Module F2.1 - Image Processing II

Lecturers and tutors

Prof. Dr. Michael Habeck (e-mail: )
Prof. Dr. Christoph Biskup (e-mail: )
Prof. Dr. Rainer Heintzmann (e-mail: t.b.a.)
t.b.a.

Components of the module

Zoom & video lectures: Lectures will be given in zoom meetings and videos. The first lecture takes place on Wednesday, April 14th, 8.15 a.m. via zoom. All following lectures will take place on Monday 10.15 a.m. - 11.45 a.m. according to the schedule at the bottom of this webpage.
Exercises: Exercises will help you to apply the knowledge learned in the lectures. See the information below for more details.
Seminars: Seminars will give you the opportunity to discuss the solutions to the exercises and remaining questions. Seminars will be organized via zoom meetings on Wednesday 8.15 p.m. - 10.00 p.m. The first seminar starts on April 21st, 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.

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 Tuesday 8.00 a.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 moodle or 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 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 this module and the exercises can be found here.

Additional material

Additional material (including recordings of the zoom meetings) is available via moodle. The link will be made available here, soon. Please, sign up to this course in Friedolin to be admitted to this room or send an E-mail to Prof. Habeck ().

Requirements to complete this module

participation in the Zoom lectures, self study of the virtual lectures and scripts
regular work on the exercises and submission of the solutions before the deadlines indicated below
regular participation in the Zoom meetings, in which the solutions to the exercises will be discussed
presentation of at least one solution of the assigned exercises in a Zoom meeting
successful participation in the written exam

Exam

Please note: date, time and location might be still subject to changes.

Date: t.b.a.
Time: t.b.a.
Location: Computer pool of the Medical Faculty

Content

Unit	Lecturer	Lectures	Online Exercises
1	Habeck/ Biskup	Zoom-meeting: Wednesday, April 14th, 8.15 a.m. Frequency domain processing of signals and images Fundamental concepts for filtering in the time/spatial domain and the frequency domain Convolution Correlation Download: Script Notebook	Download: Homework Template for the solutions Results are to be submitted until Tuesday, April 20th, 8.00 a.m.. Solutions to the exercises were discussed on Wednesday, April 21st, 8.15 a.m. via zoom
2	Habeck/ Biskup	Zoom-meeting: Monday, April 19th, 10.15 a.m. Sampling of data in one dimension Nyquist-Shannon theorem Undersampling, aliasing Resampling of data Download: Script Notebook	Download: Homework Template for the solutions Noisy cells oneliners.npz Results are to be submitted until Tuesday, April 27th, 8.00 a.m.. Solutions to the exercises were discussed on Wednesday, April 28th, 8.15 a.m. via zoom
3A	Biskup/ Habeck	Video lecture Note: There will be no zoom lecture. Have a look at the videos instead Introduction to scientific image processing Essential steps in image processing Human Vision Download: Video, Slides, Lecture Notes	Threre are no exercises related to this video lecture. But, do not forget to watch the videos of part B of this unit and to work on the respective exercises.
3B	Biskup/ Habeck	Video lecture Color Images Part1 Additive color mixing Subtractive color mixing Light sources Part2 Standardization of colors Color mixing experiments Device dependent color spaces (RGB, NTSC, CYM, CYMK) Device independent color spaces (CIE XYZ 1931, CIE Lab 1964) MATLAB functions for handling color images Download: Part1: Video, Slides, Script Part2: Video, Slides, Script Please note: The lecture material contains some information about commands to handle color images in MATLAB. Please, disregard this information. The respective Python commands will be dicussed in the next zoom lecture on May 3rd.	Download: Homework Template for the solutions Results are to be submitted until May 4th, 8.00 a.m. Sample image files: FluorescentCells01.tif FluorescentCells01.jpg FluorescentCells02.tif FluorescentCells03.tif FluorescentCells03.jpg FluorescentCells04.tif Kidney01.jpg Kidney02.jpg Jurkat.tif Solutions to the exercises were discussed in a Zoom meeting on Wednesday, May 5th, 8.15 a.m.
4	Habeck/ Biskup	Zoom-meeting: Monday, May 3rd, 10.15 a.m. Colormaps Grayscale maps Heat maps	Download: Homework Template for the solutions Solutions to the exercises will be discussed in a Zoom meeting on Wednesday, May 12th, 8.15 a.m.
5	Biskup/ Habeck	Video lecture Note: There will be no zoom lecture. Have a look at the videos instead Image Histograms Histogram plots Intensity transformations Histogram equalization Download: Video, Slides, Lecture Notes Please note: The video material contains some information about generating histograms in MATLAB. Please, disregard this information. The respective Python commands will be dicussed in the next zoom lecture.	Download: Homework (see moodle) Template for the solutions Sample image files: Gray cells.tif Oatflakes.jpg Solutions to the exercises will be discussed in a Zoom meeting on Wednesday, May 19th, 8.15 a.m.
6	Biskup/ Habeck	Video lectures Note: There will be no zoom lecture. Have a look at the videos instead Image acquisition Detectors (PMT, CCD, CMOS), Image degradation / noise Download: Lecture: Video, Slides, Script* Practical Course: Epifluorescence microscopy Practical Course: Confocal laser scanning microscopy
7		Holiday Monday, May 24th
8	Habeck/ Biskup	Zoom-meeting: Monday, May 31st, 10.15 a.m. Sampling of data in multiple dimensions Download: Script	Download: Homework Template for the solutions
9	Habeck/ Biskup	Zoom-meeting: Monday, June 7th, 10.15 a.m. Image Preprocessing Background subtraction Flatfielding Fourier-Filtering Interpolation via FFT Download: Script	Download: Homework Template for the solutions Image files for Exercise 1 FluorescentCells01.tif
10	Habeck/ Biskup	Zoom-meeting: Monday, June 14th, 10.15 a.m. Deconvolution 1/OTF-Deconvolution generalised Wiener filter, Wiener filter Maximum likelihood deconvolution, iterative minimisation Richardson-Lucy minimisation, regularisers Download: Script	Download: Homework Template for the solutions Orca.tif
11	Habeck/ Biskup	Zoom-meeting: Monday, June 21st, 10.15 a.m. Segmentation Morphology Operations Edge detection Whatershed segmentation Download: Video, Slides, Script	Download: Homework Template for the solutions
12	Habeck/ Biskup	Zoom-meeting: Monday, June 28th, 10.15 a.m. Feature extraction / Classification Labelling Object measurement Download: Script	Download: Homework Template for the solutions
13	Habeck/ Biskup	Zoom-meeting: Monday, July 5th, 10.15 a.m. Image registration Download: Script	Download: Homework Template for the solutions
14	Habeck/ Biskup	Zoom-meeting: Monday, July 12th, 10.15 a.m. Review A short last-minute checklist for the topics covered in the course will be soon available here.
	Habeck/ Biskup	EXAM (in Python) Re-EXAM (in Python or MATLAB according to your choice) Date: July 23rd, 2021. Time: 10.00 a.m.. Location: PC Pool Medical Faculty, Bachstr. 18 Please note, that during the exam we will have to obey to the corona pandemic regulations. This means that you will have to wear a face mask during the exam.
		PC Pool Medical Faculty, Bachstr. 18 t.b.a.
Additional non-compulsory topics (Note: Topics covered in the following lectures are not part of the exam)
	Habeck/ Biskup	High-end microscopy Localization Localization imaging Download: Script
	Biskup/ Habeck	MATLAB - Advanced topics GPU-Programming/CUDA GUI-Programming Download: Video, Slides, Script