Tech-Method Course:
Image Analysis I
Date
23-24-25 March 2026
Organizer
Emanuele Martini (IFOM) & Chiara Soriani (IEO)
Location
IEO Campus, Via Adamello 16 - Milan
About the Course
The goal of the Image Analysis I course is to teach students the basic theoretical concepts of image analysis and to provide them practical tools for most demanding image analysis topics, such as nuclear segmentation, tracking or co-localization. Students will learn how to perform image analysis by using ImageJ/FIJI and will familiarize with automated image analysis through FIJI macro language.
Lessons Location: Meeting Room 1+2
Introduction to Image Analysis and Objects Segmentation with Fiji
9:00 – 10:45
Introduction to digital images
Zeno Lavagnino
– How an image is obtained, sampling, monochromatic and color images, Fourier transforms
10:45 – 11:00
Break
11:00 – 13:00
Introduction to Fiji and objects segmentation
Chiara Soriani
– Introduction to Fiji’s key functionalities: installation, basic options, opening of images (Bio-Formats Import), management of simple images, export of analysed images
– Measurements of images: image calibration, set measurements parameters, creation of selections and Region Of Interest
– Processing images: geometric transformations, filters, mathematical operations
– Binarization of images: image thresholding methods, processing of binary images
– Objects segmentation and detection: Analyse particles/Find Maxima functionalities
13:00 – 14:00
Lunch Break
14:00 – 17:00
Hands-on: Nuclear segmentation and spots detection
Serena Magni
– Step-by-step creation of an image analysis workflow for nuclear segmentation and nuclear spots detection
– Step-by-step recording of macro commands within the analysis workflow
Lessons Location: Meeting Room 1+2
Macro Language and Co-localization
9:00 – 12:30
Introduction to Macro Language
Ambra Dondi & Fabrizio Orsenigo
– Introduction to macro language: What is a macro? Why do we need macros?
– How can move from a set of recorded commands to a macro for batch processing?
– Built-in functions in FIJI: basics imaging analysis functions
– Basics of programming in Fiji macro language with examples: variables, arrays, loops, conditional statements
– Import and export of files: bio-formats and bio-formats macros extensions
– Hands-on: Generalization of a series of recorded commands to create a macro for batch nuclear segmentation
12:30 – 14:00
Lunch Break
14:00 – 17:00
Colocalization
Simona Rodighiero
– Introduction to the concept of colocalization
– Co-occurrence
– Hands-on: co-occurence batch analysis
– Intensity correlation coefficient-based analyses object-based colocalization
– Hands-on: the JACoP plugin
Lessons Location: Meeting Room 1+2
Best Practices in Image Processing, Tracking and Collective Motion
9:00 – 9:50
Images for publication and guidelines for best practices in image processing
Fabrizio Orsenigo
9:50 – 10:00
Break
10:00 – 12:30
Collective Motion
Emanuele Martini (online)
– Introduction to the concepts of collective cellular mobility and motivation
– Different ways and parameters to study collective cell motility:
Wound Healing, Cell Streaming, Particle Image Velocimetry
to evaluate speed of wound closure, velocity and coordination of movement
– Hands-on: Wound Healing speed of closure extraction using Fiji
12:30 – 14:00
Lunch Break
Lessons location: Gold+Platinum Room
14:00 – 16:30
Tracking in Biology
IEO/TBD
– Introduction to the concepts of tracking and biological motivation: tracking of cells and intra-cellular objects (chromatin, proteins, exogenous probes)
– Introduction to TrackMate Software
– Technical details for tracking: objects detection & trajectories reconstruction
– Evaluation of parameters from trajectories: displacement, velocity, directionality, etc
– Mention of advanced features in tracking: mean square displacement to calculate the motion type (free-diffusion, confined, active motion) and environment material properties
– Hands-on: Tracking of nuclei using Trackmate
16:30 – 17:00
Wrap-up and Discussion