September 15, 2015 (Vol. 35, No. 16)


Strong Points: Available for Windows/OS, quickly displays 2D slices
Weak Points: Not very intuitive to use


Scientists increasingly require tools to view and manipulate large 3D imaging datasets. Knossos, a free software program developed at the Max Planck Institute for Medical Research, allows users to navigate and annotate multi-terabyte 3D volume electron microscope (EM) datasets. It does so by displaying intersecting 2D planes of the dataset—each 2D plane (XY, XZ, YZ) is shown in its own quadrant of the screen, and the 3D intersection is shown in the fourth quadrant. Using the scroll feature on the trackpad/mouse, users can easily move through the dataset in any dimension and annotate the 2D slices as they go. The software is available for both Windows and OS, and its functionality can be extended by plugins written in Python. User datasets will need to be converted into the specialized Knossos format, but if you want to quickly familiarize yourself with the program, you can take advantage of the included sample datasets.

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