Community
Workshops

Virtual (at Valencia)
Spanish & Portuguese
Advanced Optical Microscopy Meeting 2020

SPAOM2020

November 24th to 27th, 2020

General Description

Community Workshops are the signature session of SPAOM2020.
There, scientists present scientific results with a different perspective: more oriented to practical aspects, including protocols, experimental approaches, hints & tricks, or entire technological developments with a hands-on focus. Community workshops promote Open Science, open source developments and community sharing and discussions.

The format varies from a series of short talks on a specific topic, up to live demos of instruments or techniques. This year, all workshops will be streamed live, from home or from the lab.
Sessions will be introduced by a chair, and each contribution in the session will be streamed by a presenter and a team of moderators, who will interact with the audience to answer questions live.

Workshop 1:

High-Content Screening,
High-Throughput Screening

Tue 24 Nov. 13.00h – 14.00h CET Valencia

Chair:

Diego Megias

CNIO (Madrid).

Summary:

This workshop is focus on HCS technologies, from the biological questions to image analysis and data mining solutions.

Session 1:

High content and high throughput: complementary microscopies

Speakers:

Dr. Nicola Gritti & Dr. Vikas Trivedi

EMBL-Barcelona (Spain)

nicola.gritti@embl.es

Session 2:

High content image analysis with CellProfiler

Speaker:

Hugo Botelho

BioISI / University of Lisbon (Portugal)

hmbotelho@fc.ul.pt

Session 3:

Numbers for interpretation: Data analysis

Speaker:

Dr. Gadea Mata

Univ. De la Rioja (Spain)

gadea.mata@unirioja.es

Workshop 2:

Open access to Bioimaging infrastructures: Requirements, opportunities and challenges

Tue 24 Nov. 17.00h – 17.45h CET Valencia

Chair:

Timo Zimmermann

CRG (Barcelona, Spain).

Summary:

Imaging methods and technologies are continuously evolving and access provision to the latest high-end methods is challenging for single installations and facilities, and can’t even in the best case be offered for all fields. It can however be managed by combining the offer of individual sites and making them accessible to external users. This workshop aims to explore different aspects of existing open access strategies and how it is organised at different scales at the national and international level. It will be organized in two parts: short talks by key players in the field, followed by an open panel discussion.

Session 1:

Short presentations of host organizations and access provision

Panelists:

Johanna Bischoff

Euro-BioImaging

Jean Salamero

Curie Institute, Paris, France

Jana Nieder

Iberian Nanotechnology Laboratory, Braga, Portugal

Pablo Loza

Photonic Sciences Institute, Barcelona, Spain

Session 2:

Panel discussion
The panel discussion will be open for questions from the audience, but will also aim to cover what criteria are important for successful open access provision, in what fields it is most relevant and to what extent remote access is feasible in advanced imaging experiments to reduce the need for travel.

Workshop 3:

Frugal Science

Tue 24 Nov. 17.45h – 19.15h CET Valencia

Chairs:

Julien Colombelli, Gaby Martins

 

17.30h – 18.00h

Plenary Session:

Four Intros of 5 minutes to each of the following practical sessions.

18.00h – 19.00h

Parallel Sessions:

Practical Sessions / Hands-On Demos (parallel two-by-two)

18.00h – 18.30h

Session 1:

OPenT – Macro-mesoscopy with a micro-budget

Presenters:

Gabriel G Martins

Advanced Imaging Head, Instituto Gulbenkian de Ciencia (Oeiras, Portugal)

Alexandre Lopes

(co-presenter), Imaging specialist and developer

Donald Fowler

(co-presenter), Imaging specialist

18.00h – 18.30h

Session 2:

Automating multimodal microscopy with NanoJ-Fluidics

Presenter:

Romain F. Laine

MRC-LMCB/UCL/The Francis Crick Institute (London, UK)

r.laine@ucl.ac.uk

co-authors:

Pedro Matos Pereira, Ricardo Henriques

MRC-LMCB, UCL, London, UK,
The Francis Crick Institute, London, UK,
ITQB, Lisbon, Portugal
Instituto Gulbenkian de Ciência, Oeiras, Portugal

18.30h – 19.00h

Session 3:

Casper – a custom-made chamber for drug testing efficiency improvement for the Zeiss lightsheet system

Presenters:

Leonor Morgado

ABBE, Champalimaud Institute, (Lisbon, Portugal)

abbe@research.fchampalimaud.org

Co-presenters:

Davide Accardi and the ABBE team

18.30h – 19.00h

Session 4:

LEMOLISH: a benchtop LEGO-based lightsheet system for 3D mesoscopic imaging of cleared organs

Presenters:

Julien Colombelli & Sébastien Tosi

ADMCF, IRB Barcelona (Spain)

julien.colombelli@irbbarcelona.org

Workshop 4:

Lightfield Microscopy

Wed 25 Nov. 18.15h – 19.15h CET Valencia

Chairs:

Genaro Saavedra, Manuel Martinez-Corral

 

Session 1:

Design parameters of Lightfield Microscopy and of Fourier Lightfield Microscopy

Presenter:

Manuel Martinez-Corral

3DID Lab-Univ. de València (Spain)

Session 2:

Practical implementation of Lightfield Microscopes

Presenters:

Genaro Saavedra and Emilio Sanchez-Ortiga

Workshop 5:

Single particle tracking with nanobodies & iSCAT

Thu 26 Nov. 17.00h – 18.00h CET Valencia

Chair:

Pedro Matos Pereira

ITQB (Lisbon, Portugal)

Presenter:

David Albrecht

Max Planck Institute for Science of Light (Erlangen, Germany)

david.albrecht@mpl.mpg.de

Single particle tracking via fluorescently labelled nanobodies

Single particle tracking via interferometric scattering microscopy (iSCAT)

Workshop 6:

Practical Applications of Deep learning for Bioimage Analysis

Thu 26 Nov. 18.00h – 19.15h CET Valencia

Chair:

Sébastien Tosi

IRB Barcelona, Spain

Session 1:

Introduction to Deep Learning

Presenter:

Ignacio Arganda-Carreras

Universidad del Pais Vasco (Donostia-San Sebastian, Spain)

Session 2:

ZeroCostDL4Mic:
an open platform to simplify access and use of Deep- Learning in Microscopy

Presenter:

Romain F. Laine

MRC-LMCB/UCL/The Francis Crick Institute (London, UK)

co-authors:

Lucas von Chamier, Guillaume Jacquemet, Ricardo Henriques

MRC-LMCB, UCL, London, UK,
The Francis Crick Institute, London, UK,
Turku Bioscience Centre, University of Turku, Turku, Finland,
Instituto Gulbenkian de Ciência, Oeiras, Portugal

Session 3:

DeepImageJ:
a user-friendly plugin to run deep learning models in ImageJ

Presenter:

Estibaliz Gómez de Mariscal

Universidad Carlos III de Madrid (Spain)

co-authors:

C. García-López-de-Haro, L. Donati, M. Unser, A. Muñoz-Barrutia, D. Sage

Universidad Carlos III de Madrid (UC3M) and Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Spain,
École polytechnique fédérale de Lausanne (EPFL), Switzerland