webKnossos

webKnossos provides visualization and annotation of large-scale 3D electron microscopic images to support connectomics and neurite reconstruction.

Key Features:

• 3D electron microscopy visualization: Visualization of large-scale 3D electron microscopic datasets for inspection of neuronal ultrastructure.
• Flight mode (egocentric reconstruction): Implements a single-view egocentric reconstruction technique ("flight mode") for tracing and reconstructing neurites such as axons and dendrites.
• Crowdsourced annotation: Enables crowdsourced annotation by trained annotators to accelerate manual reconstruction of neuronal processes.

Scientific Applications:

• Connectomics mapping: Mapping neural connections within the mammalian cortex using annotated 3D electron microscopy data.
• Neurite reconstruction: Rapid annotation and reconstruction of axons and dendrites to build neuronal network reconstructions.

Methodology:

Uses a single-view egocentric reconstruction technique ("flight mode"); empirical reconstruction speeds reported as 1.5 ± 0.6 mm/h for axons and 2.1 ± 0.9 mm/h for dendrites, with a reported 4- to 13-fold acceleration of neurite reconstruction versus prior tools.