Coursebooks

Bioimage informatics

BIO-410

Lecturer(s) :

Sage Daniel
Seitz Arne

Language:

English

Withdrawal

It is not allowed to withdraw from this subject after the registration deadline.

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, and tracking for building a cell lineage.

The course is composed of lectures, workshops with the state-of-the-art software packages, computer sessions (programmation) and a mini-project. A personal laptop is recommended to run (open-source) bioimage software packages.

Keywords

Bioimage, microscopy, image processing, image reconstruction, image analysis, visualization, multidimensional data analysis, learning

Learning Prerequisites

Recommended courses

Important concepts to start the course

Learning Outcomes

By the end of the course, the student must be able to:

Transversal skills

Teaching methods

Lecturing with demonstration, workshops, computer laboratories, hands-on

Assessment methods

Continuous: mid-term and end-term exams and a mini-project

Resources

Moodle Link

In the programs

  • Bioengineering, 2018-2019, Master semester 2
    • Semester
      Spring
    • Exam form
      During the semester
    • Credits
      4
    • Subject examined
      Bioimage informatics
    • Number of places
      30
    • Lecture
      2 Hour(s) per week x 14 weeks
    • Project
      2 Hour(s) per week x 14 weeks
  • Bioengineering, 2018-2019, Master semester 4
    • Semester
      Spring
    • Exam form
      During the semester
    • Credits
      4
    • Subject examined
      Bioimage informatics
    • Number of places
      30
    • Lecture
      2 Hour(s) per week x 14 weeks
    • Project
      2 Hour(s) per week x 14 weeks
  • Life Sciences Engineering, 2018-2019, Master semester 2
    • Semester
      Spring
    • Exam form
      During the semester
    • Credits
      4
    • Subject examined
      Bioimage informatics
    • Number of places
      30
    • Lecture
      2 Hour(s) per week x 14 weeks
    • Project
      2 Hour(s) per week x 14 weeks
  • Life Sciences and Technologies - master program, 2018-2019, Master semester 2
    • Semester
      Spring
    • Exam form
      During the semester
    • Credits
      4
    • Subject examined
      Bioimage informatics
    • Number of places
      30
    • Lecture
      2 Hour(s) per week x 14 weeks
    • Project
      2 Hour(s) per week x 14 weeks
  • Life Sciences and Technologies - master program, 2018-2019, Master semester 4
    • Semester
      Spring
    • Exam form
      During the semester
    • Credits
      4
    • Subject examined
      Bioimage informatics
    • Number of places
      30
    • Lecture
      2 Hour(s) per week x 14 weeks
    • Project
      2 Hour(s) per week x 14 weeks

Reference week

MoTuWeThFr
8-9
9-10 BC02
10-11
11-12 BC02
12-13
13-14
14-15
15-16
16-17
17-18
18-19
19-20
20-21
21-22
Lecture
Exercise, TP
Project, other

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  • Autumn semester
  • Winter sessions
  • Spring semester
  • Summer sessions
  • Lecture in French
  • Lecture in English
  • Lecture in German