Module F1.1 - Image Processing I

Lecturers / Tutors

Microscopic Image Analysis Group: Prof. Dr. Michael Habeck ()
Biomolecular Photonics Group: Prof. Dr. Christoph Biskup
NanoImaging Group: Prof. Dr. Rainer Heintzmann

Schedule

Lectures: Wednesday 10.15 a.m. - 11.45 a.m. via zoom meetings, lectures start on Oct 20th, 2021.
Exercise: Wednesday 13.00 p.m. - 14.30 p.m. via zoom meetings, exercises start on Oct 27th, 2021.

Please, use the link below to participate in lectures and exercises:
Link: https://uni-jena-de.zoom.us/j/3372359734
The meeting-ID is 3372359734, the passcode is 133392.

Registration

A major part of this course will be organized via moodle. Please, follow this link to get to the moodle website. To enroll to moodle, it is necessary to first register via Friedolin.

To enroll for the exam, it is necessary to register via DOSIS within the first 10 weeks after the start of the lecture period. You will receive an e-mail notification as soon as the DOSIS portal is open..

Exercises

Please note:

The solutions of the exercises have to be returned via moodle before the deadline announced in the work sheets and the schedule below (usually Monday 8.00 p.m. Central European Time (CET), not Samoa Standard Time (SST) ).
Solutions to programming tasks (i.e. Python code) have to be submitted in one single “py-file”. Please, use the template which can be downloaded for each exercise from this webpage. Rename the template such that it contains your last name and the number of the week (e.g. my_name_04.py)
Only the code submitted on time via moodle will be considered for the evaluation.
The code must be unique for each person. It will be considered as plagiarism, if two or more similar solutions are submitted.

Detailed rules for the submission and presentation of the solutions to the exercises can be found here.

Additional material

Additional material (including recordings of the zoom meetings) is available via moodle.

Schedule & Contents:

Week	Lecturer	Lecture	Exercises
1 20.10.2021	Habeck/ Biskup	Introduction Introduction to digital image processing Programming languages Introduction to Python Download: Slides	Python I - Homework for next week: Install the Python 3 Anaconda distribution (Individual Edition) on your computer. It can be downloaded here: https://www.anaconda.com/products/individual. As integrated development environment (IDE) we recommend spyder, which is part of the Anaconda package. If you are not yet familiar with Python 3, please start with the free tutorial "Learn Python 3 from Scratch" at https://www.educative.io/courses/learn-python-3-from-scratch. The tutorial is free, but requires that you register with your e-mail address. with "educative". Click on the tab "Join for free" at the upper right corner of the website.
2 27.10.2021	Habeck/ Biskup	Computer hardware Milestones in computer architecture development The digital logic level Gates Boolean Algebra Implementation of Boolean functions Memory Binary and hexadecimal numbers Conversion between radices Negative binary numbers Binary arithmetic Floating-point numbers Download: Slides, Exercises Please note: A video recording of the lecture is available via moodle.	Python II Introduction to the Python IDE Introduction to Python Homework for next week: Please, note: Exercises must be submitted until Tuesday, Nov 2nd, 2021, 8.00 a.m. (CET) The template for the exercises and the solutions to the exercises are available on the moodle website of this course.
3 03.11.2021	Habeck/ Biskup	Programming I Programming in Python Debugging techniques Download: Programming I: pdf, Notebook	Python III Data types in Python Bit range of the data classes Relational operators, combining logical conditions, logical indexing Discussion of the execises of week #2 (Solutions) Homework for next week: Exercises should be submitted until Tuesday, Nov 9th, 2021, 8.00 a.m. (CET) The template for the exercises and the solutions to the exercises are available on the moodle website of this course.
4 10.11.2021	Habeck/ Biskup	Programming II Python-function programming in Python (cont.) Download: Programming II: pdf, Notebook	Python IV Discussion of the exercises of week #3 Homework for next week: Exercises should be submitted until Tuesday, Nov 16th, 2021, 8.00 a.m. (CET) The template for the exercises and the solutions to the exercises are available on the moodle website of this course.
5 17.11.2021	Habeck/ Biskup	Programming III + Graphics I Graphics features of Python Download: Programming III: pdf, Notebook Plotting I:pdf, Notebook	Python V Discussion of the exercises of week #4 Homework for next week: Exercises should be submitted until Monday, Nov 22nd, 2021, 8.00 p.m. (CET) The template for the exercises and the solutions to the exercises are available on the moodle website of this course.
6 24.11.2021	Habeck/ Biskup	Graphics II Advanced 2D plotting features 3D surface plots Download: Plotting II: pdf, Notebook	Python VI Discussion of the exercises of week #5 Homework for next week: Exercises should be submitted until Monday, Nov 29th, 2021, 8.00 p.m. (CET) The template for the exercises and the solutions to the exercises are available on the moodle website of this course.
7 01.12.2021	Habeck/ Biskup	Matrix calculus Matrix calculus with Python Matrix representation of systems of linear equations Gauss-Jordan Elimination Download: Slides: pdf, Notebook	Python VII Discussion of the exercises of week #6 Homework for next week: Exercises should be submitted until Monday, Dec 6th, 2021, 8.00 p.m. (CET) The template for the exercises and the solutions to the exercises are available on the moodle website of this course.
8 08.12.2021	Habeck/ Biskup	Optimization I χ² as a parameter for the goodness of a fit Linear regression Download: Slides: pdf, Notebook	Python VIII Discussion of the exercises of week #7 Homework for next week: Exercises should be submitted until Monday, Dec 13th, 2021, 8.00 p.m. (CET) The template for the exercises and the solutions to the exercises are available on the moodle website of this course.
9 15.12.2021	Habeck/ Biskup	Optimization II Linear regression Non-linear regression Fitting algorithms Download: Slides: pdf, Notebook	Python IX Discussion of the exercises of week #8 Homework for next week: Exercises should be submitted until Monday, Jan 3rd, 2022, 8.00 p.m. (CET) The template for the exercises and the solutions to the exercises are available on the moodle website of this course.
10 05.01.2021	Habeck/ Biskup	Optimization III "Solving" systems of m linear equations and n unkowns for m>n in Python Python toolboxes for fitting models to data Download: Slides: pdf, Notebook	Python X Discussion of the exercises of week #9 Homework for next week: Exercises should be submitted until Monday, Jan 10th, 2022, 8.00 p.m. (CET) The template for the exercises and the solutions to the exercises are available on the moodle website of this course.
11 12.01.2022	Habeck/ Biskup	Fourier Series I Review of some basics: Wave fundamentals, Complex numbers, Euler´s formula Fourier´s theorem Fourier series Download: Slides: pdf, Notebook noise_filter_v1.py (simple Version with unscaled axes in the frequency domain, see week #12 for an improved version)	Python XI Discussion of the exercises of week #10 Homework for next week: Exercises should be submitted until Monday, Jan 17th, 2022, 8.00 a.m. (CET) The template for the exercises and the solutions to the exercises are available on the moodle website of this course.
12 19.01.2022	Habeck/ Biskup	Fourier Series II Complex form of the Fourier series Discrete Fourier transform Fast Fourier Transform Download: Slides: pdf, Notebook noise_filter-v2.py (improved Version) fft_demo.py	Python XII Discussion of the exercises of week #11 Homework for next week: Exercises should be submitted until Monday, Jan 24th, 2022, 8.00 a.m. (CET) The template for the exercises and the solutions to the exercises are available on the moodle website of this course.
13 26.01.2022	Habeck/ Biskup	Frequency domain processing of signals Fundamental concepts for filtering in the time/spatial domain and the frequency domain Convolution Correlation Download Slides: pdf, Notebook	Python XIII Discussion of the exercises of week #12 Homework for next week: Exercises should be submitted until Monday, Jan 31st, 2022, 8.00 a.m. (CET) The template for the exercises and the solutions to the exercises are available on the moodle website of this course.
14 02.02.2022	Habeck/ Biskup	Frequency domain processing of images Fundamental concepts for filtering images in the time/spatial domain and the frequency domain Convolution Correlation Download Slides: pdf, Notebook	Mock Exam: Mock Exam: pdf Template for the solution: py Solutions: pdf, py
14 18.02.2020	Habeck/ Biskup	Exam Group I (PC-Pool Bachstr.)* 9.30 - 12.00	Group II (Lecture Hall Bachstr.)* 12.00 - 14.30
		A link to the results of the exam will be available here. xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx	Sample image files: FluorescentCells01.tif FluorescentCells02.tif FluorescentCells03.tif FluorescentCells04.tif Kidney01.jpg Kidney02.jpg Jurkat.tif

* A list of the students belonging to either group is available on the moodle site of this course (Link). If your student ID is not mentioned in one of the lists, but if you believe that you have fulfilled all prerequisites to participate in the exam, please send an e-mail to . Mention "Image Processing Exam" as subject in the header of your e-mail.

A discription about how to find the way to the PC Pool or the lecture hall can be found here.

Please note also, that you will have to wear a face mask (medical surgical mask or FFP2 mask) during the exam. If you have any signs/symptomps that might be indicative for COVID (i.e. elevated temperature, fever or chills, cough, shortness of breath, loss of taste or smell) we ask you to refrain from coming to the exam. See a medical doctor and send his/her medical certificate to Dr. Babovsky.