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AIIVM

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

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

Introduction and networking activity (Pizzagalli)

1

9:00 - 10:00

Physics of 2-photon intravital microscopy (Morone)

1

10:30 - 11:30

Intravital imaging of the immune system (Gonzalez)

1

11:45 - 12:45

Image formation / histograms / Properties of digital images (Barbera / Morone)

1

14:00 - 15:00

The role of Open Data and Open Source in biomedical research , FAIR principles and IMMUNEMAP project (Pizzagalli / Barbera)

1

15:10 - 15:45

FIJI introduction (Morone)

1

15:45 - 17:00

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

Exercise 1

  • Which histogram is saturated
  • Thresholding
  • Use pixel inspector

2

9:00 - 9:30

Image analysis pipeline, quantification of cell motility, dynamism, and interaction (Pizzagalli)

2

9:30-10:30

The possibilities of Machine Learning in IVM (Pizzagalli)

2

10:45-11:30

Excercise 2 (Morone / Pulfer / Barbera Pizzagalli)

  • cell detection (classical / Otsu etc)
  • Thresholding with TWS
  • stardist
  • trackmate
  • automatic tracking with trackmate
  • computation of measures: collective (i.e. preferential direction) and individual cell behavior (i.e. change of speed)

2

14:00 - 17:00

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

Exercise: track-based measures on neutrophil chemotaxis

Exercise: migration differences between WT and KO cells in spleen

 

9:00 – 10:30

Discussion Exercise 1 (Pizzagalli)

Contact analysis in Exercise 1 (Pizzagalli)

Advanced analysis without tracking (of/recruitment) (Pizzagalli)

3

10:45 - 11:00

Image processing techniques (Pulfer)

3

11:15 - 12:15

Exercise 3

  • Quantify the recruitment in vessels
  • Analyze whole LN images with OF
  • Apply the bayes coloc plugin by Alain (cell-cell interaction)
  • Imaris workshop (tracking, coloc, heatmaps, and cell-cell interaction)

3

14:00 - 17:00

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

Inside AI: neural networks and clustering (Pizzagalli)

4

9:00 – 10:00

Trends in computer vision: classic, deep learning, generative (Pulfer)

4

10:05 - 11:00

Action recognition applied to immune cells (Pizzagalli)

  • Review of motility patterns displayed by immune cells in vivo and their biological meaning
  • Application of action recognition to quantify neutrophil dynamics and migration morpho-phenotypes

4

11:15 - 12:15

Exercise 4 (Pulfer / Pizzagalli)

  • Usage of the apoptosis detection program (incl. challenge)
  • Discussion on the limits and potential usage of Deep Learning in IVM
  • Neutrophil swarm detection

4

14:00 - 16:00

Discussion on good practices for IVM analysis (Barbera + Pizzagalli)

4

16:15 - 17:00

DAY 5: June 18th: Workshop and conclusion

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.
- Quantification of neutrophil swarm dynamics via unsupervised machine learning.

5

9:00 - 12:00

Exam

5

14:00 - 15:00

Concluding remarks

5

15:30 - 16:30

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