Advanced microscopic techniques and nanotechnology

A.Y. 2020/2021
Overall hours
Learning objectives
The course is meant to be an introduction for students to all the different and biotechnologically relevant techniques that requires a particular knowledge of their physical, computational and technological basis.

The course is then designed so that, starting from the introduction of some scientifically and technological fundamental concepts, it shows the working principle and the aim of different and relevant technologies.

The topics included in the course can be divided in three main parts.
Expected learning outcomes
In this class the student: (i) learns about the physical quantities of importance in the field of Biotechnologies, with a specific emphasis on thermodynamic quantities, and about their units of measurements; (ii) learns to use such quantities in quantitative problems; (iii) learns about the physical and technological foundations of optical microscopy and fluorescence.
Course syllabus and organization

Single session

Lesson period
First trimester
All classes planned during the first trimester will be given as frontal teaching and as distance synchronous learning. In case of a new suspension of frontal lectures, all students will be asked to move to distance synchronous learning..
Each hour of lesson will be divided into 45' of formal teaching followed by 15' of discussion/interaction/question time. All lessons will be recorded and made available for students on the indicated platforms (i.e. Ariel, TEAMS, etc).

The program and the reference material will not change

Unless otherwise specified, exams will be organized in classroom but if the student is unable to reach the building for COVID-related issues, other forms might be considered (this only apply for exams scheduled until the 31st December - 2020).
Course syllabus
Introduction on the resolution of optical microscopes
Effects of the finite resolution on images
Introduction to confocal microscopy
Optical processes and techniques that can overcome the resolution limit, such as: non linear microscopy, STED,TIRF,PALM, SNOM.
introduction to nanotechnology
Nanoparticles:quantum dots, nanomag, metallic nanoparticles. General concepts, stability and bioconiugation. Optical tweezers for micro-manipulation
Microfluidics: miniaturization of lab apparatus (Lab-on-a-chip technologies), microfluidic technologies based on flux and droplets. Diffusion and mixing. Notable examples of micro-mechanicals applications.
Atomic force microscopy
Later-free optical Biosensors for the detection of not marked molecules and interactions between not marked molecules. Introduction to SPR based techniques and to methods that use guided light.
Introduction to the fundamentals of computer graphics aimed to the comprehension of the informations contained in images with examples taken from microscopy, gel electrophoresis and medical diagnostic.
Colorimetry: color spectrum, Gamut, chromatic coordinates, gamma value of displays, RGB, CMYK.
Digital image types: (es. BMP,TIF,GIF,JPG)
Lossy and lossless compression
Images stacks over space (3D stacks) and time (movies). Movie file types.
Volumes and surface renderings. Tomography.
Introduction to ImageJ software as a tool to:
- extract quantitative information from an image (measurement of bands on a gel electrophoresis image, particle counting, border detection)
- Punctual, local and global filtering
- False color images applied to multi-fluorescence detection.
- Stack visualization and reslicing
- Timelapse and measurements on images over time
Prerequisites for admission
Students are required to have some knowledge of: basics of optics (basic properties of light: speed, frequency, wavelength, refraction), basic properties of lenses (focal length, image formation), basic structure of the optical microscopes (objective, eyepiece, magnification, upright or inverted structure, illumination). Those who do not have these elements of knowledge are required of an effort of personal study. During the first hour of the class, the required elements of knowledge will be listed, together with web sites that can be used for the study material, in case no other reference book is available to the students.
Teaching methods
The course comprised three main topics: microscopy, nanotechnology, and digital images. The first two are given through lessons, while the third is developed in a combination of lessons and hands-on experiences. Students will be asked to analyze digital images made available by the teachers through the Ariel platform. Hands-on exercises will be carried on by single students or by pairs of students, as they prefer. For the exercises it will be possible to use the computers own by the students. This will be discussed and decided by the students during the first lesson.
The teaching material includes: pdf files with the slides used during the lessons and articles. The articles are either review papers or applications of the various technologies introduced in the class. Within slides students will find comments - not used during the lessons - that summarize the contents, aimed at helping studying.
Teaching Resources
On the course website you will find the files of the slides used in the lectures and a selection of review articles on topics drawn from important international magazines. The part of the hands-on practice using the ImageJ software that is available online without the need for licenses.
Assessment methods and Criteria
The examination is in written form, and it consists in open questions. Each student will receive three questions, chosen from a list of about 60, previously divulged to the students. The three questions will be about the three main sections of the class: microscopy, nanotechnology, digital images. The duration of the test is one hour and 30 minutes. The evaluation will focus on the capacity of the student to describe in short the key elements of the answer to the questions. The evaluation will take into account the congruity of the answer to the question, and the clarity of the answer. The outcome of the evaluation will be made available to the student through the online system of the University.
FIS/07 - APPLIED PHYSICS - University credits: 6
Practicals: 16 hours
Lessons: 35 hours