Presentation materials
The SAMJ Annotator is a new plugin for ImageJ, Fiji, and Icy that offers user-friendly access to advanced image-segmentation models. These transformer-based models, including the Segment Anything Model (SAM) variants, have shown exceptional performance in segmenting complex and heterogeneous objects in natural images.
With SAMJ Annotator, users can easily annotate objects using manual prompts...
Unlock spatial transcriptomics with our open-source pipeline, generating single-cell datasets from microscopy images. Our modular pipeline streamlines workflows by integrating image registration, segmentation, RNA peak-calling, spot-decoding and visualization steps. With our flexible framework, customize your workflow to meet project requirements. Seamlessly process data using Nextflow, ideal...
Paintera is a tool specializing in dense annotation of large 3D images. In this workshop, users will create multiscale label datasets, and learn to use the various tools and annotation modes that Paintera provides. This will include semi-automated segmentation with Segment Anything and 3D annotations with Shape Interpolation in arbitrary orientation, which can be leveraged to quickly generate...
"Lightsheet microscopy is a rapidly developing and spreading technology that now enables imaging of very large, fixed samples such as adult mouse brains at single-cell. Previously, we developed the BigStitcher software that efficiently handles and interactively reconstructs large lightsheet acquisitions up to the terabyte range. However, new types of image acquisitions use modes such as...
❗ IMPORTANT INFO FOR THE WS ❗
For the workshop, it is recommended to have the following software installed on your laptops:
• DL4MicEverywhere (https://github.com/HenriquesLab/DL4MicEverywhere). Please launch the Notebook: U-Net_2D_Multilabel_ZeroCostDL4Mic.ipynb
• Docker (DL4MicEverywhere will install it automatically the first time you launch it, but if this does not work, you can...
We will present "motile" (https://funkelab.github.io/motile/) and its napari plugin for the tracking of objects in image sequences. The plugin allows users to go from a segmentation (e.g., of cells or nuclei) to a full tracking solution (e.g., a lineage tree) within a few clicks. Motile uses integer linear programs (ILPs) to solve tracking problems and comes with many useful costs and...
QuPath is a popular open-source platform for visualizing, annotating and analyzing complex images - including whole slide and highly multiplexed datasets. It's especially useful for digital pathology applications, but can also be used for a wide range of other tasks (albeit mostly 2D... for now).
This work will introduce QuPath's main features, concepts and interface. It will show examples of...
ScaleFEx℠ is an open-source Python pipeline designed for extracting biologically relevant features from single cells in large image-based high-content imaging screens. Optimized for efficiency, it can easily handle datasets containing millions of images and several Tbs of data with reduced overhead and minimal redundancy. In our upcoming workshop, we will demonstrate how to install, configure,...
