Michael Hooker Microscopy Facility (MHMF.ORG)

Using Volocity

These are terse notes on using Volocity are (more) specific to version 4.4.

1.  Using Volocity

• Start Volocity
• Create or open a library

2.  Loading Images

• Zeiss database:
  • File -> Open -> New Library
  •  In the white area of the Library window
    • Right-click
    • Select Create -> Image Sequence
    • A blank Image Sequence window will appear
  • Drag and drop the desired .lsm file into the Image Sequence window
    • Indicate the number of color channels and time/channel naming order (usually "Channels, then Z-series...") when prompted and press OK
    • You should see one thumbnail for each color channel in the Image Sequence window.  You will probably have to expand the window to see them all if there are more than one.
• Leica series:
  • File -> Open -> New Library
  • Load image sequences by either:
    • Dragging the .lei file into the white space
  • or
    • In the white area of the Library window
    • Right-click
    • Select Create -> Image Sequence
    • Double click on the Image Sequence Entry
    • A blank Image Sequence window will appear
    • In a Windows folder window, highlight all images from .tif series images
    • Drag and drop the group of images into the Image Sequence window
      When prompted,
    • Indicate the number of color channels and time/channel naming order (usually usually "Channels, then Z-series, then time) and press OK
  • You should see one thumbnail for each color channel in the Image Sequence window.  You will probably have to expand the window to see them all if there are more than one.
• Olympus confocal series in .oif format:
  • If images are in .oib format make an .oif version using the Olympus FV10 software on \\Sutton (or install and use the free FV10-asw 2.0c viewer on your PC computer)
  • File -> Open  (or  File -> New Library)
  • File -> Import  the .oif file (or drag the .oif file from Windows Explorer into the Volocity Library window pane)
  • May need to change channel colors
  • May need to check that image dimensions are correct (right click on image and hit properties)
• Importing Olympus 3D time series stacks (4D image data) e.g. MATL data (multi area time lapse z-stacks)
  • After a MATL has completed just dragging the append folder to the Library windows pane will provide a fairly well organized 4-D series.
    • Color for channels will need to be manually set.  This is best done after all the tracks are imported, then selecting all the volumes so that color is changed on all track volumes at once.
      • Choose one or more spliced sequences
      • Tool -> Change Colors - select appropriate color for one channel at a time
  • - or -
  • If volumes need to be manually assembled or the MATL has not completed or an append series has not been generated:
    • Drag .oif files into gray Library area  (or File -> Import - select .oif files)
    • Select library items there are part of the same image series (i.e. have same dimensions, e.g. 3-D stacks at different times, but not different positions)
    • Right click on selection and choose Splice Sequences
    • Choose one or more spliced sequences
    • Tool -> Change Colors - select appropriate color for one channel at a time
• C-Imaging series -e.g. Spinning Disk Confocal Stacks, Fluorescence Dissecting/Macro-scope
  • Talk to facility personnel
• Biorad PIC format
  • Contact Michael
  • Or just click and drag the .pic files into an image sequence window.
• Free standing tiff files
  • Contact Michael

3.  Displaying orthogonal view (Image tab)

• Cropping
• Changing channel colors - targeting channel -

4.  Rendering

• Mode
• Brightness
• Density (Opacity)
• Black level

5.  Create Movie Sequence

• Right-click in the white space of the Library window
  • Create a new Movie Sequence
• A window “Untitled Sequence” will open
• Insert actions (rotating, zooming, etc), durations, etc.
  • IMPORTANT NOTE:  The orientation of the image as it is displayed in the Image Window is the starting point for the Movie Sequence.
    • To ensure consistent rotation, orientation, etc. in subsequent plays of the movie, always reset the image view to zero rotation. 
    • To reset image view, right-click on the image and select Reset View.
• When movie sequence is complete, select newly created sequence rectangle in the image database
• Go to menu bar item Sequence -> Make Movie
  • NOTE:  This will apply the highlighted Movie Sequence to ALL of the Image Sequence files open from the image database library!
  • The movie will be added to the Library with a folder icon
• Export Movies from created folder
  • Right-click on the Movie file (in the Library Window)
  • Choose Export
    • Select options and choose codec.  On Windows XP 64 bit only the "Microsoft Indeo 1" or "Intel IYUV" codecs are available.  Save in this format and use another program (e.g. QuickTimePro) on another computer to convert to, preferably, uncompressed or the Cinepak codec in order to be compatible with Power Point on a Windows XP (standard 32 bit) computer.  For Apple users convert to a QuickTime format.

		Copyright 2001-12  Dr. M. Chua, Office of Research, School of Medicine, University of North Carolina, Chapel Hill, NC 27599
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