PlantSeg
A tool for cell instance aware segmentation in densely packed 3D volumetric images, originally developed for plant tissues.
What is PlantSeg?
PanSeg is a specialized bioimage analysis tool for cell instance aware segmentation in densely packed 3D volumetric images. It uses a two-stage segmentation strategy combining neural networks with segmentation algorithms to accurately separate individual cells in complex biological tissues. Originally developed for plant cell segmentation from confocal and light sheet microscopy, it has been expanded to handle animal cells as well.
Researchers and biologists working with 3D microscopy data who need automated, accurate segmentation of densely packed cells in plant or animal tissues.
PanSeg provides a ready-to-use pipeline with pre-trained models specifically optimized for challenging 3D biological images, eliminating the need for extensive manual annotation or model training. Its two-stage approach delivers superior accuracy in separating touching cells compared to traditional segmentation methods.
Overview
A tool for cell instance aware segmentation in densely packed 3D volumetric images
Use Cases
Best For
- Segmenting plant cell tissues from confocal microscopy images
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