Introduction to Image Analysis

Overview
Program
Faculty
Venue
Partners
Poster
Private Area
Contact

Overview

This course aims at providing researchers who are initiating microscopy-based projects with fundamental skills on digital imaging and biological image analysis. The course incorporates theoretical lectures as well as hands-on exercises which present key concepts and demonstrate image analysis procedures on Fiji/ImageJ, the reference open source image bioimage analysis software. Finally, trainees will learn about selecting regions of interest using artificial intelligence methods as well as recording and automating image processing workflows. Trainees will be exposed to images produced by transmission, epifluorescence and confocal microscopes. At the end of the course, trainees will be able to use Fiji/ImageJ to open, visualize and perform basic image processing and analysis procedures on their own biological images to extract quantitative information.

Program

4 November 2024

Session 1: Working with ImageJ
9h30 – 11h00	Fiji and ImageJ ImageJ interface Basic concepts and common tasks Opening, visualizing and saving an image
11h00 – 11h20	Break
11h20 – 12h30	Exercises
12h30 – 14h00	Lunch
Session 2: Multi-dimensional images
14h00 – 15h00	5D images: x, y, z, channels and time Basic operations
15h00 – 15h15	Break
15h15 – 16h30	Exercises

5 November 2024

Session 3: Quantitative bioimage analysis
9h30 – 11h00	Images as a source of data Regions of interest Line profile ROI Manager
11h00 – 11h20	Break
11h20 – 12h30	Exercises
12h30 – 14h00	Lunch
Session 4: Spatial measurements in ImageJ
14h00 – 15h00	Pixel spatial calibration Setting a scale bar Measurement types
15h00 – 15h15	Break
15h15 – 16h30	Exercises

6 November 2024

Session 5: Image pre-processing and segmentation
9h30 – 11h15	Basics of linear filtering Thresholding Basics of Binary filtering Object counting
11h15 – 11h30	Break
11h30 – 12h30	Exercises
12h30 – 14h00	Lunch
Session 6: Advanced Segmentation
14h00 – 15h00	Labkit Stardist
15h00 – 15h15	Break
Session 7: Introduction to automation
15h15 – 16h15	Using the macro recorder Introduction to batch processing Best practices in reporting bioimage quantification
16h15 – 17h00	Exercises

Faculty

Anna Pezzarossa

Champalimaud Foundation

Website

Hugo Botelho

Faculdade de Ciências da Universidade de Lisboa

Website

José Rino

Gulbenkian Institute for Molecular Medicine

Website

Luís Marques

Faculdade de Ciências da Universidade de Lisboa

Website

Manuel Tanqueiro

Gulbenkian Institute for Molecular Medicine

Website

Patrícia Rodrigues

Gulbenkian Institute for Molecular Medicine

Website

Pedro Campinho

Champalimaud Foundation

Website

Telmo Pereira

NOVA Medical School

Website

Gabriel Martins

Gulbenkian Institute for Molecular Medicine

Website

Venue

The course will take place at FCUL from 4^th to 6^th of November 2024.

We will be meeting at 4.2.07 (Building C4, 2nd Floor, room number 7). This is within the main library building. There are multiple options for meals inside and outside the FCUL campus.

FCUL is located next to Campo Grande and Cidade Universitária. We recommend traveling by public transportation. There is parking for private vehicles, but spots are always in high demand.