Advanced microscopic techniques and nanotechnology
A.Y. 2024/2025
Learning objectives
The course is meant to be an introduction to biotechnologically relevant techniques that requires a particular knowledge of their physical, computational and technological basis.
The course aims at giving describing the principles and the potentials of a selection of advanced optical microscopy techniques and of nanotechnologies. The course also aims at providing a basic understanding and training of quantitative image analysis.
The topics included in the course can be divided into three main sections.
The course aims at giving describing the principles and the potentials of a selection of advanced optical microscopy techniques and of nanotechnologies. The course also aims at providing a basic understanding and training of quantitative image analysis.
The topics included in the course can be divided into three main sections.
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.
Lesson period: First trimester
Assessment methods: Esame
Assessment result: voto verbalizzato in trentesimi
Single course
This course cannot be attended as a single course. Please check our list of single courses to find the ones available for enrolment.
Course syllabus and organization
Single session
Responsible
Lesson period
First trimester
Course syllabus
ADVANCED OPTICAL MICROSCOPY
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 time resolved fluorescence and FLIM microscopy
NANOTCHNOLOGY
Aims and uses of nanoparticles in biomedicine.
Nanoparticles: quantum dots, nanomag, metallic nanoparticles, polymer particles, liposomes.
General concepts, stability, bioconiugation, cell internalization.
Optical tweezers for micro-manipulation.
Atomic force microscopy.
Later-free optical biosensors. Introduction to SPR-based techniques.
Micromechanical devices.
QUANTITATIVE ANALYSIS OF IMAGES
Introduction to the fundamentals of computer graphics aimed to the understanding and elaboroation of the informations contained in images.
Colorimetry: color spectrum, Gamut, chromatic coordinates, gamma value of displays, RGB, CMYK.
Digital image types: (es. BMP,TIF,GIF,JPG)
Lossy and lossless compression
ImageJ interface introduction, Image visualization (Look Up Tables, Brightness and Contrast), Pixel Statistics.
Processing examples (FFT and filtering)
An example of a quantitative analysis: electrophoretic gel
Object recognition I : image segmentation and particle analysis
Multidimensional images from color channels to image stacks
Video processing
Best Fitting procedures. Fitting a model into quantitative data extracted from a digital image. Extraction of experimental parameters and confidence levels.
Object Recognition II: Training a convolutional Netural Networks for the automatic recognition of objects in image. Image annotation.
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 time resolved fluorescence and FLIM microscopy
NANOTCHNOLOGY
Aims and uses of nanoparticles in biomedicine.
Nanoparticles: quantum dots, nanomag, metallic nanoparticles, polymer particles, liposomes.
General concepts, stability, bioconiugation, cell internalization.
Optical tweezers for micro-manipulation.
Atomic force microscopy.
Later-free optical biosensors. Introduction to SPR-based techniques.
Micromechanical devices.
QUANTITATIVE ANALYSIS OF IMAGES
Introduction to the fundamentals of computer graphics aimed to the understanding and elaboroation of the informations contained in images.
Colorimetry: color spectrum, Gamut, chromatic coordinates, gamma value of displays, RGB, CMYK.
Digital image types: (es. BMP,TIF,GIF,JPG)
Lossy and lossless compression
ImageJ interface introduction, Image visualization (Look Up Tables, Brightness and Contrast), Pixel Statistics.
Processing examples (FFT and filtering)
An example of a quantitative analysis: electrophoretic gel
Object recognition I : image segmentation and particle analysis
Multidimensional images from color channels to image stacks
Video processing
Best Fitting procedures. Fitting a model into quantitative data extracted from a digital image. Extraction of experimental parameters and confidence levels.
Object Recognition II: Training a convolutional Netural Networks for the automatic recognition of objects in image. Image annotation.
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.
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 exam will be in written form and composed of two parts regarding to the two parts of the course: 1. conceptual foundations, 2. technologies.
The test for the conceptual foundations is composed by two quantitative problems and two theory questions.
During the exam, problems and questions are projected in the classroom in sequence, allowing between them the time required for answering (15-20 minutes each).
We will evaluate: the ability to correctly set up the problem by clarifying which equations are used and why, the quantitative processing ability to arrive at the correct result, the correct use of units of measurements..
The test relative to the technology part consists of: a question on the conversion between quantities describing light, 5 closed-ended questions ("true or false") and the request for a diagram describing the operation of a phenomenon or a device described in class.
In the final classes of the course, an mid term test is scheduled for the technologies part.
The test for the conceptual foundations is composed by two quantitative problems and two theory questions.
During the exam, problems and questions are projected in the classroom in sequence, allowing between them the time required for answering (15-20 minutes each).
We will evaluate: the ability to correctly set up the problem by clarifying which equations are used and why, the quantitative processing ability to arrive at the correct result, the correct use of units of measurements..
The test relative to the technology part consists of: a question on the conversion between quantities describing light, 5 closed-ended questions ("true or false") and the request for a diagram describing the operation of a phenomenon or a device described in class.
In the final classes of the course, an mid term test is scheduled for the technologies part.
FIS/07 - APPLIED PHYSICS - University credits: 6
Practicals: 16 hours
Lessons: 35 hours
Lessons: 35 hours
Professor:
Bellini Tommaso Giovanni
Shifts:
Turno
Professor:
Bellini Tommaso GiovanniProfessor(s)