Volume Segmenter

Segment 3-D grayscale or RGB volumetric images

Description

The app can be used to create and refine a binary or semantic segmentation mask for a 3-D grayscale or an RGB image using automated, semi-automated, and manual techniques.

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Open the Volume Segmenter App

• MATLAB^® Toolstrip: Open the Apps tab, under Image Processing and Computer Vision, click the Volume Segmenter app icon.

• MATLAB command prompt: Enter volumeSegmenter.

Examples

Load Volume and Labeled Volume into the Volume Segmenter

1. Load a volume into the workspace.

   load(fullfile(toolboxdir('images'),'imdata','BrainMRILabeled','images','vol_001.mat'));
   

2. Load the corresponding labeled volume into the workspace.

   load(fullfile(toolboxdir('images'),'imdata','BrainMRILabeled','labels','label_001.mat'));
   

3. Open the Volume Segmenter specifying both the volume and the labeled volume.

   volumeSegmenter(vol,label)

Related Examples

• Create Binary Mask Using Volume Segmenter
• Create Semantic Segmentation Using Volume Segmenter

Programmatic Use

volumeSegmenter

volumeSegmenter opens a volume segmentation app.

volumeSegmenter(V)

volumeSegmenter(V) opens the Volume Segmenter app, loading the volume V into the app. Volume V is a scalar valued m-by-n-by-p or m-by-n-by-p-by-3 image of class uint8, uint16, uint32, int8, int16, int32, single, or double.

volumeSegmenter(V,L)

volumeSegmenter(V,L) opens the Volume Segmenter app, loading the volume V and the labeled volume L into the app. The labeled volume L is a scalar valued m-by-n-by-p image of class logical, categorical, uint8, uint16, uint32, int8, int16, int32, single, or double.

volumeSegmenter(___,'Show3DDisplay',TF)

volumeSegmenter(___,'Show3DDisplay',TF) logical value that specifies whether the Volume Segmenter includes a visualization of the 3-D volume in the app. The default value is true. However, the default is false on platforms where 3-D display is not supported, such as, Linux platforms, or on Windows platforms that use software versions of OpenGL.

Version History

Introduced in R2020b

R2021a: Support for blocked images

The Volume Segmenter app now accepts blockedImage objects as input for segmentation. Use blocked images when a volume is too large to fit into memory. By using blocked images, you can segment volumes without running out of memory.

After loading the blocked image into Volume Segmenter, you can use the same set of tools the app offers for nonblocked images to segment regions of the volume. This includes the use of automated methods, working block-by-block through each slice. Use the Blocked Image tab in Volume Segmenter to specify the block you want to work on, and to mark that block completed. Volume Segmenter automatically calculates the percent of blocks that are done. Volume Segmenter combines your work across blocks to create masks. For more information, see Work with Blocked Images Using Volume Segmenter.