Join us for an engaging hands-on workshop at the Image to Knowledge Conference, where we will introduce participants to our collective efforts in the AI4Life project, a Horizon Europe-funded initiative to make AI tools accessible to the bioimage community and bridge the gap between life scientists and computational experts. This workshop brings the opportunity for participants to discover and...
OME-Zarr is a community-backed file format that is well suited for storing and sharing images. WEBKNOSSOS is an open-source tool for visualizing, annotating and sharing large multi-dimensional images. In this workshop, we will give an intro to the OME-Zarr format and provide a hands-on walkthrough the basics of WEBKNOSSOS including data upload, volume annotation (including AI-based...
During the game the players (The Scientists), team up against a game master (Reviewer#3). For a prompted biological question, the Scientists have to prepare an Experiment Plan using a deck of cards. Their plan will be reviewed and challenged by Reviewer#3 using their own deck. During this workshop attendees will play coLoↄ the board game in small teams of Scientist and the Reviewer will either...
In this interactive workshop, we will explore ultrack, a cutting-edge multi-hypothesis tracking framework designed for cell tracking across multiple microscopy modalities. Participants will begin by learning the core principles that drive ultrack's robust performance, including its ability to handle multiple input types such as intensity images, segmentation masks, contours or a combination of...
Together with the participants, we will explore the BioImage Model Zoo: an accessible, user-friendly repository of FAIR, pre-trained deep learning models. We will go through the current model collection, check models by their descriptions in cards, try them out on the website and in partner desktop tools such as ilastik and DeepImageJ. We will communicate with the AI chatbot for tips on image...
In this workshop we propose to learn the principles of phasor analysis of Fluoresce Lifetime Microscopy (FLIM) data as well as to perform image analysis of FLIM data with this approach using (F)luorescence (L)ifetime (U)l(t)imate (E)xplorer (FLUTE) a new open source and user-friendly GUI that we recently developed [1,2]. Using FLUTE, participants will learn the basis of FLIM calibration,...
The workshop aims to introduce pymmcore-plus, a Python package designed for controlling microscopes via the open-source software Micro-Manager within a pure Python environment. It is an extension of pymmcore, the original Python 3.x bindings for the C++ Micro-Manager core and, as such, it operates independently of Java, eliminating the need for Java dependencies. Throughout the workshop, we'll...
In this workshop we will go over basics of using BigTrace plugin to extract and analyze filament/vessel/neurite-like structures in large 3D multicolor (timelapse) datasets. It will be focused on volumetric dataset navigation, creation of ROIs and their analysis: measurements of intensity and geometrical properties, subvolume extraction and post-processing.
