Manual

SNT is ImageJ’s framework for tracing, visualization, quantitative analyses and modeling of neuronal morphology. For tracing, SNT supports modern multidimensional microscopy data, semi-automated and automated routines, and options for editing traces. For data analysis, SNT features advanced visualization tools, access to all major morphology databases, and support for whole-brain circuitry data.

BIIGLE is a web-based software for image and video annotation that enables collaborative research on large datasets. It offers tools for manual and computer-assisted annotation, quality control and the collaboration on custom taxonomies to describe objects. BIIGLE is freely available and can be installed in cloud environments, a local network or on mobile platforms during research expeditions. The public instance on biigle.de is free for non-commercial use.

TissUUmaps is a browser-based tool for fast visualization and exploration of millions of data points overlaying a tissue sample. TissUUmaps can be used as a web service or locally in your computer, and allows users to share regions of interest and local statistics.

BiaPy is an open source Python library for building bioimage analysis pipelines. 

BiaPy contains ready-to-use solutions for the tasks of semantic segmentation, instance segmentation, object detection, image denoising, single image super-resolution, self-supervised learning and image classification. 

btrack is a Python library for multi object tracking, used to reconstruct trajectories in crowded fields. btrack implemented a residual U-Net model coupledd with a classification CNN to allow accurate instance segmentation of the cell nuclei. To track the cells over time and through cell divisions, btrack developed a Bayesian cell tracking methodology that uses input features from the images to enable the retrieval of multi-generational lineage information from a corpus of thousands of hours of live-cell imaging data.