This workshop will give an introduction into the ImageJ-based visual programming language JIPipe. Attendees will be guided step-by-step through the process of building batch processing workflows of ImageJ-functions and JIPipe-exclusive features. All demonstrations will be based on already published projects.
The clEsperanto project equips users and developers with GPU-accelerated image-processing components. It ships a library with which you will be able to build fast bioImage analysis scripts, by leveraging modern GPUs.
Positioned as a classical Image Processing library, it is built on a framework that makes it available in many language (Python, Java, C++), in many software platforms (Fiji,...
The workshop will involve live coding, showing how one can use a Jupyter notebook for exploratory data analysis in napari and then make simple widgets based on that. The target is someone who has some familiarity with the napari application and bioimage analysis in Python and wants to take the next steps to customize/extend the napari GUI. For this, magicgui will be introduced as a way to...
Deriving scientifically sound conclusions from microscopy experiments typically requires batch analysis of large image data sets. Once the analysis has been conducted it is critical to visually inspect the results to identify errors and to make scientific discoveries. Leveraging the ImgLib2/BigDataViewer ecosystem we developed a platform in which large image data sets can be conveniently...
In life sciences, tracking objects within movies is crucial for quantifying the behavior of particles, organelles, bacteria, cells, and entire organisms. However, tracking multiple objects across numerous movies and analyzing the objects’ movements can be challenging. This workshop aims to demonstrate the effective utilization of TrackMate for object tracking across multiple movies through...
Explore Omega, an advanced conversational agent designed to enhance bioimage analysis through large language models. Participants will learn how to converse with Omega to perform basic image processing and analysis tasks, from basic filtering to more advanced tasks such as segmenting cell nuclei, creating custom image processing widgets, and applying denoising algorithms. Additionally, the...
QuPath is a popular open-source platform for visualizing, annotating and analyzing complex images - including whole slide and highly multiplexed datasets. QuPath is inspired and influenced by ImageJ and Fiji, but also quite different.
This workshop will show how experienced ImageJ and Fiji users can benefit from QuPath, and vice versa. It will show how to use ImageJ and QuPath together...
The question "How thick is my biological object?" is more difficult to answer than it appears on first sight. In this workshop we will use different methods to calculate width profiles of 2D and 3D objects and learn about their differences. We will use FIJI/ImageJ in the workshop.
