cod. 1011780

Academic year 2023/24
2° year of course - Second semester
- Simonetta CROCI
Academic discipline
Fisica applicata (a beni culturali, ambientali, biologia e medicina) (FIS/07)
A scelta dello studente
Type of training activity
Student's choice
21 hours
of face-to-face activities
3 credits
course unit

Learning objectives

The educational objectives of the course aim to provide students with a solid foundation of practical skills in using ImageJ for processing and analyzing images acquired by various microscopy techniques through the use of plug-ins and can be listed as follows:

- Learn how to properly install ImageJ on your computer and configure initial settings.

- Gain a thorough understanding of the internal structure of ImageJ and its main functionalities.

- Become familiar with ImageJ's user interface and identify the most commonly used functions, including those located in the menu bar.

- Learn how ImageJ handles color and grayscale images, as well as the handling of complex images such as Z Stack, multichannel images, and over time.

- Learn how to use linear and nonlinear spatial filters, mathematical operations, point operations, and geometric transformations to process images in ImageJ.

- Gain skills to analyze images in ImageJ, including spatial calibration, manual measurements, thresholding, counting and automatic measurements, intensity and color analysis, and visualization and export of results.

- Gain knowledge of the plugin concept, including its definition, installation, configuration and use of specific plugins to extend ImageJ functionality.


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Course unit content

The course focuses on using ImageJ, covering several aspects. It begins with installing and configuring the software on your computer. The logical and functional structure of ImageJ is examined, as well as the key functions of the user interface. The types of images supported are described and the handling of complex images, such as Z Stack and multichannel images, is addressed. Practical examples are provided to enhance images acquired with various microscopy techniques. Spatial filters, mathematical operations, point operations, and geometric transformations are presented. Image analysis includes spatial calibration, manual measurements, defining thresholds, counting structures such as cells and nuclei, and automatic measurements of various quantities. The concept of plugins is also explained, with instructions for installing, configuring, and using the most common plugins.

Full programme

IMAGEJ on your computer. Overview of the logical and functional structure of IMAGEJ . User interface: where the most commonly used functions are located.
Types of images handled by IMAGEJ ; The graphic formats supported directly by IMAGEJ.
The internal management of complex images (Z Stack).
Enhancing an image: adjusting brightness and contrast, false color tables,
modifying dynamic depth (gray levels), distribution curves
Process an image: Linear and nonlinear spatial filters, mathematical operations,
point operations, geometric transformations (rotation, scaling, perspective).
:Analyzing an image :
- spatial calibration
- Manual measurements
- Selection of parameters to be measured
- Threshold definition - methods and principles
- Automatic counting and measurement
- Intensity analysis
- Color analysis
- Visualization and export of results
What is a macro?
What is a Plugin?
how to install and configure it
How to use it ( with examples of the most commonly used ones)


Slide e appunti delle lezioni

Teaching methods

Lectures will be held in-person, in compliance with safety standards. Lecture materials will be deposited on the specific platform with restricted student access (Elly) and will include iconographic presentations, supporting audio-video or video recordings of lectures.
During the lecture, topics contained in the module syllabus will be illustrated and commented on with examples using ImageJ on images. During class and on a voluntary basis, students will be able to perform the same analyses presented with their own computer

Assessment methods and criteria

he assessment of achievement of the module objectives will involve a 30 min written test in which you will be asked to answer a series of closed-ended questions.
The final grade will be announced following the written test directly in Esse3.
Students with DSA/BSE must contact Le Eli-che in advance: support for students with disabilities, D.S.A., B.E.S. (

Other information

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