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Biological Engineering - ImageJ Intensive course - MB100P10

Title:	4EU+ Biological Engineering - ImageJ Intensive course
Czech title:	Bioengineering - kurz ImageJ
Guaranteed by:	Biology Section (31-101)
Faculty:	Faculty of Science
Actual:	from 2023 to 2023
Semester:	summer
E-Credits:	3
Examination process:	summer s.:
Hours per week, examination:	summer s.:1/2, Ex [HT]
Capacity:	20
Min. number of students:	unlimited
4EU+:	yes
Virtual mobility / capacity:	no
State of the course:	taught
Language:	English
Note:	enabled for web enrollment

Guarantor:	Mgr. Ondřej Šebesta Mgr. Zuzana Burdíková, Ph.D.
Teacher(s):	RNDr. Barbara Elsnicová, Ph.D. Mgr. Roman Leontovyč, Ph.D. Mgr. Jan Pačes Ing. Martin Schätz, Ph.D. Mgr. Ondřej Šebesta

Opinion survey results Examination dates SS schedule

Annotation -

Last update: RNDr. Veronika Sacherová, Ph.D. (12.05.2023)

This course will provide a comprehensive understanding of the usage of the open-source software ImageJ for
scientific image analysis. The course will cover everything from basic manipulations to custom scripting. Students
will learn how to create functional workflows for the analysis. The course is suitable for total beginners as well as
for intermediate users. The course will be held in hybrid mode for a maximum of 20 students in personal
attendance and virtually unlimited students online.

Literature -

Last update: RNDr. Veronika Sacherová, Ph.D. (12.05.2023)

ImageJ study

https://imagej.nih.gov/ij/docs/examples/index.html

Requirements to the exam -

Last update: RNDr. Veronika Sacherová, Ph.D. (11.05.2023)

Examination based on project report.

Syllabus -

Last update: RNDr. Veronika Sacherová, Ph.D. (12.05.2023)

Lesson 1: Image Formation in microscopy modalities, resolution and super-resolution, noise, image dimensions, file formats, workflows, image preprocessing, image restoration, image processing, segmentation, object classification, measurements, statistics, data visualization, data management, FIJI introduction.

Lesson 1: Basic image handling in FIJI

Lesson 2: Preparing images for analysis

Lesson 3: Basic measurements and image segmentation

Lesson 4: Machine learning techniques and advanced image processing and segmentation

Lesson 5: CLIJ GPU accelerated analysis, FIJI customization

Lesson 6: Introduction to macro language, scripting, and batch processing

Lesson 7: Programming fundamentals, writing scripts in macro language

Lesson 8: Writing custom scripts for batch analysis

Lesson 9: Colocalization analysis

Lesson 10: Advanced microscopy techniques analysis and image processing

Lesson 11: Implementation FIJI in large workflows, using imageJ in computing cluster

Lesson 12: Students projects presentation

Schedule ticket:

Schedule scheduled
Schedule ticket	Date	From - To	Education type	Theme	Teacher	Files	Note
23bMB100P10p1	Thu 22.02.2024	9:00 - 9:45	lecture	Basic image handling in FIJI	Mgr. Ondřej Šebesta
	Thu 29.02.2024	9:00 - 9:45	lecture	Preparing images for analysis	Mgr. Ondřej Šebesta
	Thu 07.03.2024	9:00 - 9:45	lecture	Basic measurements and image segmentation	Mgr. Ondřej Šebesta
	Thu 14.03.2024	9:00 - 9:45	lecture	Machine learning techniques and advanced image processing and segmentation	Ing. Martin Schätz, Ph.D.
	Thu 21.03.2024	9:00 - 9:45	lecture	Colocalization analysis	Mgr. Ondřej Šebesta
	Thu 28.03.2024	9:00 - 9:45	lecture	Introduction to macro language, scripting, and batch processing	Mgr. Ondřej Šebesta
	Thu 04.04.2024	9:00 - 9:45	lecture	Programming fundamentals, writing scripts in macro language	Mgr. Ondřej Šebesta
	Thu 11.04.2024	9:00 - 9:45	lecture	Writing custom scripts for batch analysis	Mgr. Ondřej Šebesta
	Thu 18.04.2024	9:00 - 9:45	lecture	CLIJ GPU accelerated analysis, FIJI customization	Ing. Martin Schätz, Ph.D.
	Thu 25.04.2024	9:00 - 9:45	nothing	Deans Day
	Thu 02.05.2024	9:00 - 9:45	lecture	Advanced microscopy techniques analysis and image processing	Mgr. Ondřej Šebesta
	Thu 09.05.2024	9:00 - 9:45	lecture	Implementation FIJI in large workflows, using imageJ in a computing cluster	Mgr. Roman Leontovyč, Ph.D.
	Thu 16.05.2024	9:00 - 9:45	lecture	Students projects presentation	Mgr. Ondřej Šebesta