Michael Hooker Microscopy Facility (MHMF.ORG)

Volocity - 3D & Time Lapse Viewing, Analysis, Quantitation, Tracking and Deconvolution

What is Volocity:

Volocity (Improvision/Perkin Elmer) is a 3D and time lapse (4D) imaging program for volume visualization, analysis, object measurement, tracking, colocalization analysis and deconvolution.  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 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 called:

• \\Zernike high performance work station - (Windows x64 bit, 512 MB OpenGL video, 4GByte RAM).  Will do movie black level fades and other green button functions.
• \\Nomarski (Volocity version 5.1)
• \\Snell (version 4.4) Will not do movie black level & intensity changes - use \\Zernike
• On your computer!  You will need to obtain an activated account.  Obtain the Volocity software from the Improvision web site and connect to the ai.med.unc.edu:15002 license server (see section 1. below).  For adequate performance your computer should have sufficient RAM and a high performance OpenGL video card.

Who Can Use Volocity:

Users will need to arrange to have access to this software with 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.  Pathology Olympus microscope users should contact Bob on how to use Volocity Acquisition.  In the future use of the Visualization and Quantification and Restoration (deconvolution) licenses will cost $3.50 each per hour, or $7.00 per hour for both.  Much analysis done only requires one license and not both.  The Volocity LE viewer is free, but an activated account is required.

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 - $3.00/hr  (Deconvolution is also available at on the workstation call \\Normaski using SimplePCI or Metamorph)
• Combined Modules
  • Volocity Vis & Quant - 3D rendering and measurement, tracking & co-localization - $5.00/hr
  • Volocity Vis & Restor - Deconvolution $5.00/hr
  • Volocity Vis & Quant & Restor - Deconvolution $6.50/hr
  • Volocity Acquisition - Dept. of Pathology MSL users only

• Instant access username=guest password=Volocity(LE).  Please contact facility personnel (Michael or Neal) and obtain a permanent account.

0.  Notices:

• Volocity now uses a 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 to obtain an account (He may respond to after hours requests, if available).
• Improvision (Volocity) Technical Support Desk 866-310-0932   (781-402-0134   781-402-0251 fax    781-403-0211)
• Volocity's latest available manual:
  • http://www.improvision.com/support/guides/volocity.php
  • Volocity's January 14, 2009 manual is also available here:  http://physiology.med.unc.edu/Resources/Volocity/Volocity5UserGuide-090114.pdf
• Application examples from Improvision
• \\Zernike - Volocity has been downgraded to version 4.3.2 in order to gain some movie making functionality lost in version 4.4
• \\Snell  -  Volocity 4.4 is installed and allows correct Leica confocal stack importation, which version 4.3 does not
• \\Nomarski - Volocity 5.1 interface is significantly different from previous version 4

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

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 2001-09  Dr. M. Chua, Office of Research, School of Medicine, University of North Carolina, Chapel Hill, NC 27599
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