Introductory image processing on biological images using python.

This is an image processing practical for students with an interest in analysing biologically derived images. It is written in the language python and utilises jupyter notebook for annotation and visualisation of the code. The practical is beginner level, although some knowledge of python is recommended. In this practical students will learn to open single images as well as multi-page tiff files. Users will then learn to apply simple thresholding to an image and image-stacks and will learn to apply a variety of image filters to process the data. The practical is accompanied by lecture slides which give an introduction to image processing.
This training material was developed as model user case for the GBI/ELIXIR/EuBI/NEUBIAS hackathon 2018 hosted at Cambridge University.

Resource type: Jupyter notebook, PDF

Target audience: Bioimage Analysts, Image Analysts, Computer Vision scientists, bioinformaticians, computational scientists, Biophysicists, Biologists, Microscopists, Python for Biologists, PhD students

Difficulty level: Beginner

Licence: MIT License

Authors: Dominic Waithe

Contributors: Anatole Chessel, Volker Baecker

DOI: 10.5281/zenodo.1292101

Introductory image processing on biological images using python. https://tess.elixir-europe.org/materials/introductory-image-processing-on-biological-images-using-python A jupyter notebook python practical designed to give students a introduction to opening and processing image files derived from biological samples. Anatole Chessel Volker Baecker Bioimage Analysts Image Analysts Computer Vision scientists bioinformaticians computational scientists Biophysicists Biologists Microscopists Python for Biologists PhD students