How To Reconstruct Neurons in 3D
Quantitative morphology can be used as an important cell type descriptor and as a proxy for connectivity. We have recently used it to describe the properties of transcriptomically-defined cell types in mouse and human cortex and as one of the multiple characteristics used to define a set of integrated morpho-electric-transcriptomic (MET) cell types in mouse visual cortex.
Follow the links presented here to access our open-source software, protocols, and analysis scripts for generating and analyzing image-based, quantitative, 3D morphologies for your own research.
Vaa3D-Terafly-Mozak
'Vaa3D' is short for the “3D Visualization-Assisted Analysis” software suite. It is a versatile tool in 3D/4D/5D Image Visualization and Analysis software. For neuron morphology reconstruction, it is the main program that hosts our reconstructing software. It contains many more tools than are listed below; for more information click here.
TeraFly is program used for interactive 3D visualization of terabytes of 3D and 4D (3D spatial information plus color) images, as well as 5D (4D plus time) image series, with subsecond response times from both local and remote data sources. TeraFly instantly translates simple computer-mouse actions (e.g., drags and scrolls) performed directly in the volumetric space of a 3D viewer into translation, rotation and zoom for the 3D volumes of interest displayed at the appropriate image resolution (Bria, Iannello, Onofri, Peng 2016).
Mozak is a tool used for visualization and reconstruciton of cell neurites from 3D image stacks. These traced neurites, or reconstructions, are saved in the swc file format, which can be exported and analyzed for morphological features (e.g. branch points, end points, x-y extent, etc). More information about swc files can be found here.
All the tools are wrapped in in the Vaa3D software package listed below, along with protocols, analysis tools, and data generated using these tools.
Computer Requirements
CPU: Equivalent of Intel i5 5th gen or better
GPU: Dedicated GPU recommended, but can handle Intel UHD Graphics 620
Memory: 16 GB RAM - RAM will be limiting factor for speed when transferring images from tiff to Terafly format
Monitor: A larger monitor is preferred, we find 27" to 32" idea
Get Started
Below are links for the software download, along with protocols and example stacks.
Vaa3D Download
Reconstruction Protocol
Example raw inverted image stack and Terafly format files for a mouse cortical excitatory cell
Learn More About Vaa3D
Analysis
When measured correctly, morphological features effectively quantify the idiosyncratic characteristics of neurons we observe when examining them under the microscope or in 3D images and reconstructions. These features are key in a variety of analyses such as creating distinct classes of neurons based on morphological features through unsupervised clustering, or analyzing the relationship between morphology, electrophysiology and transcriptomics. The skeleton keys package supports the skeletal analysis of neuron morphologies. It is used to perform a series of analysis steps in a consistent and scalable manner and can be found at this link, skeleton keys package.
Our Data
Viewers
Patch-seq viewer
Cell Types Database (patch-clamp)
Access
Published patch-seq datasets
BICCN human neocortical patch-seq
BICCN full morphology (fMOST)
Protocols
Scaled, high fidelity electrophysiological, morphological, and transcriptomic cell characterization
White Papers
Signature morphoelectric properties of diverse GABAergic interneurons in the human neocortex
Morphoelectric and transcriptomic divergence of the layer 1 interneuron repertoire in human versus mouse neocortex
Human neocortical expansion involves glutamatergic neuron diversification
Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells
Classification of electrophysiological and morphological neuron types in the mouse visual cortex
Beyond Vaa3D
Mozak is a scientific discovery game about neuroscience. 3D image stacks are posted on the website so players can reconstruct neurons and capture their morphology. Informational guide to playing Mozak, as well as general information about gameplay can be found on the website. Players from beginner to expert levels of experience can participate in general tracing or enter different challenges. Click on the links to learn more.
Reconstruction Gamified on Mozak
Have Questions?
If you have a question, please post at Allen Brain Map Community Forum and Allen Institute scientist will help you out!
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