PlantSeg is a tool for cell instance aware segmentation in densely packed 3D volumetric images. The pipeline uses a two stages segmentation strategy (Neural Network + Segmentation). The pipeline is tuned for plant cell tissue acquired with confocal and light sheet microscopy. Pre-trained models are provided.
Ultrack is a versatile and scalable cell tracking method designed to address the challenges of tracking cells across 2D, 3D, and multichannel timelapse recordings, especially in complex and crowded tissues where segmentation is often ambiguous. By evaluating multiple candidate segmentations and employing temporal consistency, Ultrack ensures robust performance under segmentation uncertainty. Ultrack's methodology is explained here.
Tools for segmentation and tracking in microscopy build on top of Segment Anything. Segment and track objects in microscopy images interactively with a few clicks.
Spine Analyzer allows to semi-automatically segment dendritic spines in 3D+t images and to measure their volumes and the intensities of the signal within in different channels over time.
The authors present an ImageJ-based, semi-automated phagocytosis workflow to rapidly quantitate three distinct stages during the early engulfment of opsonized beads.
