High-throughput Digital Brain Atlasing for Model Systems: Worm, Fly, Mouse, and Human

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• Dr Hanchuan Peng, Allen Brain Institute
• Monday 06 October 2014, 13:00-17:00
• Bryan Matthews Room, Physiology Building, Department of Physiology, Development and Neuroscience, Downing Site.

If you have a question about this talk, please contact ptg25.

Lecture and Workshop - Registration required

Lecture (1pm-2pm)

Hanchuan Peng (Allen Institute, Associate Investigator).

High-throughput Digital Brain Atlasing for Model Systems: Worm, Fly, Mouse, and Human

Vaa3D software Workshop (2:15pm to 5pm)

Sign up: To register, send an email to ptg25@cam.ac.uk

What is Vaa3D: Vaa3D is a free and open source cross-platform (Mac, Linux, and Windows) tool for visualizing large-scale (gigabytes, and 64-bit data) 3D image stacks and various surface data. It is also a container of powerful modules for 3D image analysis (cell segmentation, neuron tracing, brain registration, annotation, quantitative measurement and statistics, etc) and data management.

What is the workshop for: This will be a hands-on tutorial (remember to bring your laptop). The following functions of Vaa3D will be demonstrated in an interactive manner.

• Introduction: from 2D to 3D visualization. ● Multidimensional medical and microscopy image visualization: visualize a 3D multicolor image, visualize a 5D image data set such as a series of multicolor 3-D images. ● Turning the computer mouse into a 3D Virtual Finger: 3D point pin-pointing algorithm (PPA) and 3D curve drawing algorithm (CDA) ● Generate, quantify, measure and annotate 3D surface meshes. ● Plugin generation: how to write a simple plugin to instantly manipulate a 3D image ● Stitching of large-scale images ● Visualization of terabyte-scale 3-5D images ● Automatic neuron reconstruction: semi-automatic and fully automatic neuron reconstruction for regular and large-scale images.

This talk is part of the Cambridge Neuroscience Seminars series.

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