 2

TimeMonday 22 JulyTuesday 23 JulyWednesday 24 JulyThursday 25 JulyFriday 26 July
9.00-
10.00
Keynote lecture on
Imaging biology

Christian Tischer
Optogenetics in morphogenesis

Daniel Krueger
Keynote lecture on light-sheet microscopy

Lars Hufnagel
Imaging cancer initiation: one cell at a ti

Ashna Alladin
Student presentations preparation time
10.00-
11.00
The basics: pixels, filters, morphology

Sanjana Singh
Intro to machine learning

Fynn Beuttenmueller
Keynote on EM imaging

Julia Mahamid
Chasing space and mapping time: on tracking and kymographs

Paul Gerald Sanchez
Student presentations preparation time
COFFEE BREAKCOFFEE BREAKCOFFEE BREAKCOFFEE BREAKStudent presentations preparation time
11.00-
12.00
From Images to data: Denoising, filtering and segmentation

Philipp Walch
Ways of Seeing – Machine Learning for Images

Jose Almeida
Extending the Depths of Light-Sheet Microscopy with Adaptive Optics

Dimitri Kromm
Deep learning

Anna Kreshuk
Student presentations preparation time
12.00-
13.00
LUNCHLUNCHLUNCHLUNCHLUNCH
13.00-
17.00
Practicals: Image Analysis

Anna Kreshuk, Fynn Beuttenmueller, Ben Story
Practicals: Image Analysis

Anna Kreshuk, Fynn Beuttenmueller, Ben Story
Focus PracticalsFocus PracticalsStudents presentations

Wrap-up and Feedback session
17.00-
20.00
Food for thought with Manfred LautenschlägerDinnerDinnerDinnerFarewell BBQ

There’s no programme activites during the weekend


Microscopy Building module

This module will introduce you to basic concepts in microscopy, and teach you how to assemble your own microscope. The lectures will focus on physical principles, as well as describe the application of various microscopy methods for current research in biology. In the practical, you will build your own wide-field fluorescence microscope, evaluate it’s optical performance and test it on various biological samples.

Imaging module

This module will introduce the basic principles of developmental biology, with emphasise on imaging approaches that capture the cellular and molecular mechanisms by which a fertilized zygote transforms into a mature organism. Topics covered will include cell mechanics, cell-cell communication and tissue morphogenesis across diverse multicellular organisms. The lab practical will consist on live imaging the metamorphic process of a sea anemone that gradually transforms the spherical embryo into an elongated tubular body.

Image Analysis module

This module will give an introduction to how microscopy images can be processed to extract biological information. We will look into both classical filters and machine learning-based methods and try them all out on the Nematostella samples imaged in the previous module.

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