Pre-Hackathon

Pre-symposium AI4Life Workshop & Hackathon: Trends in AI for super-resolution microscopy

The pre-symposium Workshop & Hackathon will be held on August 26th-27th, 2024, at the Institute Gulbenkian de Ciência (IGC) in Oeiras, Portugal and will be co-hosted by AI4Life. The event will focus on the latest AI trends for super-resolution microscopy, particularly Single-Molecule Localization Microscopy. The workshop is organized by Estibaliz Gómez de Mariscal and co-led by experts in the field, and will provide an opportunity for participants to share some of the latest developments in AI and super-resolution microscopy, and discuss practical problems and needs in a collaborative environment. It is an excellent opportunity for researchers to engage with experts and peers in the community, and foster the cross-pollination of ideas and methodologies for AI-enhanced microscopy. Join us for dynamic discussions about next-generation microscopy imaging and machine learning-enabled image-driven discovery!

Registration

Registration is free but mandatory. Please fill in the form below to register for the event. The deadline for registration is July 5th, 2024. As there are a limited number of places available, we encourage you to register as soon as possible. The application will be reviewed on a rolling basis, and you will be notified of the outcome of your application by July 10th, 2024.

Participants

The workshop is open to all researchers, from students to senior scientists, who are interested in learning about the latest trends in AI for super-resolution microscopy. We particularly encourage applications from researchers who are working on the development of new algorithms for image analysis, and from those who are interested in applying AI to their own research. Please note that this event is not a course on AI for microscopy.

Invited speakers

Alon Saguy
Technion, Israel Institute of Technology
Israel

Estibaliz Gómez-de-Mariscal
Instituto Gulbenkian de Ciência
Portugal

Prof. Guillaume Jacquemet
Åbo Akademi University
Finland

Prof. Arrate Muñoz-Barrutia
Universidad Carlos III de Madrid
Spain

About Alon Saguy: is PhD candidate at the Technion under the supervision of Prof. Yoav Shechtman. In his PhD, Alon developed various computational methods to analyze microscopy images, especially in the domain of super-resolution microscopy. In recent years, Alon has focused on improving the spatiotemporal resolution of microscopy methods using deep learning models.

About Estibaliz Gómez-de-Mariscal: is a postdoctoral researcher at the Henriques Lab, Instituto Gulbenkian de Ciência. She is interested in the development of deep learning models for microscopy, and in the application of these models to biological problems. She is also a co-founder of the AI4Life initiative, which aims to foster the development of AI in the life sciences.

About Guillaume Jacquemet: earned his PhD from the University of Manchester, UK, and then carried postdoctoral training at the University of Turku, Finland. He currently serves as an Associate Professor at Åbo Akademi University. His laboratory uses and develops live imaging and image analysis methodologies to investigate how cancer cells interact with and respond to their surroundings during metastasis.

About Arrate Muñoz-Barrutia: is a Full Professor in the Bioengineering Department at Universidad Carlos III de Madrid, a senior researcher at the Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM) and IEEE Fellow. She has a long-standing career in the field of biomedical image analysis with a particular emphasis on user-friendly tools for deep learning-based image processing in the life sciences, such as deepImageJ and SAMJ, as well as the organisation of image processing challenges such as the Cell Tracking Challenge and ANHIR. Arrate is co-founder and member of the steering committee of AI4Life.

Schedule

Time	Day 1 (August 26th)		Day 2 (August 27th)
09:00 - 09:30	Arrival and check-in at Library building	9:15 - 9:30	Arrival, Q&A, debriefing - Protagoras room
09:30 - 10:00	AI4Life Introduction (E. Gómez-de-Mariscal)	9:30 – 10:00	Alon Saguy
10:00 - 10:30	Guillaume Jacquemet	10:00 – 10:15	Nils Mechtel
10:30 - 10:45	Coffee break in the Library building	10:15 – 10:30	Cecilia Zaza
10:45 - 11:00	Clément Cabriel	10:30 – 10:45	Hyoungjun Park
11:00 - 11:15	Tayla Shakespeare	10:45 – 11:00	Coffee break in the Library building
11:15 - 11:30	Nour Mohammad Alsamsam	11:00 – 12:00	Working groups*
11:30 - 11:45	Christophe Spahn
11:45 - 12:00	Discussion and working groups assignment
12:00 - 13:30	Lunch - IGC cantina	12:00 - 13:30	Lunch and group picture - IGC cantina
13:30 - 16:15	Working groups*	13:30 - 16:00	Working groups*
16:15 - 16:30	Coffee break in the Library building	16.00 - 16.30	Coffee break in the IGC cantina
16:30 - 17:00	Arrate Muñoz-Barrutia	16:30 - 17:45	Elders table - Democritus room
17:00 - 18:30	Hands-on tutorial in groups*	17:45 - 18:00	Wrap up - Democritus room
18:30 - 19:00	Lessons of the day and discussion	18:00 -	Sunset in Carcavelos beach
19:00 - 19:30	Guided visit to the lab
19:30 -	Dinner at IGC in the cantina

* Hands-on session will be split into two groups: 1) Newbies: a didactic hands-on using deep learning for microscopy image analysis (e.g., dl-segmentation, virtual staining, deepstorm, decode etc.) using ZeroCostDL4Mic. (Instructor: Estibaliz Gómez de Mariscal, in Protagoras room) 2) Advanced: method containerisation and dissemination through the BioImage Model Zoo with DL4MicEverywhere. (Instructors: Iván Hidalgo-Cenalmor, Mariana Ferreira, in the BioInformatics Computers room)

* Working in groups sessions are dedicated to working in a hackathon mood. Potential topics you can bring are: - The integration of the BioImageIO packages into super-resolution microscopy pipelines. - Compatibility of BioImgaeIO with SOTA DL-methods in bioimaging that need specific post-processing pipelines. - Cross-compatibility between the BioEngine, Hypha and DL4MicEverywhere. - Integration of cell tracking and particle tracking DL methods in BioImageIO. - Point-cloud AI for microscopy. - Integration of recent virtual staining pipelines in BioImageIO as user-friendly notebooks. - DL-methods for (multicolor) single-molecule localisation. - DL-methods and assessment of obtained results for cross-modality translation. - Super-resolution microscopy data simulation.

Organising committee

Beatriz Serrano-Solano, European Molecular Biology Lab (EMBL) & Euro-Bioimaging Bio-Hub
Estibaliz Gómez-de-Mariscal, Instituto Gulbenkian de Ciência (IGC)
Iván Hidalgo-Cenalmor, Instituto Gulbenkian de Ciência (IGC)
Inês Geraldes, Instituto Gulbenkian de Ciência (IGC)
Mariana Ferreira, Instituto Gulbenkian de Ciência (IGC)
Ricardo Henriques, Instituto Gulbenkian de Ciência (IGC)

Venue and your stay

The Instituto Gulbenkian de Ciência (IGC) will be the host institution for the "AI4Life workshop: Trends in AI for super-resolution microscopy" workshop, located in Oeiras, Portugal, close to the sea and quickly accessible from the capital city of Lisbon, where SMLMS 2024 will happen from August 28th. The IGC is a multidisciplinary research institute, that invests in innovative training, and transforming society through science. It is part of Fundação Calouste Gulbenkian, a foundation with charitable, artistic, educational and scientific aims.

Address

Instituto Gulbenkian de Ciência

Rua da Quinta Grande, 6

2780-156, Oeiras, Portugal

Google maps

Further information about the venue

How to get to Instituto Gulbenkian de Ciência (IGC)?

From the airport (Aeroporto Humberto Delgado, Lisboa):

The metro station can be found outside the Arrivals at Terminal 1 in Lisbon Airport. Metro tickets can be purchased at vending machines in the Airport station and have a cost of 1.50€ (plus 0,50€ for the card - paid only once; can be reused).

1 - Take the metro (red line) towards São Sebastião and get off in Alameda (~16 minutes trip).

2 - In Alameda, take the metro (green line) towards Cais do Sodré (~8 minutes trip).

3 - Get off in Cais do Sodré and walk to the train terminal to take the train towards Cascais and get off in Oeiras (17 or 24 minutes trip depending on the train). Train.-,Train,-tickets%20cost%201.95) tickets cost 1.95€.

4 - Get off in Oeiras train station and take the exit to your left. The Oeiras train station is located at a safe walking distance from the IGC (6 minutes).

5 - Cross the road to the side of the street where you will find a pharmacy and a restaurant.

6 - Keep walking until you get to an intersection with traffic lights.

7 - Turn left again and cross the road. Welcome to the IGC!

Check how to get to IGC from the metro station using Google Maps here

Where to stay

These are accommodations located close by:

In Carcavelos:

By train: ~13 minutes walking to the Carcavelos Train Station http://bit.ly/abla-carcavelostrain-map + 6 minutes to Oeiras Train Station + 6 minutes walking to IGC - http://bit.ly/igc-oeiras-map.

Walking: ~40 min walking

Hotel Riviera

Address: R. Bartolomeu Dias, 2775-551 Carcavelos

Phone: + 351 21 458 6600

Email: reservas@rivierahotel.pt

Hotel Praia Mar

Address: R. Gurué 16, 2775-581 Carcavelos

Phone: + 351 21 458 5100

Email: antonio.romeiro@almeidahotels.pt

Abla Guesthouse

Address: Praceta Infante Dom Henrique 80, 2775-004 Carcavelos

Phone: + 351 214548114

In Parço de Arcos

By train: ~10 minutes walking to the Parço de Arcos Train Station Carcavelos Train + 6 minutes to Oeiras Train Station + 6 minutes walking to IGC - http://bit.ly/igc-oeiras-map.