Image data science with Python and Napari
PHYS-647 / 2 crédits
Enseignant(s): Manley Suliana, Invited lecturers (see below), Andò Edward Carlo Giorgio
Langue: Anglais
Frequency
Only this year
Summary
This course introduces students to the basics of image data science using Napari and Python. Students will learn image filtering, segmentation and feature extraction. Other topics include supervised and unsupervised machine learning techniques for object classification and clustering.
Content
The goal of this course is to introduce students to the basics of image data science using Napari and Python. The students will learn how to setup Conda environments, install Python libraries and setup Jupyter notebooks for scientific image and data analysis. We will start with a crash-course in Python basics. Afterwards, core concepts of image analysis such as image filtering, segmentation and feature extraction will be taught with the interactive image analysis software Napari. The students will then learn how to reproduce interactively assembled image analysis workflows using Python and Jupyter lab. Finally, we will introduce the students to supervised and unsupervised machine learning techniques for object classification and clustering. Using these techniques the students will be enabled to differentiate objects such as cells with different phenotypes using object-based measurements and state-of-the-art data science methods.
Note
Lecturers: Robert Haase and Till Korten (Technische Universität Dresden)
Host: S. Manley
Keywords
Python, Napari, bio-image analysis
Learning Prerequisites
Required courses
Minimal python skills
Learning Outcomes
By the end of the course, the student must be able to:
- to analyze microscopy images, e.g. segmenting nuclei in one image channel and measuring intensity in another channel
- Apply this to a folder of images
- Do basic statistics, compare conditions
Dans les plans d'études
- Nombre de places: 30
- Forme de l'examen: Exposé (session libre)
- Matière examinée: Image data science with Python and Napari
- Cours: 16 Heure(s)
- Exercices: 16 Heure(s)