A neurite tracer is a program that extracts the 3D structures of neurons from stacks of electron micrographs of brain tissue, so neuroscientists can infer the connectivity of neurons in a certain volume of the brain without having to manually go through the pictures.
The program works by taking a series of micrographs, and for each picture it traces the contours of neurites (The cellular membranes). Then, the contours are concatenated together into a single 3D models. The resulting models are emitted as a .pov file (Voxels), each model with a different color to ensure they can be told apart.
This is free software distributed under the terms of the MIT License.
This image is from the paper 3D Segmentation of Neurons from Electron Micrographs by Nathaniel Thomas (MIT), and shows approximately how the program should behave.
Left is the source image, right is the tracing of its neurites. The source image is a cross section of a rat’s visual cortex taken with an electron microscope. The resolution is 26.4 nm in both the vertical and horizontal directions.
Left is the original micrograph, right is the tracing of its neurites (2D slices only).
- TrakEM2: Provides annotated electron micrographs of brain tissue slices of the Drosophila melanogaster (Fruit fly).
- Denk-Horstmann dataset: Two thousand slices of rodent cortical tissue.
- 3D Segmentation of Neurons from Electron Micrographs
- Serial Block-Face Scanning Electron Microscopy to Reconstruct Three-Dimensional Tissue Nanostructure
- Machines that learn to segment images: a crucial technology for connectomics
- To the creators of the incredible OpenCV open-source computer vision library.
Copyright © 2012-2013 Fernando Borretti
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