Artificial intelligence applied to intravital video microscopy, 4th edition
11 - 13 December 2024
This workshop will cover theoretical and practical aspects regarding the application of A.I. -based methods for the analysis of intravital imaging data.
We will focus on the migration and interaction of immune cells observed in vivo, explaining how to get accurate tracking analysis, or how to extract insights from videos without using cell tracking.
Moreover, we will discuss the importance of Open Source and Open Data resources.
The topics and tools presented in this workshop can be applied also for other imaging modalities and cell types but a basic knowledge in microscopy is recommended.
How: Online via Google meet
When: December 11th – 13th
9:00 - 17:00 Switzerland time zone
18 places available, served on a first come first served basis.
Contact: For questions do not hesitate to contact us at This email address is being protected from spambots. You need JavaScript enabled to view it. with the subject of the email ai-ivm2024
Organizers:
Prof. Santiago Fernandez Gonzalez
Prof. Rolf Krause
Dr. Diego Ulisse Pizzagalli
Temtative Program
DAY 1: December 11th. Introduction, intravital imaging and Open Data
Learning objectives. Understanding the applications and advantages of intravital microscopy / the importance of Open Data research / Practice with immunemap platform and other tools
09:00 - 10:00 Introduction
10:00 - 11:15 Principles of fluorescence and intravital microscopy
11:15 - 11:30 Coffee break
11:30 - 12:30 Studying the immune system in vivo, surgical models and applications
12:30 - 14:00 Lunch Break
14:00 - 16:00 Open Data research, FAIR principles and Immunemap
DAY 2: December 12th: Analysis with tracking.
Learning objectives. Understanding what can be extracted from IVM data using the classical image analysis pipeline (tracking and track measures), challenges and new perspectives.
09:00 - 10:00 Cell motility and cell-to-cell interaction metrics.
10:30 - 10:45 Coffee break
10:45 - 12:30 Practical session 2: Exercises to quantify motility
12:30 - 14:00 Lunch Break
14:00 - 15:00 Tracking with FIJI/Trackmate
15:00 - 17:00 Image processing and supervised machine learning techniques to facilitate cell detection and tracking
DAY 3: December 13th: Analysis without tracking.
Learning objectives. Understanding how image processing and computer vision techniques can be applied to analyze IVM data without necessarily using of cell tracking
09:00 - 10:15 Recent trends in computer vision methods - discussion
10:15 - 10:30 Coffee break
10:30 - 12:00 Apoptosis detection via machine learning
12:00 - 13:00 Lunch Break
13:00 - 14:00 Unsupervised learning to identify motility patterns
14:00 - 16:00 Practical session 3: Analyzing cell migration without tracking
16:10 - 17:00 Conclusion
PAST EDITIONS
Artificial intelligence applied to intravital video microscopy, 3rd edition
13 - 15 November 2023
This workshop will cover theoretical and practical aspects regarding the application of A.I. -based methods for the analysis of cell motility from microscopy data, with a focus on immune cells observed in vivo. Moreover, we will discuss the importance of Open Source and Open Data resources in image-driven immunological research.
The methods presented in the workshop can be applied also to other cell types and imaging modalities. A basic understanding of microscopy is recommended.
How: Best would be to attend in presence, with practical cases to be solved in small groups. We will provide data and tools. You have to bring your own laptop. You can also bring your own data to be analyzed with the help of the peers.
For those who cannot come to Lugano in person we will leave open the possibility to connect via Google meet, attending lectures and watching the demonstrations. However, interactions may be restricted.
Link to attend online https://meet.google.com/qiq-yuug-vif
Where: USI Campus EST, Via La Santa 1, 6962 Lugano – Switzerland
Organizers:
Prof. Santiago Fernandez Gonzalez
Prof. Rolf Krause
Dr. Diego Ulisse Pizzagalli
Confirmed speakers:
Pau Carrillo Barbera (University of Edinburgh)
Raffaella Fiamma Cabini (University of Pavia & USI Lugano)
Diego Morone (IRB Bellinzona)
Santiago Fernandez Gonzalez (IRB Bellinzona)
Mariaclaudia Nicolai (USI Lugano)
Elisa Palladino (IRB Bellinzona)
Diego Ulisse Pizzagalli (USI Lugano)
Alain Pulfer (IRB Bellinzona)
Inge Wortel (Radboud University)
Contact: For questions do not hesitate to contact us at This email address is being protected from spambots. You need JavaScript enabled to view it.
DAY 1: November 13th. Introduction, intravital imaging and Open Data
Learning objectives. Understanding the applications and advantages of intravital microscopy / the importance of Open Data research / Practice with immunemap platform and other tools
09:00 - 10:00 Introduction - DUP
10:00 - 11:15 Principles of fluorescence and intravital microscopy – DM
11:15 - 11:30 Coffee break
11:30 - 12:30 Studying the immune system in vivo, surgical models and applications - SFG
12:30 - 14:00 Lunch Break
14:00 - 15:00 Open Data research, FAIR principles and Immunemap DUP + EP
15:00 - 17:00 Practical session 1 in small groups: Reuse of datasets and Open source tools
DAY 2: November 14th: Analysis with tracking.
Learning objectives. Understanding what can be extracted from IVM data using the classical image analysis pipeline (tracking and track measures), challenges and new perspectives.
09:00 - 09:45 Basic measures of cell motility and cell-to-cell interaction. DUP+MN
10:15 - 10:30 Advanced metrics of cell motility + introduction to CelltrackR. IW
10:30 - 10:45 Coffee break
10:45 - 12:30 Practical session 2: Exercises to quantify motility
12:30 - 14:00 Lunch Break
14:00 - 15:00 Tracking with FIJI/Trackmate – PCB
15:00 - 16:00 Practical session 3: Practice with FIJI and Trackmate
16.00 - 17.00 Deep learning based cellular action recognition (mock dissertation - AP)
DAY 3: November 15th: Analysis without tracking.
Learning objectives. Understanding how image processing and computer vision techniques can be applied to analyze IVM data without necessarily using of cell tracking
09:00 - 10:15 Image processing and supervised machine learning techniques to
- facilitate cell detection and tracking DUP+RFC
- quantify motility when it is impossible to track individual cells DUP
10:15 - 10:30 Coffee break
10:30 - 12:00 Unsupervised machine learning technique for
- cell segmentation RFC
- cell swarming analysis DUP
- identification of main motility patterns DUP
12:00 - 13:00 Lunch Break
13:00 - 14:00 Discussion: recent trends in computer vision methods
14:00 - 16:00 Practical session 3: Analyzing cell migration without tracking
16:10 - 17:00 Conclusion
Artificial intelligence applied to intravital microscopy of the immune system, 2nd edition 16 - 18 May 2022
This workshop will cover theoretical and practical aspects regarding the application of A.I. -based methods for the analysis of intravital imaging data.
We will focus on the migration and interaction of immune cells observed in vivo, explaining how to get accurate tracking analysis, or how to extract insights from videos without using cell tracking.
Moreover, we will discuss the importance of Open Source and Open Data resources in image-driven immunological research.
The topics and tools presented in this workshop can be applied also for other imaging modalities and cell types but a basic knowledge in microscopy is recommended.
How: Blend modality. Best would be to attend in presence, with practical cases to be solved in small groups. We will provide data and tools and can offer a few workstations to be used but is encouraged to bring your own laptop. You can also bring your own data to be analyzed. For those who cannot come to Bellinzona we will leave open the possibility to connect via Zoom and watch the demonstrations.
When: May 16th – 18th, optional excursion on May 19th
Where: Institute for Research in Biomedicine, Via Francesco Chiesa 5, CH-6500 Bellinzona (Switzerland) / or online on Zoom (we will do the possible to let you following, but consider that technical issues may arise for the practical sessions)
Registration: up to May 8th 2022 23:59 CEST at https://forms.gle/x3XqkdqG7PxMBVH56 15 places available, served on a first come first served basis. You will receive a confirmation via email.
Cost: Free of charge
Contact: For questions do not hesitate to contact us at This email address is being protected from spambots. You need JavaScript enabled to view it. with the subject of the email ai-ivm2022
Program is in CEST timezone. Program can be subjected to changes, here you will always find the most updated schedule.
DAY 1: May 16th. Introduction to intravital microscopy (IVM).
Learning objectives. Understanding the applications and advantages of intravital microscopy / Understanding the importance of Open Data research / Practice with the immunemap platform
08:45-09:15: Walk-in and welcome of participants
9:15-10:15: Introduction of the course and Ice-breaker activity (Pizzagalli DU)
10:15-11:15: Technical Introduction to IVM (Morone D)
11:15-11:30 Coffee break
11:30-12:30: Surgical models and biological applications of IVM (Virgilio T)
12:30-14:00: Lunch Break
14.00-14:25: Summary of the concepts presented during the morning, Q&A session (Pizzagalli DU)
14:30-15:15: Introduction to cell tracking and open data research (Pizzagalli DU)
15:15-15:45: Coffee break
15:45-16:00: Presentation of immunemap (Palladino E / Ceni K)
16:00-17:00: Practical session 1: Use of immunemap and open data resources (Palladino E / Ceni K / Thelen B)
DAY 2: May 17th: Analysis with tracking.
Learning objectives. Understanding which type of information can be extracted from IVM data using the classical image analysis pipeline, challenges and new perspectives
9:00-10:30: Classical image analysis pipeline, artifacts, quality requirements (Pulfer A)
10:30-10:45 Coffee break
10:45-12:00: The relevance of cell tracking in life sciences, motility parameters (Pizzagalli DU)
12:30-14:00: Lunch Break
14.00-14:25: Summary of the concepts presented during the morning, Q&A session (Pizzagalli DU)
14:25-15:00: Practical session 2a, Facilitating automatic tracking using computer-assisted colocalization (Pizzagalli DU)
15:00-16:00: Practical session 2b, Analysis of motility measures and cell-to-cell interaction (Pizzagalli DU)
16:00-16:15 Coffee break
16:15-17:30: Practical session 2c, Manual tracking and crowd-based tracking using immunemap. Manual tracking in FIJI/Trackmate and Imaris on request. (Ceni K, Carrillo-Barbera P, Palladino E).
DAY 3: May 18th: Analysis without tracking.
Learning objectives. Understanding how image processing and computer vision techniques can be applied to analyze IVM data without the usage of cell tracking
9:00-10:30: From pixels to cell actions (Pizzagalli DU)
10:30-10:45 Coffee break
9:00-10:30: Recent trends in computer vision methods (Pulfer A)
12:30-14:00: Lunch Break
14.00-14:25: Summary of the concepts presented during the morning, Q&A session (Pizzagalli DU)
14:25-15:45: Practical session 3: Advanced analysis of cell migration (Motility heatmaps, Optical flow, Tracklet-based action recognition, Colocalization, Cell death detection, Swarm detection) (Pizzagalli DU, Pulfer A)
15:45-16:00: Coffee break
16:15-16:45: Practical session 4: Unsupervised machine learning to identify migration modalities (Pizzagalli DU)
16:45-17:00: Conclusion
DAY 4: May 19th: Social activity
09:00–12:00: Visit to the castles of Bellinzona
Organizers:
Dr. Santiago Fernandez Gonzalez - Institute for Research in Biomedicine (CH)
Dr. Diego Ulisse Pizzagalli - Institute for Research in Biomedicine and Euler Institute, USI (CH)
Tutors:
Dr. Pau Carrillo-Barbera – The University of Edinburgh (UK)
Kevin Ceni – Institute for Research in Biomedicine (CH)
Diego Morone – Institute for Research in Biomedicine (CH)
Elisa Palladino – Institute for Research in Biomedicine (CH)
Alain Pulfer – Institute for Research in Biomedicine and ETH Zurich (CH)
Benedikt Thelen – Euler institute (CH)
Dr. Tommaso Virgilio - Institute for Research in Biomedicine (CH)
---- MATERIAL FROM PREVIOUS EDITION (2021) ----
Description
This summer school covered theoretical and practical aspects regarding the analysis of immune cell migration and interaction, using intravital microscopy and new A.I.-based methods. We had 18 participants (4 from USI, 14 external), from 4 european countries including BSc, MSc, PhD students, postdocs and imaging specialists.
Organizers. Dr. Santiago Fernandez Gonzalez, Dr. Diego Ulisse Pizzagalli, dr. Pau Carrillo Barbera
Tutors. Diego Morone, Alain Pulfer, Kevin Ceni, Benedikt Thelen
Supported by. IRB PhD program Cell Migration PhD program USI - Biomedical PhD program IMMUNEMAP consortia Euler Institute
Program
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DAY 1: June 14th. Introduction to intravital microscopy (IVM). Learning objectives. Understanding the applications and advantages of intravital microscopy / Understanding the importance of Open Data research / Practice with the immunemap platform |
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Introduction and networking activity (Pizzagalli) |
1 |
9:00 - 10:00 |
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Physics of 2-photon intravital microscopy (Morone) |
1 |
10:30 - 11:30 |
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Intravital imaging of the immune system (Gonzalez) |
1 |
11:45 - 12:45 |
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Image formation / histograms / Properties of digital images (Barbera / Morone) |
1 |
14:00 - 15:00 |
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The role of Open Data and Open Source in biomedical research , FAIR principles and IMMUNEMAP project (Pizzagalli / Barbera) |
1 |
15:10 - 15:45 |
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FIJI introduction (Morone) |
1 |
15:45 - 17:00 |
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DAY 2: June 15th: Analysis with tracking. Learning objectives. Understanding which type of information can be extracted from IVM data using the classical image analysis pipeline, challenges and new perspectives |
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Exercise 1
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2 |
9:00 - 9:30 |
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Image analysis pipeline, quantification of cell motility, dynamism, and interaction (Pizzagalli) |
2 |
9:30-10:30 |
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The possibilities of Machine Learning in IVM (Pizzagalli) |
2 |
10:45-11:30 |
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Excercise 2 (Morone / Pulfer / Barbera Pizzagalli)
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2 |
14:00 - 17:00 |
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DAY 3: June 16th: Analysis without tracking. Learning objectives. Understanding how image processing techniques working at pixel-level can be applied to analyze IVM data without the usage of cell tracking |
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Exercise: track-based measures on neutrophil chemotaxis Exercise: migration differences between WT and KO cells in spleen |
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9:00 – 10:30 |
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Discussion Exercise 1 (Pizzagalli) Contact analysis in Exercise 1 (Pizzagalli) Advanced analysis without tracking (of/recruitment) (Pizzagalli) |
3 |
10:45 - 11:00 |
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Image processing techniques (Pulfer) |
3 |
11:15 - 12:15 |
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Exercise 3
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3 |
14:00 - 17:00 |
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DAY 4: June 17th: Beyond tracking. Learning objectives. Understanding how computer vision methods for action recognition can be applied to analyze IVM data without the usage of cell tracking |
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Inside AI: neural networks and clustering (Pizzagalli) |
4 |
9:00 – 10:00 |
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Trends in computer vision: classic, deep learning, generative (Pulfer) |
4 |
10:05 - 11:00 |
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Action recognition applied to immune cells (Pizzagalli)
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4 |
11:15 - 12:15 |
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Exercise 4 (Pulfer / Pizzagalli)
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4 |
14:00 - 16:00 |
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Discussion on good practices for IVM analysis (Barbera + Pizzagalli) |
4 |
16:15 - 17:00 |
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DAY 5: June 18th: Workshop and conclusion |
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Workshop: analyze data by participants (Pizzagalli): - Quantification of leukocyte migration within and outside blood vessels via track-based measures and pixel classification. - Analysis of DCs – Macrophage interaction via supervised spectral unmixing, contact analysis, and bayesian colocalization. |
5 |
9:00 - 12:00 |
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Exam |
5 |
14:00 - 15:00 |
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Concluding remarks |
5 |
15:30 - 16:30 |