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)
Session 2:
High content image analysis with CellProfiler
Speaker:
Hugo Botelho
BioISI / University of Lisbon (Portugal)
Session 3:
Numbers for interpretation: Data analysis
Speaker:
Dr. Gadea Mata
Univ. De la Rioja (Spain)
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)
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)
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)
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
In this section of the workshop, we will discuss two distinct and complementary approaches to observe biological samples: high content microscopy and light sheet microscopy, and highlight the pros and cons of each. We will touch upon the biologically relevant information that can be obtained in each technique, thus providing a set of guidelines to choose the experimental approach best suited for the sample of interest.
Description
In this section we will use CellProfiler to batch analyze a 3D imaging dataset. We will introduce the recently released CellProfiler 4 and present the major changes in this version. Then, we will design a custom analysis pipeline to segment objects, extract quantitative features and export a results table. We will also show how the analysis pipeline can be customized to address advanced analytical requirements and allow annotation with experimental metadata.
Refs:
https://github.com/hmbotelho/SPAOM2020-ws1-high-content-screening
https://cellprofiler.org
Description
In this part, we will see how to process the data obtained from the image analysis. We will work with Excel to get a fast visualization to start to interpret our results, and we will work with Orange to approach the Machine Learning techniques to analyze our data.
Optical Projection Tomography (OPT) is a technique still vastly unexplored in biomedical research. OPT has been instrumental for establishing high-quality virtual atlases for several vertebrate embryos or for expediting efforts such as the International Mouse Phenotyping Consortium to characterize thousands of mouse phenotypes. Here we will show a simplified version of the OPenT, simple/inexpensive to build and operate and capable of producing isometric macro & mesoscopic level 3D datasets of high-quality, anatomical detail and visual impact. The OPenT can be built with basic knowledge on electronics and optics, and ImageJ operation. OPT also allows 3D imaging or non-fluorescent samples and does not require stitching and fusion of different views, thus saving enormous time and computational/data handling resources. In this demonstration we show the prototype, how to build it, discuss advantages/challenges, considerations about sample preparation and introduce a new ImageJ script and workflow for pre-processing OPT datasets.
Combining and multiplexing microscopy approaches is crucial to understand cellular events, but requires elaborate workflows. We developed a robust, open-source approach for treating, labelling and imaging live or fixed cells in automated sequences. NanoJ-Fluidics is based on low-cost Lego hardware controlled by ImageJ-based software, making high-content, multimodal imaging easy to implement on any microscope with high reproducibility. We will demonstrate how easy it is to build a pump set and how you can use it in your experiments.
Ref:
https://www.nature.com/articles/s41467-019-09231-9
https://github.com/HenriquesLab/NanoJ-Fluidics

The ABBE Platform of the Champalimaud Foundation developed an innovative imaging chamber for drug testing in long term in vivo imaging using the Zeiss lightsheet system. The chamber is optically transparent, biocompatible and of small inner volume (~3 mL), which improves the efficiency of drug testing studies. During this workshop we will show the technical characteristics of the chamber, how to make it and how to use it from its assembling to image acquisition.

Description
Whole organism imaging is pursued by life scientists to study cells in their natural “in tissue” context, but the challenges associated with in toto imaging of centimeters-sized organs, combined with consequent instrumentation costs, somehow still impair global access to such analysis. Here, we propose an affordable lightsheet device and imaging framework, LEMOLISH (LEGO-based Motorized Lightsheet microscope) aimed to enable anyone to equip the lab with a easy-to-mount benchtop solution, and to enter the game of 3D imaging of very large scale cleared samples, for a starting cost standing below immunostaining costs, and 100- to 200-fold below commercial or highly customized systems. We will present the features of the instrument in a live hands-on demo from the lab to offer participants a close-up view on its building blocks and acquisition strategy.
(from November 2020: https://legolish.org/lemolish/)

Description
Two designs of Lightfield Microscope are shown. The conventional Lightfield Microscope captures at each shot an array of thousands microimages, from which the perspective views are computed. On the contrary, the Fourier Lightfield Microscope captures directly, at each shot, the collection of orthographic perspective views. The two modes are compared in terms of resolution, depth of field and computation time. Besides, practical hints on how to setup the two microscopes are given.
Description
In direct streaming from the 3DID Lab., University of Valencia, it is shown how to setup the two modes of lightfield microscope. The microscopes are implemented in open architecture on an optical table. The importance of the fine adjustment of some parameters, like the illumination or the microlenses conjugation, are shown. Then, some imaging experiments are performed in real time, and the resulting 3D images are shown and compared.
Deep learning, the latest extension of machine learning, has pushed the accuracy of algorithms to unseen limits, especially for perceptual problems such as the ones tackled by computer vision and image analysis. This workshop will cover the foundations of the field, the communities organized around it, and some important tools and resources to get started with these techniques. Two successful deep learning bioimage analysis platforms will then be presented, with hands-on examples that will cover how to set them up for daily use. No prior programming knowledge is required to follow the workshop.
Deep Learning (DL) methods are powerful analysis tools for microscopy. However, the need to access computational resources and the complexity in setting these up often lead to an accessibility barrier for most biology-focused laboratories.Here, we present ZeroCostDL4Mic, a DL platform which considerably simplifies access and use of DL for microscopy. For this, we exploit the computational resources provided by Google Colab: a free, cloud-based service accessible through a web browser. ZeroCostDL4Mic allows researchers without coding expertise to use some of the most powerful DL networks available today, for e.g. segmentation, denoising, artificial labelling, super-resolution microscopy, object detection and image-to-image translation. Importantly the platform allows the user to perform every step of the process necessary to DL: training and use of the models, quality control of the network output as well as integration within larger analysis pipelines.
The use of Deep Learning models requires previous programming knowledge and expertise, which makes them unapproachable to the general public. We present DeepImageJ [1], an open-source project that enables the generic use of pre-trained deep learning models provided by their developers in FIJI/ImageJ. The plugin acts as a software layer between TensorFlow and FIJI/ImageJ with all the technicalities hidden behind a user-friendly interface. In this workshop we show the two main functionalities of DeepImageJ: (1) a model importer tool that gathers all critical information from developers to get a correct image processing, and (2) a user-oriented tool that runs a selected model on an image batch. The plugin can also be called in a standard ImageJ/Fiji macro, which permits its inclusion as a standard plugin in image analysis workflows. This design facilitates the use of DNN models by end-users.