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)
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.
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
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
9:00-9:30: Introduction of the tutors and the course (Pizzagalli DU)
9:30-10:15: Ice-breaker activity (Pizzagalli DU)
10:30-11:30: Technical Introduction to IVM (Morone D)
11:30-12:30: Biological applications of IVM (Gonzalez SF)
12:30-14:00: Lunch Break
14:00-15:15: Open Data research and presentation of immunemap (Pizzagalli DU)
15:15-15:45: Coffee break
15:45-17:00: Practical session 1: Use of immunemap (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
14:00-15:15: Practical session 2a: Manual tracking using FIJI/Trackmate (Carrillo-Barbera P), Imaris (Palladino E), immunemap (Ceni K)
15:30-16:00: Practical session 2b: Facilitating automatic tracking using computer-assisted colocalization (Pizzagalli DU)
16:15-17:00: Practical session 2c: Analysis of motility measures (Pizzagalli DU)
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
10:45-12:30: Recent trends in computer vision methods (Pulfer A)
12:30-14:00: Lunch Break
14:00-16:15: Practical session 3: Analyzing cell migration without tracking (Motility heatmaps, Action recognition, Optical flow, Colocalization)
16:30-17:00: 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)
Elisa Palladino – Institute for Research in Biomedicine (CH)
Alain Pulfer – Institute for Research in Biomedicine and ETH Zurich (CH)
Benedikt Thelen – Euler institute (CH)
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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 |