Bioimage informatics
Summary
The course provides a comprehensive overview of methods, algorithms, and computer tools used in in computational bioimaging and bioimage analysis. It exposes the fundamental concepts and the practical computer solutions to extract quantitative information from multidimensional images.
Content
To investigate biological processes, bioimage informatics emerges as a growing field on the interface between microscopy, signal-processing, and computer science. The recent microscopes are producing large volumes of high-resolution multidimensional data (up to 5D). Therefore, algorithms and software tools are needed to automatically extract quantitative data from these images.
The course gives the theoretical concepts and practical aspects of the most common image reconstruction and image analysis techniques. It explains how to code algorithms and to deploy software tools to build an automatic analysis workflow (mainly in ImageJ/Fiji). The lecture is tailored to the needs of life sciences and driven by biological questions.
Addressed topics include (but not restricted to): presentation of microscopy modalities, digital images, multi-dimensional data (3D, time, multiple channels) manipulation, 3D image-processing algorithms, 5D visualization, reconstruction, deconvolution, denoising, stitching, visual feature detection, segmentation, active contours, image analysis workflow, pixel classification, machine learning, deep learning for image analysis, and tracking of particles.
The course is composed of lectures, workshops, practives, and a mini-project. A personal laptop is recommended to run (open-source) image analysis software.
Keywords
Bioimage, microscopy, image processing, image reconstruction, image analysis, visualization, multidimensional data analysis, machine learning, deep learning
Learning Prerequisites
Required courses
- Baisc knowledge in programming
Assessment methods
20% Homework, individual
- In the first half of the semester: 4 homeworks on computer (2 weeks)
40% Mini-project by groups of 2-3 students
- In the second half of the semester: Development of an image analysis tool for a real application in biology
40% End-term exam, individual
- written exam with handwritten notes
In the programs
- Semester: Spring
- Exam form: Written (summer session)
- Subject examined: Bioimage informatics
- Lecture: 2 Hour(s) per week x 14 weeks
- Project: 2 Hour(s) per week x 14 weeks
- Semester: Spring
- Exam form: Written (summer session)
- Subject examined: Bioimage informatics
- Lecture: 2 Hour(s) per week x 14 weeks
- Project: 2 Hour(s) per week x 14 weeks
- Semester: Spring
- Exam form: Written (summer session)
- Subject examined: Bioimage informatics
- Lecture: 2 Hour(s) per week x 14 weeks
- Project: 2 Hour(s) per week x 14 weeks
- Semester: Spring
- Exam form: Written (summer session)
- Subject examined: Bioimage informatics
- Lecture: 2 Hour(s) per week x 14 weeks
- Project: 2 Hour(s) per week x 14 weeks
- Semester: Spring
- Exam form: Written (summer session)
- Subject examined: Bioimage informatics
- Lecture: 2 Hour(s) per week x 14 weeks
- Project: 2 Hour(s) per week x 14 weeks
- Semester: Spring
- Exam form: Written (summer session)
- Subject examined: Bioimage informatics
- Lecture: 2 Hour(s) per week x 14 weeks
- Project: 2 Hour(s) per week x 14 weeks
- Semester: Spring
- Exam form: Written (summer session)
- Subject examined: Bioimage informatics
- Lecture: 2 Hour(s) per week x 14 weeks
- Project: 2 Hour(s) per week x 14 weeks
- Semester: Spring
- Exam form: Written (summer session)
- Subject examined: Bioimage informatics
- Lecture: 2 Hour(s) per week x 14 weeks
- Project: 2 Hour(s) per week x 14 weeks
- Semester: Spring
- Exam form: Written (summer session)
- Subject examined: Bioimage informatics
- Lecture: 2 Hour(s) per week x 14 weeks
- Project: 2 Hour(s) per week x 14 weeks
- Semester: Spring
- Exam form: Written (summer session)
- Subject examined: Bioimage informatics
- Lecture: 2 Hour(s) per week x 14 weeks
- Project: 2 Hour(s) per week x 14 weeks
- Exam form: Written (summer session)
- Subject examined: Bioimage informatics
- Lecture: 2 Hour(s) per week x 14 weeks
- Project: 2 Hour(s) per week x 14 weeks