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17ABBKZS - Conventional Imaging Systems

20.3.2020 - distance learning instruction No. 1 - the majority of lectures will be performed as online lectures via MS Teams on Thursday. Please, see details below.

But there are the following exceptions:  lectures headed by external experts willn´t be performed as online, i.e. on 16.3., 23.3. and 30.3.2020 (all Mondays). These lectures will be replaced by means of the study documents including lectures comments, animations and videos, and some questions (quiz). You will receive these documents later.

As regards exercises I will send you set of tasks, because of exercises on 19.3., 26.3. and 2.4.2020 (all Thursdays) are cancelled. See original timeschedule (https://harm.fbmi.cvut.cz/B192/17ABBKZS/tut ). As regards visit at Academy of Science, it´s problem. I will sent you actual info later.

On the relevant course webpage there are all lectures. Some of them will be updated as soon as possible. You will receive emails.

All requirements for course completion are valid and there is no problem to perform assessment and exam via MS Teams and Moodle.

Detailed description of the MS Teams is below. But in case when you have MS Teams installed, there is required to find the relevant team (course) only.

MS Teams details

The typical name of the team is Predmet-B192-17ABBKZS, i.e. course-semester-course_code.

App Teams is available via webpage (Login: username@cvut.cz + CTU password - the same for all all below mentioned cases):

https://ist.cvut.cz/en/our-services/microsoft-teams/ , link GO TO SERVICE, or via dowmloadable app https://ist.cvut.cz/en/our-services/microsoft-teams/ ,  download TEAMS or app for mobiles and tablets with OS Android and iOS (the same format of login).

Android
https://play.google.com/store/apps/details?id=com.microsoft.teams

iOS
https://apps.apple.com/cz/app/id1113153706

In every case you will receive info about all courses that will use MS TEAMS from relevant teachers.

All lectures and exercises have to be perfomed within the valid timeschedule only!

22.3.2020 - distance learning instruction No. 2 - mandatory tasks within the exercises (tutorial will be organized on Th 9.4.2020)

1. Task 1 - see PDF file below in section Exercises

2. Task 2 - 2D convolution for the input image of the Siemens star (see ZIP file within the section Others)
Detailed instructions:
- use Matlab function conv2,
- use convolution kernel as matrix 16x16 with 1/256 elements (see function ones),
- there is required to illustrate changes of the brightness (black-white interface into the white-black interface and vice versa) based on the phase changes.

3. Task 3 - MTF graph for imaging systems with transfer properties as LPF (modelled by matrix 16x16 with 1/256 elements) where the input image has to be used 2D sine or 2D square signal (see PPT file with support and results within the section Others)
Detailed instructions:

  1. You need to create image with 2D sine. Some examples are used within the lower left corner. There are used two sines, i.e. at the input and at the output. Input sine is sharp and output is blurred.
  2. Blurring can be performed by 2D convolution.
  3. After that you can apply method of cross-profile, i.e. in Matlab matrix you can select and display graph of intensity along the relevant row. These profiles will be related to the sharp sine (red graph) and blurred sine (blue graph).
  4. You will compute ratio of the red/blue amplitude.
  5. After that you can create graph of MTF, i.e. function of MTF (mentioned ratio) versus spatial frequency.

All points, inputs and results are included and illustrated within the attached presentation that is your help and set of hints.

Some experiences:

1. generate 2D sine with spatial frequency SF1, it will be input image for the imaging systems (this system has transfer function like low pass filter, from this follows kernel of the 2D convolution).
2. apply 2D conv function (low pass filter - 16x16 matrix with 1/256) to the image under 1 (conv means, that the simulated imaging systems has transfer properties the same as LPF, but in 2D)
3. apply brightness image profile function for selected row within the matrix under 1 (red curve within the presentation PPT)
4. apply brightness image profile function for selected row within the matrix under 2, i.e. after the 2D convolution onto to the blurred image (blue curve within the presentation PPT)
5. compute value of the MTF for the SF1, i.e. amplitude of blue one - see point 3/amplitude of the red one - see point 4 (it´s math operation division), you will obtain the first point of the MTF curve for SF1 (there is required to use function improfile and from this profile you have to find amplitudes of red and blue profiles within the presentation)
6. repeat points 1-5 for the next SF2
7. repeat points 1-5 for the next SF3
8. repeat points 1-5 for the next SF4
9. repeat points 1-5 for the next SF5
10. plot the MTF function (5 points) versus spatial frequency (from SF1 to SF 5, 5 values)

24.3.2020 - distance learning instruction No. 3 - exercises in Academy of Sciences was cancelled

9.4.2020 - distance learning instruction No. 4 - TV imaging systems fundamentals PDF file was uploaded (see section Others)

16.4.2020 - distance learning instruction No. 5 -  lectures (confocal microscopy, superresolution microscopy and electron microscopy) and relevant materials were uploaded (see section Others)

Code Completion Credits Range Language
17ABBKZS Z,ZK 4 2P+2C English
Enrollement in the course requires an successful completion of the following courses:
Physics II (17ABBFY2)
Lecturer:
Jiří Hozman (guarantor), Tomáš Dřížďal, Martin Rožánek
Tutor:
Jiří Hozman (guarantor)
Supervisor:
Department of Biomedical Technology
Synopsis:

Electromagnetic radiation spectrum and relationship to the modalities of medical diagnostic imaging systems. Fundamentals of imaging theory. Application of 2D FT. Transmission properties of imaging systems. Optical imaging systems including microscopic. Television imaging systems (including video endoscopic imaging systems). Basic digital image pre-processing methods. Infrared imaging systems (thermal imaging/IR imaging systems). X-ray imaging systems. Gamma imaging systems. Lectures and especially the laboratory exercises provide students with an overview of the principles of image formation in medicine for conventional imaging systems and methods. There are described methods for image data sensing, digitization and subsequent processing and principles of function and properties of sensing image devices in context, which is especially relevant from the interdisciplinary point of view of the whole course and study specialization.

Knowledge, skills and competences:

The student is able to explain the basic physical principle of the given modalities and knows its layout including the principle of image formation.

The student is able to assess, on the basis of standard definition of technical parameters that imaging system meets the physician requirements for selected modality. Such knowledge is a prerequisite to the correct process technology selection and application of the modalities as well as the minimum necessary to ensure the required quality of the resulting image data.

Requirements:

Course requirement:

Physics from the point of view of the interaction of radiation with matter, particle physics, optics, and from this follows the requirements for a prerequisite for registration of the course. The theory of systems it is also suitable for.

Assessment and exam requirements:

Participation is mandatory on all exercises. Non-participation is possible for serious reasons only (to be substantiated).

At the end of each lesson (exercise in PC lab), the fulfilled assignment must be given to the teacher for the current week.

It is not possible to take the exam without obtaining the credit and enrolling it in the CTU IS KOS.

The exam is based on the written test and this one consists of a two variants of questions. The so called MCQ, i.e. ABC answer variant (one answer is correct only) with 1 point, i.e. 0 or 1 point. Marking multiple answers means 0 points, no answer means 0 points, bad answer means zero points. The second variant of answers includes the so called open questions (important questions), i.e. 5 points (0 to 5 points). Correct answer can be assessed from 0 to 5 points based on quality of the answer. The whole test consists of a total of 36 questions, of which 20 MCQ (abc) for 1 point and 16 open questions for 5 points. There is required minimum 50 points and there is available max. 100 points. Assessment of the test according to ECTS table (classification grades) is given in the CTU Study and examination code. The total time reserved for the test is 120 minutes. After the test, this one is corrected and there is possible to improve the whole test result if the test result is at the grade boundaries (typically max. by -2 points).

Syllabus of lectures:

1. Classifications of imaging systems, methods and techniques. Illustration of individual imaging modalities.

2. Fundamentals of imaging theory. Transmission properties and functions of imaging systems (PSF, MTF, FWHM).

3. Optical imaging systems

4. Fluorescence microscopy

5. Confocal laser microscopy

6. High-end super-resolution microscopic systems STED and N-SIM

7. Electron microscopy (TEM, EELS)

8. Television imaging systems.

9. Chain for image sensing and digitization. Basic digital image pre-processing methods.

10. Endoscopic imaging systems

11. Infrared imaging systems

12. X-ray imaging systems - sources, layout, parts description, X-ray spectrum, X-ray detectors.

13. X-ray imaging systems - X-ray - TV systems (Image Intensifiers - II), angiography (DSA), digital radiography (DR)

14. Conventional gamma imaging systems (Anger type gamma camera).

Syllabus of tutorials:

1. Matlab computations within the imaging systems

2. Transfer properties and functions of imaging systems (PSF, OTF, MTF, PTF, FWHM). 2D FT applications

3. Optical imaging systems

4. Fluorescence microscopy

5. Confocal laser microscopy

6. High-end superresolution microscopy - STED a N-SIM

7. Elektron microscopy (TEM, EELS)

8. Television imaging systems

9. Image signal sensing and digitization chain. Fundamental methods for image preprocessing

10. Endoscopic imaging systems

11. Infrared imaging systems

12. X-ray imaging systems - power supplies, arrangement, description of main parts, X-ray spectrum, X-ray detectors

13. X-ray imaging systems - X-ray-TV systems, angiography (DSA), digital radiography

14. Conventional gama imaging systems (Anger gammakamera)

The exercises will take place both in the PC classroom (lab), in the laboratory of CTU FBME as well as in the Academy of Sciences of the Czech Republic, v.v.i., in the IMG institute in Prague 4, Krč, specifically in the laboratories involved in the Czech Bioimaging Group.

Study Objective:

The aim of the course is to acquaint students with general fundamentals of imaging process theory, sensing methods, evaluation and processing of image information, image signal properties, principles of image formation, structure and general quantitative assessment of the quality of conventional imaging modalities used in medicine and the resulting limitations and risks.

Study materials:

Mandatory:

[1] Image Sensing and Digitization - Microscopy Imaging Systems [online]. Jiří Hozman. Poslední změna 18. 10. 2013 [cit. 2017-09-27]. URL: http://webzam.fbmi.cvut.cz/hozman/

[2] Webb's physics of medical imaging. 2nd ed. Editor M. A. FLOWER. Boca Raton: CRC, c2012. Series in medical physics and biomedical engineering. ISBN 978-0-7503-0573-0. (1st ed. is also available in library)

Recommended:

[3] HRAZDIRA, Ivo a Vojtěch MORNSTEIN. Fundamentals of biophysics and medical technology. 2nd, rev. ed. Brno: Masaryk University, 2012. ISBN 978-80-210-5758-6.

Study tools:

Image Sensing and Digitization - Microscopy Imaging Systems - educational SW MIPS [online]. Jiří Hozman. Last change 18. 10. 2013 [cit. 2017-09-27]. URL: http://webzam.fbmi.cvut.cz/hozman/

Note:
The course is a part of the following study plans:
Downloads:

Lectures - link: 

Image Sensing and Digitization - Microscopy Imaging Systems - educational SW MIPS | http://webzam.fbmi.cvut.cz/hozman/

Principles of BW television systems (educational video - use Save as) | http://webzam.fbmi.cvut.cz/hozman/AKK/BW_television_principle.mov

Principles of color television systems (educational video - use Save as) | http://webzam.fbmi.cvut.cz/hozman/AKK/color_TV_principle.mov

Image sensors (educational video - use Save as) | http://webzam.fbmi.cvut.cz/hozman/AKK/image_sensors.mov

Image displays (educational video - use Save as) | http://webzam.fbmi.cvut.cz/hozman/AKK/image_displays.mov

Others - link: 

Time schedule of 17ABBKZS (lectures) in SS AY 2019/2020 V1 (15.2.2020) | https://harm.fbmi.cvut.cz/B192/17ABBKZS/lec

Time schedule of 17ABBKZS (exercises) in SS AY 2019/2020 V1 (15.2.2020) | https://harm.fbmi.cvut.cz/B192/17ABBKZS/tut

Distance learning instructions No. 5 - 16.4.2020 (ZIP file) | http://webzam.fbmi.cvut.cz/hozman/lectures_microscopy.htm