News

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

 

Date:

6^th October 2014 (Monday)

 

Location:

Bryan Matthews Room,

Physiological Laboratory, PDN Department

 

 

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.

 

Posted on 18/09/2014