Mandatory registration by May 22nd 2021 23:59 CEST
Link: https://forms.gle/jYHBTNej7kDJ4QX96

Description

This summer school will cover theoretical and practical aspects regarding the analysis of immune cell migration and interaction using intravital microscopy and the application of new A.I.-based methods.
Basic knowledge in imaging is recommended.

Organizers. Dr. Santiago Fernandez Gonzalez, Dr. Diego Ulisse Pizzagalli, Pau Carrillo Barbera
Can apply. PhD students (3 ECTS)
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

9:00-9:30: Introduction of the tutors and the course.

9:30-10:30: Interactive activity to know each student and background.

10:30-11:00: Technical Introduction to IVM

11:00-12:00: Biological application of IVM

12:00-14:00: Lunch Break

14:00-15:00: Presentation of immunemap

15:00-17:00: Practical session 1: Use of immunemap

 

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

9:00-10:30: Classical image analysis pipeline

10:30-10:45 Coffee break

10:45-12:00: The relevance of cell tracking in life sciences

12:00-14:00: Lunch Break

14:00-16:00: Practical session 2: Analyzing cell migration with manual and automatic cell tracking

16:00-17:00: Discussion and networking activity

 

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

9:00-10:30: Advanced analysis - Theory

10:30-10:45 Coffee break

10:45-12:00: Image processing

12:00-14:00: Lunch Break

14:00-16:00: Practical session 2: Analyzing cell migration without tracking (Optical Flow, Colocalization, Heatmaps…)

16:00-17:00: Discussion and networking activity

 

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

9:00-10:30: Trends in computer vision methods – Theory

10:30-10:45 Coffee break

10:45-12:00: Application of computer vision methods to IVM data analysis and immunology

12:00-14:00: Lunch Break.

14:00-16:00: Practical session 2: Analyzing IVM data with action recognition

16:00-17:00: Discussion and networking activity

 

DAY 5: June 18th: Conclusion

09:00 – 12:00: Workshop - Analyze your own data (if you do not have we can provide or form groups)

15:00-16:00: Evaluation - Summer School Quiz

16:00 – 17:00: Concluding remarks

 

A collection of intravital microscopy videos of immune cells along with their tracks (3d) manually annotated by multiple operators
RAW data available as Imaris IMS, TIF sequences, and Cell Tracking Challenge (CTC) format
Ground truth available as CSV files and Cell Tracking Challenge (CTC) format

link: http://www.nature.com/articles/sdata2018129

 More coming soon

Welcome to immunemap.org!
The cloud platform that makes intravital microscopy videos of the immune system Findable, Accessible, Interoperable, Reusable (FAIR).

Here you can find

  • An excellent collection of 2P-IVM videos captured in different organs and experimental conditions, including RAW microscopy videos, physical metadata, and biological details specific for immunological research.
  • Manual tracking and annotations.
  • Analysis tools that can be downloaded or executed directly from the browser

IMMUNEMAP centralizes data from an international network of research laboratories, opening new perspectives for data-driven immunological research.
Example usages:

  • Data-driven discovery of novel mechanisms of the immune system.
  • Development of computer vision methods
  • Defining experimental standards for intravital imaging experiments in different organs and research models.

The website is under development
For the moment you can check our initial collection "Leukocyte Tracking Database", meant to support the development of cell tracking methods http://www.ltdb.info


NEWS: Join our online Summer School
"Artificial intelligence methods applied to the analysis of intravital microscopy videos of the immune system"
June 14th - 18th 2021
https://forms.gle/UMtCx266JhDuheJ38

Cell action recognition (track-based)

This tool detects and counts the actions of neutrophils as described in Pizzagalli et al. Frontiers in Immunology (2019)
https://www.frontiersin.org/articles/10.3389/fimmu.2019.02621/abstract

  • Program for Windows (coming soon)
  • MATLAB script (download) - Requires Matlab to be executed
  • Imaris XTension (coming soon)

Semi-supervised Colocalization

This tool creates an additional imaging channel, specific for the cells of interest.

The user can draw a few lines on the cells of interest and other lines on the background.
The program will automatically separate them into 2 classes.

Useful when cells appear in more than one acquisition channel.

Please publish modules in offcanvas position.

Free Joomla! templates by Engine Templates