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Instruction for Using 3D Data Set

General uses the Samurai Microtome, a browser client for 3-dimensional image sets hosted on a Neuroterrain Atlas server at Drexel University ( It is designed to present the slice views of the data set so that the images appear as if they are coming directly from the microtome. These slices can be displayed at any arbitrary angle and position. Navigation through the embryo is done simply by clicking and dragging the virtual knife, or by clicking on the image. The Samurai Microtome has been developed in Java, so that it can be used on any computer with Java support. You’ll need the Java2SE5 or later Java environment to use the SamuraiMicrotome.

Download Samurai Microtome

  1. Go to:Neuroterrain web site.
    Click on Available Technologies
  2. Go to SamuraiMicrotome Neuroterrain Atlas browser
    Click on Zip archive of SamuraiMicrotome
    Open and download file.
  3. Extract the file Samurai_Microtome.jar (last version)
    Move file to desktop or application folder.

Navigating 3D Data Set

  1. Click on Samurai_Microtome to open Virtual Knife.
  2. Click on File, and then Connect.
  3. Connect to
  4. Connect to EPMBA Gestational Day 12.
  5. Choose from the middle buttons to look at horizontal, sagittal or coronal orientation.
  6. For navigation, use either mouse click and drag, or move red virtual knife in its window.
  7. Use either of three buttons on left to pivot knife about the x, y or z axis.
  8. Note buttons to undo or redo former actions (C-shaped symbols).
  9. Note buttons to enlarge or decrease image (magnifying glass).