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Seg3D 1.x Tutorial

A more up-to-date tutorial is available from the CIBC workshop held in January 2009.

This presentation is a good introduction to segmentation.

The CVRG wiki also has a good Seg3D tutorial.

The User Interface

The Seg3D consists of three panels from left to right. These are the tools pane, the visualization pane, and the volumes pane.

Figure 1 Seg3D User Interface.

Tools Pane

The tools pane is used to set various parameters and execute image processing operations. It changes to match the current active tool. For instance if the Brush Tool is active then the tools pane contains controls for the brush size.

Visualization Pane

The visualization pane as illustrated in Figure 1 contains four different viewing windows. However, it is possible to to change the layout of the visualization pane with the options available under the Views menu. There are three different slice view modes and a volume rendering mode available.

The slice windows are where interactive drawing operations take place. By default right clicking in one and dragging the mouse changes the contrast. Clicking with the middle mouse button places the crosshairs and adjusts the other slices to match their location within the volume. The left mouse button allows you to zoom and pan in on the slices.

The volume rendering window defaults to just showing the active slices in their relative positions within the volume. Because volume rendering and isosurfacing can be slow these options are turned off by default. To enable volume rendering just click the cloud icon in the volume rendering window. By default the volume will be rendered with a translucent grayscale colormap. The Tools->Isosurface menu item can be used to isosurface all of the current segmentations. However if you do it without a segmentation there will be nothing to see. The mouse buttons in the volume rendering window also default to basic zoom and rotation of the volume.

Volumes Pane

The volumes pane is used to modify which volumes are active. Volumes in Seg3D refer to data volumes and their perspective segmentations. The toplevel volumes are data volumes and the label volumes (segmentations) are indented to the right of the data volume they correspond to. Volumes are drawn in order from top to bottom and may occlude each other. It is recommended that you just select one data volume to be visible (the eye icon) at a time. Also be aware that only the first data volume loaded is currently volume rendered due to limitations in the current volume renderer.

Getting Started

Loading Data

Use the File->Open Volume menu item to pull up a file open dialog. Select your dataset. For example if you downloaded the AA-Paw.mhd dataset from the Download area selecting this file would open the mouse paw used in the Capecchi use case. After loading the new data volume will appear in the volumes pane.

Start A New Segmentation

Click on the new volume icon next to the volume entry in the volume pane. This will create a new subvolume attached to the selected data volume. Select the Tools->Brush Tool menu entry to start the brush tool, then make sure the new label volume is active. Now you can start painting your segmentation on the slice views. The '<' and '>' keys can be used to move up and down within the volume by one slice at a time as you paint.

Save Your Work

Select the File->Save Session menu item and pick a name for your session from the standard save file dialog. Your data will be saved in the same directory as the directory as a NRRD file per volume and a file containing the current Seg3D state. You can load it again with the File->Load Session dialog later.

Seg3D currently saves the data volumes as floating point NRRD files and smooshes each segmentation into a 32 bit unsigned int NRRD. Each label volume will correspond with a bit in one of the segmentation NRRD files. The label volume contains which bit value it is using.

Thresholding Example

See the new Seg3D tutorial.