Download 3D Image processing with MorphoGraphX User manual

User Guide
1. Introduction to MorphoGraphX
MorphoGraphX is an open source platform for the visualization and processing of 3D image
data. MorphoGraphX can manipulate 3D image stacks and use them to extract curved surfaces
(2½D) from them or segment data in full 3D.
Some definitions
•
Stack. A stack corresponds to a 3D image of a biological sample. There can be 2 stores
associated with each stack, corresponding for example to the original 3D image and the
same data after image processing. The size of a stack is defined in voxels, which are the
equivalent of pixels for 3D images.
•
Store. There are 2 stores in each stack. Usually the original sample is loaded into the
main store. Once the original stack has been modified by a function, the result (e.g. the
3D image after blurring) is stored separately in the work store, without over-writing the
original image in the main store. Each store has a separate color, brightness,
transparency, etc.
•
Mesh. A mesh is a triangulated curved surface. Typically the mesh is extracted from a
stack after some image processing operations are performed on it. Currently
MorphoGraphX can handle 2 stacks (each with a main and work store) and 2 associated
meshes in a single session.
•
Process. Most operations in MorphoGraphX are performed by processes. There are 3
kinds of processes, “Mesh”, “Stack”, and “Global”. They are named after what they can
modify. Processes can be organized by users into custom pipelines called tasks.
User interface in MorphoGraphX
Start a MorphoGraphX session with the example data loaded by clicking on the
“example_session.mgxv” file in the “Kierzkowski_2012” folder.