Author/Creator: Karin Sasaki, Jonas Hartmann
Curated By: Jonas Hartmann
Field(s): image analysis
DescriptionTeaches the basics of bio-image processing, segmentation and analysis in python. The main part is a pipeline for the automated segmentation of 2D confocal fluorescence micrographs of membrane-labeled cells. Students develop the pipeline themselves by following provided exercises and guidelines. An example solution is also provided. The included pre-tutorial revisits some basic concepts of python coding, array computation and image processing. Optional advanced content includes examples of vectorization, multiprocessing and cluster computation, as well as an intro to feature extraction and advanced analysis of single-cell segementation data.
Level: Beginner, Intermediate
Format: Online (browser-based)
Time Required: 8-20 hours
Prerequisites: Python 2.7. Basic python knowledge required. Basics in image processing and segmentation encouraged. A pre-tutorial explains some basic concepts of array computation and image processing.
Last Curated: 17.07.2016