Interactive Open-source Image Analysis and Scientific Plotting Workshop

In recent years, increasingly sophisticated Python tools have become available for otherwise tedious, manual image analysis tasks. At the same time, it is becoming increasingly difficult for non-specialized Python-programmers to gain access to these methods, as there is often little standardization and interoperability between projects. In that circumstance, napari has taken the stage, offering advanced multidimensional image data visualization and simple creation of graphical user interfaces for image analysis workflows.

Our workshop aims to make end users familiar with the napari viewer itself and its plugin ecosystem. This includes a tour through napari's visualization layers as well as a collection of interoperable tools for image machine-learning-driven segmentation, feature extraction and unsupervised-machine learning methods for feature exploration. More specifically, we will show how to open n-dimensional data in napari, how to perform semantic and instance segmentation, how to extract features from objects in different channels, how to use these features to classify these objects, and finally how to save and plot these results with open-source libraries/software.

The workshop aims at life scientists and facility staff members who wish to improve their proficiency in image visualization, image analysis and graph plotting with napari plugins and other open-source tools. Our workshop will make attendants more confident and proficient in developing modern image analysis workflows using open-source tools. Knowledge in Python is recommended, but not required.