StarDist is an AI-based tool for object detection with star-convex shapes in 2D and 3D. Intended for cell nuclei detection/segmentation in microscopy images, it can be used via the stand-alone Python software package, or with the provided plugins for other common image analysis software suites (e.g., Fiji, napari, QuPath).
Prismatic is a CUDA/C++/Python GPU+CPU software package for fast image simulation in high resolution and scanning transmission electron microscopy (HRTEM & STEM) that includes a graphic user interface.
AFT is an open-source workflow to quantify alignment of fibrillar features in bioimages. It allows for evaluation of alignment lengthscale and works with a number of different imaging modalities.
SR-Tesseler is an open-source interactive single molecule localisation microscopy clustering tool based on Voronoï tesselation, that allows for segmentation and quantification of localisation-based super-resolution microscopy data.
PlantSeg is a tool for cell instance aware segmentation in densely packed 3D volumetric images. The pipeline is tuned for images acquired with confocal and light sheet microscopy and can be used to segment both plant and animal tissues.
