search

reconstrue / brightfield

Reconstruction of biocytin-stained neurons detected in brightfield microscopy image stacks
http://reconstrue.com
Apache License 2.0
2 stars 1 forks source link

Vaa3D: repro whatever pipeline they use inside the Allen #36

Open JohnTigue opened 4 years ago

JohnTigue commented 4 years ago

Allen Institute's Morphology technical white paper:

Serial images (63X magnification) through biocytin-filled neurons were evaluated for quality, and cells that passed a quality threshold entered a detailed morphological analysis workflow. Reconstructions of cell dendrites and the initial segment (spiny neurons) or complete axon (aspiny neurons) were generated for a subset of neurons using a 3D Visualization-Assisted Analysis (Vaa3D) workflow. The automated 3D reconstruction results were then manually curated using the Mozak extension of Vaa3D.

Whelp, can Vaa3D be spun-up somehow on Colab?

JohnTigue commented 4 years ago

ShuTu could be the curator's editor of the SWC files.

JohnTigue commented 4 years ago

Adaptive Image Enhancement for Tracing 3D Morphologies of Neurons and Brain Vasculatures (The Gray-scale Distance Transformation (GSDT) paper. Zhou, 2014:

All codes for our adaptive image enhancement are available in open source and can be found on Vaa3D (RRID:nlx_156012) source code repository.

Well there you go. Allen process. Just how to get Vaa3D plugins running on Colab? Need to feed the plugin? Mocking the Vaa3D engine? or maybe even be able to deploy parts of Vaa3D.