Michael Hooker Microscopy Facility (MHMF.ORG)

Volocity - 3D & Time Lapse Viewing, Analysis, Quantitation, Tracking and Deconvolution
Note: This information page is available on line at: http://microscopy.unc.edu/Volocity

What is Volocity:

Volocity (Improvision/Perkin Elmer) is a 3D and time lapse (4D) imaging program for:

• Volume visualization - volume rendered, ray tracing, orthogonal views, maximum projection, stereo, VR
• Analysis
• Object measurement
• Tracking (including 3-D)
• Co-localization analysis
• Deconvolution - blind and measured point spread function

It can use data from diverse sources such as confocal microscopes & widefield microscopes.  Volocity can easily import z-series &/or time lapse image sequences with from the Zeiss 510 or Leica SP2/SP5 or Biorad or Perkin Elmer confocal programs with meta data, C-Imaging data, as well as .tif image format image series.

Where can it be Used:

Volocity is installed on the image processing workstations in the Michael Hooker Microscopy Facility:

• \\Schott  \\Brewster high performance work stations - (Windows X64 bit, 8 GByte RAM, 512 MB OpenGL video). 
• \\Nomarski (Volocity version 5.3.1 or later)
• \\Snell (Volocity version 4.4) Will not do movie black level & intensity changes (green button functions) - use \\Schott or \\Nomarski  or  \\Brewster
• \\Zernike - Please note that this computer failed. Data stored on it has been recovered to a server.
• On your computer!  You will need to have both an MHmicroscopy account and also have it activated to use the Volocity license server.  Obtain the Volocity software from the Improvision web site (or try this download page) and connect to the ai.med.unc.edu:15002 Michael Hooker Microscopy license server (see section 1. below).  For adequate performance your computer should have sufficient RAM (>= 1 GBytes or with Vista >= 2 GBytes) and a high performance OpenGL video card.

Who Can Use Volocity:

Users will need to arrange to have access to this software from facility personnel before being able to use the license server.  Most users will use their MHmicroscopy user name and password, which must be activated for use with Volocity by facility personnel.  If you do not have an MHmicroscopy account please fill out this New User Information form and then contact Michael or Neal.  In the future use of the Visualization and Quantification and Restoration (deconvolution) licenses will cost $3.00, $5.00 & $6.50 per hour for 1, 2 & 3 modules respectively.  Much analysis done only requires one license and not two or all three.  The Volocity LE viewer and image database organizer is free, but an activated account is required. 

License Availability:

Volocity module licenses are available individually on a first come first served basis to users with Volocity activated MHmicroscopy accounts.  Licenses availability is shown at: http://ai.med.unc.edu:15003

Getting your MHmicroscopy account activated or a new account for using the Volocity License server:

• Contact Michael or Neal
• Available Modules (please choose selected modules carefully in order to have the desired features available):
  • Volocity (Volocity LE) - "Light Edition" Image importing, cropping, resizing, viewing and image library organization only - Instant access to Volocity (LE) - free
  • Volocity Visualization (Vis) - 3D rendering - $3.00/hr
  • Volocity Quantitation (Quant) - Measurement, tracking & co-localization - $3.00/hr
  • Volocity Restoration (Restor) - Deconvolution  (Deconvolution is also available at on the workstation call \\Normaski using SimplePCI or Metamorph) - $3.00/hr
• Combined Modules
  • Volocity Vis & Quant - 3D rendering and measurement, tracking & co-localization - $5.00/hr
  • Volocity Vis & Restor - 3D & Deconvolution - $5.00/hr
  • Volocity Vis & Quant & Restor - Deconvolution - $6.50/hr
• For (LE) light version only instant access  username=guest password=Volocity(LE).  Please contact facility personnel (Michael or Neal) and obtain a permanent account.

0.  Notices:

• Volocity uses an on line license server to assign a user a license instance to run the program.  See section 1. below.
• Users who have not used Volocity via the license server should contact Michael or Neal to obtain an account (Michael is happy to respond to after hours requests, if available).
• Improvision (Volocity) Technical Support Desk 866-310-0932   (781-402-0134   781-402-0251 fax )
• Volocity's latest available manual:
  • Dec 2009 version 5.3 manual:
    • http://microscopy.unc.edu/Resources/Volocity/VolocityUserGuide53.pdf
  • From Perkin Elmer/Improvision/Volocity web site :
    • http://www.improvision.com/support/guides/volocity.php
• Application examples from Improvision
• \\Snell  -  Volocity 4.4 is installed and allows correct Leica confocal stack importation, which version 4.3 does not
• \\Nomarski - Volocity 5.3 (32-bit) or later. WindowsXP with 3.4 GByte RAM
• \\Schott - Volocity 5.3 (64 bit) on Windows 7 (64-bit) 2x CPU, 8 GByte RAM, Video nVidia 8800 + 640 MB.
• \\Brewster - Volocity 5.3 (64bit) on Windows 7 (64-bit) 4x CPU, 4 GByte RAM, Video nVidia 8600 + 256 MB+shared RAM

1.  Using Volocity

1.1  Connecting to the license server:

• Start Volocity
• If the "Connect to the license server at" shows ai.med.unc.edu or 152.19.83.97 then enter your MHMF user account name and password
• 
• And choose an appropriate configuration - Generally Vis or Vis+Quant or Vis+Restoration or Vis+Quant+Rest  (Restoration=deconvolution)

• 3D Visualization

  or

  Acquisition (Pathology Department only)

  • If the server is not listed as ai.med.unc.edu or 152.19.83.97 then press the ESC key and press the Server button
  • 
  • Enter ai.med.unc.edu and port 15002 (not port 15003 which is the availability status web page)
  • 
• Skip downloading any new software and just push the Continue button
• 
• Volocity should run if a license is available

1.2  Opening/Creating a Volocity Image Library:

Loading Images  |  Displaying orthogonal view  |  Rendering  |  Creating a movie sequence

 

2.  Access to Volocity

Please contact MHMF personnel in order to setup an account

3.  Links:

• Improvision  (http://improvision.com)
• Volocity manual:
  • Latest available: http://www.improvision.com/support/guides/volocity.php
  • Volocity's January 14, 2009 manual:  http://physiology.med.unc.edu/Resources/Volocity/Volocity5UserGuide-090114.pdf

		Copyright 2001-10  Dr. M. Chua, Office of Research, School of Medicine, University of North Carolina, Chapel Hill, NC 27599
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