CIBC:Seg3D:Documentation:UseCase:Dougherty
This page describes a typical use case for the collaboration with Matthew Dougherty's lab at the National Center for Macromolecular Imaging, Baylor College of Medicine. The typical user will be segmenting electron microscopy datasets.
Contents
Using Seg3D
Download and Install Seg3D
A source archive of Seg3D 1.13 beta is available with the MRC reader and views renamed from axial, saggital and coronal to xy, yz, xz. Build the source archive by following these instructions. An OS X disk image built from this code is also available.
The MRC reader is also available from our Subversion repository.
Using Seg3D
Loading MRC Data
Load dataset using File->Open Volume. Seg3D supports a number of file formats and will select the correct reader based on the file extension.
Manipulating the view
Use the zoom buttons to zoom in or out of 2D views. It may be necessary to use the autoview button to reset the layer view
Filters
Running the Median Filter (try radius = 2) removes some of the noise from the sample dataset (b11g309b-rec-bin4.mrc). Good window/level tool settings for the sample data after running the Median Filter are: windows=1852, level=1198. Start segmenting by creating a new layer from the layer created by the Median Filter.
