DaCapo is a deep learning library tailored to expedite the training and application of existing machine learning approaches on large, near-isotropic image data. It addresses the need for scalability and 3D-aware segmentation networks, and is developed with a modular and open-source framework for training and deploying deep learning solutions at scale. DaCapo breaks through terabyte-sized...
BigWarp is an intuitive tool for non-linear manual image registration that can scale to terabyte-sized image data. In this workshop, participants will learn to perform image registration with BigWarp, apply transformations to large images, import and export transformations to and from other tools, and fine-tune the results of automatic registration algorithms. BigWarp makes heavy use of the...
In this workshop, we will introduce users to CellProfiler, a software that allows you to create reproducible image analysis workflows without knowing how to code. Users will be introduced to how to input multi-channel data into CellProfiler, how to perform image processing, object finding, and measurement steps, as well as how to create reproducible outputs.
In this workshop, we present computational tools, workflows and pipelines for the processing and analysis of multiplexed tissue imaging data. In the first part of the workshop, we discuss commonly used analysis strategies and present a set of existing pipelines for multiplexed image processing, including MCMICRO (Schapiro et al., 2022), Steinbock (Windhager et al., 2023) and PIPEX...
In some cases, meshes have advantages over the use of voxels for image analysis (lightweight representation, surface features, ...)
In this workshop, participants will learn:
- How to pass from a voxels representation to a mesh, and vice-versa.
- How to use Blender and Napari as well as some dedicated Python modules to filter, process or extract measures from meshes.
The workshop will introduce PlantSeg 2.0: a new version of the popular PlantSeg tool for segmentation of cells in tissues based on membrane staining, in 2D and in 3D. Together with the participants, we will step through the new napari-based GUI, learning to choose pre-trained networks, set the parameters, correct the results and launch headless jobs. No prior experience with PlantSeg is needed.
We - Jerome Mutterer and Jan Brocher - would like to introduce participants in this joint hands-on workshop to discover the flexible potential of ImageJ or Fiji alongside Inkscape for crafting scientific figures, slides, or posters. Our aim is not only to effectively incorporate traditional elements such as scale bars or labels but also to integrate reproducible content whenever possible. The...
This hands-on workshop will introduce you to CytoDL, a powerful deep learning framework developed by the Allen Institute for Cell Science. CytoDL is designed to streamline the analysis of biological images, including 2D and 3D data represented as images, point clouds, and tabular formats. We will cover (A) Getting single cell and nucleus instance segmentations from image datasets from the...
