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Vaa3D Workshop Series

Purpose

This meeting series will feature some recent progresses of the widely used Vaa3D system (http://vaa3d.org). The audience could be interested biologists, computer scientists who want to study or use Vaa3D effectively and discuss application cases of Vaa3D. This event is being organized as a weekly meeting series, rotating in the day time of America and Asia to provide convenience for people to participate. The meetings' date, time, and how-to-join are the following.

Schedule

Up-coming

Please look forward to!

How to join

Zoom Meeting:

https://us02web.zoom.us/j/6543029624?pwd=bWdESGZqSHZLWCthUGhyMDVtS1QvUT09

Past meetings

Monday, June 21, 2021

  • Dr. Yimin Wang: "Vaa3D is the Right Tool for Big Biodata Visualization and Analysis" download here
  • Dr. Liya Ding: "Automated Neuron Tracing in Vaa3D" download here

Monday, June 21, 2021

  • 8:00 AM -9:00 AM PST
  • 11:00 AM - 12:00 PM EST
  • 11:00 PM - 0:00 AM Beijing Time.

Monday, June 28, 2021 

  • Dr. Lijuan Liu: "How to produce precise full neuronal reconstructions efficiently through Vaa3D-TeraVR platform" download here

  • Dr. Shuxia Guo: "Make sense of swc files: information extraction via Vaa3D" download here
     
    Monday, June 28, 2021

  • 7:00 PM -8:00 PM PST

  • 10:00 PM - 11:00 PM EST

  • Tuesday, June 29, 2021 10:00 AM - 11:00 AM Beijing Time.  

Tuesday, July 6, 2021

  • Dr. Peng Xie: "Generation of 3D models with Vaa3D" download here
  • Dr. Zongcai Ruan: "Transform SWC to 3D surface model" download here

Tuesday, July 6, 2021

  • 8:00 AM -9:00 AM PST
  • 11:00 AM - 12:00 PM EST
  • 11:00 PM - 0:00 AM Beijing Time.

Monday, July 12, 2021

  • Dr. Yufeng Liu: "Extend Your Research with Vaa3D Plugins" download here
  • Dr. Hanchuan Peng: "Evolving Vaa3D: The Best is Yet to Come" download here

Monday, July 12, 2021

  • Tuesday, July 13, 2021 10:00 AM - 11:00 AM Beijing Time
  • 7:00 PM -8:00 PM PST
  • 10:00 PM - 11:00 PM EST.

Monday, July 19, 2021

  • Dr. Liya Ding: "How to apply APP2?" download here
  • Attendees practice under our guidance

Monday, July 19, 2021

  • 8:00 AM -9:00 AM PST
  • 11:00 AM - 12:00 PM EST
  • 11:00 PM - 0:00 AM Beijing Time.

Monday, July 26, 2021

  • Dr. Yimin Wang: "Visualizing big bio data using Vaa3D-TeraFly" download here
  • Attendees practice under our guidance

Monday, July 26, 2021

  • Tuesday, July 27, 2021 10:00 AM - 11:00 AM Beijing Time
  • 7:00 PM -8:00 PM PST
  • 10:00 PM - 11:00 PM EST.

Monday, August 2, 2021

  • Dr. Lijuan Liu: "How to reconstruct 3D neurons in accuracy and efficiency using Vaa3D" download here
  • Attendees practice under our guidance

Monday, August 2, 2021

  • 8:00 AM -9:00 AM PST
  • 11:00 AM - 12:00 PM EST
  • 11:00 PM - 0:00 AM Beijing Time.

Monday, August 9, 2021

  • Dr. Peng Xie: "Generation of 3D models with Vaa3D" download here
  • Attendees practice under our guidance

Monday, August 9, 2021

  • Tuesday, August 10, 2021 10:00 AM - 11:00 AM Beijing Time
  • 7:00 PM -8:00 PM PST
  • 10:00 PM - 11:00 PM EST.

Monday, August 16, 2021

  • Dr. Shuxia Guo: "Make sense of swc files: information extraction via Vaa3D" download here
  • Attendees practice under our guidance

Monday, August 16, 2021

  • 8:00 AM -9:00 AM PST
  • 11:00 AM - 12:00 PM EST
  • 11:00 PM - 0:00 AM Beijing Time.

Monday, August 23, 2021

  • Dr. Zongcai Ruan: "Transform SWC to 3D surface model" download here
  • Attendees practice under our guidance

Monday, August 23, 2021

  • Tuesday, August 24, 2021 10:00 AM - 11:00 AM Beijing Time
  • 7:00 PM -8:00 PM PST
  • 10:00 PM - 11:00 PM EST.

Monday, August 30, 2021

  • Dr. Yufeng Liu: "Extend Your Research with Vaa3D Plugins" download here
  • Attendees practice under our guidance

Monday, August 30, 2021

  • Tuesday, August 31, 2021 10:00 AM - 11:00 AM Beijing Time
  • 7:00 PM -8:00 PM PST
  • 10:00 PM - 11:00 PM EST.

Monday, September 6, 2021

  • Dr. Liya Ding: "Automated Neuron Tracing in Vaa3D" download here
  • Attendees practice under our guidance

Monday, September 6, 2021

  • Tuesday, September 7, 2021 10:00 AM - 11:00 AM Beijing Time
  • 7:00 PM -8:00 PM PST
  • 10:00 PM - 11:00 PM EST.

Monday, September 13, 2021

  • Dr. Hanchuan Peng: "Evolving Vaa3D: The Best is Yet to Come" download here
  • Discussion

Monday, September 13, 2021

  • Tuesday, September 14, 2021 10:00 AM - 11:00 AM Beijing Time
  • 7:00 PM -8:00 PM PST
  • 10:00 PM - 11:00 PM EST.

Tuesday, September 21, 2021

  • Xiang Liu, Linlu Xu and Chao Song (Peking University): "Zebrafish whole-brain imaging and neural signal data processing"
  • Yibing Wang and Xing Long (Peking University): "PACT reconstruction result show in 3D for better performance and photoacoustic image enhance and improvement"

Monday, September 21, 2021

  • Wednesday, September 22, 2021 10:00 AM - 11:00 AM Beijing Time
  • 7:00 PM -8:00 PM PST
  • 10:00 PM - 11:00 PM EST.

Monday, September 27, 2021

  • Sumit Nanda (George Mason University): "Using a Vaa3D multi-signal plug-in to quantify neuronal cytoskeleton" download here
  • Ty Hergenreder (University of Michigan): "Analyzing the morphology of whole Chandelier cells in mouse brains" download here

Monday, September 27, 2021

  • 8:00 AM -9:00 AM PST
  • 11:00 AM - 12:00 PM EST
  • 11:00 PM - 0:00 AM Beijing Time.

Tuesday, October 12, 2021

  • Keivan Moradi (University of California): "Image enhancement for light sheet microscopy: towards automated neuronal reconstruction" download here
  • Discussion

Tuesday, October 12, 2021

  • Wednesday, October 13, 2021 10:00 AM - 11:00 AM Beijing Time
  • 7:00 PM - 8:00 PM PST
  • 10:00 PM - 11:00 PM EST.

Monday, October 18, 2021

Monday, October 18, 2021

  • Tuesday, October 19, 2021 10:00 AM - 11:00 AM Beijing Time
  • 7:00 PM - 8:00 PM PST
  • 10:00 PM - 11:00 PM EST.

Monday, October 25, 2021

  • Yiwei Li: "Building a Vaa3D plugin to do neuron refinement" download here
  • Sujun Zhao: "Quality Control for Reconstructions of Neuron Morphology at Whole Mouse Brain Level" download here

Monday, October 25, 2021

  • Tuesday, October 26, 2021 10:00 AM - 11:00 AM Beijing Time
  • 7:00 PM - 8:00 PM PST
  • 10:00 PM - 11:00 PM EST.

Monday, November 1, 2021

  • Xiangqiao Ye: "How to write a Vaa3D plugin" download here
  • Yingxin Li: "Vaa3D usage summary and tracing algorithm extension" download here

Monday, November 1, 2021

  • Tuesday, November 2, 2021 10:00 AM - 11:00 AM Beijing Time
  • 7:00 PM - 8:00 PM PST
  • 10:00 PM - 11:00 PM EST.

Monday, November 8, 2021

  • Yanyan Guo: "How to use TeraStitcher and NeuronStitcher" download here
  • Yuanyuan Song: "How to use TeraFly to improve the efficiency and quality of reconstruction" download here

Monday, November 8, 2021

  • Tuesday, November 9, 2021 10:00 AM - 11:00 AM Beijing Time
  • 6:00 PM - 7:00 PM PST
  • 9:00 PM - 10:00 PM EST.

Monday, November 15, 2021

  • Yaping Wang: "How to generate high-quality neuronal reconstructions semi-automatically through Vaa3D" download here
  • Shengdian Jiang: "Radius Estimation and Bouton Detection of whole brain neurons" download here

Monday, November 15, 2021

  • Tuesday, November 16, 2021 10:00 AM - 11:00 AM Beijing Time
  • 6:00 PM - 7:00 PM PST
  • 9:00 PM - 10:00 PM EST.

Monday, November 22, 2021

  • Jiangshan Liang and Luchen Deng: "Vaa3D , Update to QT6" download here

Monday, November 22, 2021

  • Tuesday, November 23, 2021 10:00 AM - 11:00 AM Beijing Time
  • 6:00 PM - 7:00 PM PST
  • 9:00 PM - 10:00 PM EST.

Monday, November 29, 2021

Monday, November 29, 2021

  • Tuesday, November 30, 2021 10:00 AM - 11:00 AM Beijing Time
  • 6:00 PM - 7:00 PM PST
  • 9:00 PM - 10:00 PM EST.

Monday, December 6, 2021

  • Shize Chen: "Create a plugin to mix images" download here
  • Lulu Yin: "Reconstruction and quality control of neuron morphology in Vaa3D" download here

Monday, December 6, 2021

  • Tuesday, December 7, 2021 10:00 AM - 11:00 AM Beijing Time
  • 6:00 PM - 7:00 PM PST
  • 9:00 PM - 10:00 PM EST.

Monday, December 13, 2021

Monday, December 13, 2021

  • Tuesday, December 14, 2021 10:00 AM - 11:00 AM Beijing Time
  • 6:00 PM - 7:00 PM PST
  • 9:00 PM - 10:00 PM EST.

Monday, December 20, 2021

  • Zhixi Yun: "Some simple operations combining Vaa3D and programming language" download here
  • Jingzhou Yuan: "The usage of Vaa3D plugins" download here

Monday, December 20, 2021

  • Tuesday, December 21, 2021 10:00 AM - 11:00 AM Beijing Time
  • 6:00 PM - 7:00 PM PST
  • 9:00 PM - 10:00 PM EST.

Monday, December 27, 2021

  • Ye Zhong: "The OPT Metric: Comparing Multiple Reconstructions of the Same Neuron" download here
  • Yichen Guo: "Basic use of Vaa3D" download here

Monday, December 27, 2021

  • Tuesday, December 28, 2021 10:00 AM - 11:00 AM Beijing Time
  • 6:00 PM - 7:00 PM PST
  • 9:00 PM - 10:00 PM EST.

Monday, January 3, 2022

  • Gaoyu Wang: "The implementation of APP2 in Vaa3D" download here
  • Feng Xiong: "Neuron morphology analysis with Vaa3D" download here

Monday, January 3, 2022

  • Tuesday, January 4, 2022 10:00 AM - 11:00 AM Beijing Time
  • 6:00 PM - 7:00 PM PST
  • 9:00 PM - 10:00 PM EST.
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