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3-D Volumetric Image Processing

Filter, segment, and perform other image processing operations on 3-D volumetric data

Perform pixel operations, local filtering, morphology, and other image processing, on 3-D data sets.

Apps

Volume Viewer	View volumetric data and labeled volumetric data
Volume Segmenter	Segment 3-D grayscale or RGB volumetric images (Since R2020b)

Functions

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Volume Display

`volshow`	Display volume
`sliceViewer`	Browse image slices (Since R2019b)
`orthosliceViewer`	Browse orthogonal slices in grayscale or RGB volume (Since R2019b)
`obliqueslice`	Extract oblique slice from 3-D volumetric data (Since R2020a)
`viewer3d`	Create 3-D viewer object (Since R2022b)
`Surface`	Display surface in 3-D viewer (Since R2022b)
`Light`	Light source (Since R2023b)

Image Import and Conversion

`adaptthresh`	Adaptive image threshold using local first-order statistics
`blockedImage`	Big or multiresolution image made from discrete blocks (Since R2021a)
`dicomread`	Read DICOM image
`dicomreadVolume`	Create 4-D volume from set of DICOM images
`dicomContours`	Extract ROI data from DICOM-RT structure set (Since R2020a)
`imbinarize`	Binarize 2-D grayscale image or 3-D volume by thresholding
`niftiinfo`	Read metadata from NIfTI file
`niftiwrite`	Write volume to file using NIfTI format
`niftiread`	Read NIfTI image
`tiffreadVolume`	Read volume or time series image stack from TIFF file (Since R2020b)

Image Arithmetic

`imabsdiff`	Absolute difference of two images
`imadd`	Add two images or add constant to image
`imdivide`	Divide one image into another or divide image by constant
`immultiply`	Multiply two images or multiply image by constant
`imsubtract`	Subtract one image from another or subtract constant from image

Geometric Transformations and Image Registration

`affineOutputView`	Create output view for warping images (Since R2019b)
`affinetform3d`	3-D affine geometric transformation (Since R2022b)
`imcrop3`	Crop 3-D image (Since R2019b)
`imref3d`	Reference 3-D image to world coordinates
`imregister`	Intensity-based image registration
`imregdemons`	Estimate displacement field that aligns two 2-D or 3-D images
`imresize3`	Resize 3-D volumetric intensity image
`imrotate3`	Rotate 3-D volumetric grayscale image
`imwarp`	Apply geometric transformation to image
`rigidtform3d`	3-D rigid geometric transformation (Since R2022b)
`simtform3d`	3-D similarity geometric transformation (Since R2022b)
`transltform3d`	3-D translation geometric transformation (Since R2022b)
`transformPointsForward`	Apply forward geometric transformation
`transformPointsInverse`	Apply inverse geometric transformation

Image Filtering and Enhancement

`fibermetric`	Enhance elongated or tubular structures in image using Frangi vesselness filter
`fspecial3`	Create predefined 3-D filter
`histeq`	Enhance contrast using histogram equalization
`imadjustn`	Adjust intensity values in N-D volumetric image
`imboxfilt3`	3-D box filtering of 3-D images
`imfilter`	N-D filtering of multidimensional images
`imgaussfilt3`	3-D Gaussian filtering of 3-D images
`imhistmatchn`	Adjust histogram of N-D image to match histogram of reference image
`imnoise`	Add noise to image
`integralBoxFilter3`	3-D box filtering of 3-D integral images
`integralImage3`	Calculate 3-D integral image
`medfilt3`	3-D median filtering

Morphology

`bwareaopen`	Remove small objects from binary image
`bwconncomp`	Find and count connected components in binary image
`bwmorph3`	Morphological operations on binary volume
`bwskel`	Reduce all objects to lines in 2-D binary image or 3-D binary volume
`imbothat`	Bottom-hat filtering
`imclose`	Morphologically close image
`imdilate`	Dilate image
`imerode`	Erode image
`imopen`	Morphologically open image
`imreconstruct`	Morphological reconstruction
`imregionalmax`	Regional maxima
`imregionalmin`	Regional minima
`imtophat`	Top-hat filtering
`offsetstrel`	Morphological offset structuring element
`strel`	Morphological structuring element
`watershed`	Watershed transform

Image Segmentation

`activecontour`	Segment image into foreground and background using active contours (snakes) region growing technique
`bfscore`	Contour matching score for image segmentation
`dice`	Sørensen-Dice similarity coefficient for image segmentation
`gradientweight`	Calculate weights for image pixels based on image gradient
`graydiffweight`	Calculate weights for image pixels based on grayscale intensity difference
`imsegfmm`	Binary image segmentation using fast marching method
`imsegkmeans3`	K-means clustering based volume segmentation
`jaccard`	Jaccard similarity coefficient for image segmentation
`superpixels3`	3-D superpixel oversegmentation of 3-D image

Image Analysis

`bwselect3`	Select objects in binary volume
`edge3`	Find edges in 3-D grayscale volume
`imgradient3`	Find gradient magnitude and direction of 3-D image
`imgradientxyz`	Find directional gradients of 3-D image
`imhist`	Histogram of image data
`regionprops3`	Measure properties of 3-D volumetric image regions

Image Augmentation for Deep Learning

`blockedImageDatastore`	Datastore for use with blocks from `blockedImage` objects (Since R2021a)
`centerCropWindow3d`	Create cuboidal center cropping window (Since R2019b)
`randomCropWindow3d`	Create randomized cuboidal cropping window (Since R2019b)
`randomAffine3d`	Create randomized 3-D affine transformation (Since R2019b)
`randomPatchExtractionDatastore`	Datastore for extracting random 2-D or 3-D random patches from images or pixel label images

Topics

Display Volumes

Explore 3-D Volumetric Data with Volume Viewer App
View perpendicular cross-sections of 3-D volumetric data and adjust the rendering to reveal structures within the volume.
Explore 3-D Labeled Volumetric Data with Volume Viewer
View 3-D labeled volumetric data, and adjust the visualization such as the opacity and colormap, using the Volume Viewer app.
Display Interior Labels by Clipping Volume Planes
Interactively clip a quadrant of a volumetric image to expose a surface within the volume.
Display Interior Labels by Adjusting Volume Overlay Properties
Adjust the transparency of labeled volumetric data and the rendering style to reveal labels on the interior of the volume.
Display Volume Using Cinematic Rendering
View volumes with photorealistic lighting and shadows using cinematic rendering.
Display Translucent Volume with Advanced Light Scattering
This example shows how to display translucent volumes using realistic light scattering.
Remove Objects from Volume Display Using 3-D Scissors
This example shows how to interactively remove unwanted regions in a 3-D display, such as a patient bed in a CT scan, by using 3-D scissors.
Display Large 3-D Images Using Blocked Volume Visualization
This example shows how to display large 3-D image volumes using a blockedImage object and the volshow function.
Explore Slices from 3-D Image Volume with Anisotropic Voxel Spacing
Display slices from a 3-D image volume with voxel spacing that varies between spatial dimensions.

Process and Analyze Volumes

Create Binary Mask Using Volume Segmenter
This example shows how to segment a volume in the Volume Segmenter app.
Work with Blocked Images Using Volume Segmenter
Segment a volumetric image that could be too large to fit into memory by converting the volume to a blocked image.
Compute 3-D Superpixels of Input Volumetric Intensity Image
Convert 3-D MRI data into a grayscale intensity image of superpixels.
Preprocess Volumes for Deep Learning (Deep Learning Toolbox)
Read and preprocess volumetric image and label data for 3-D deep learning.

Featured Examples

Register Multimodal 3-D Medical Images

Align two volumetric images using automatic intensity-based image registration.

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Segment Lungs from 3-D Chest Scan

Perform a 3-D segmentation using active contours (snakes) and view the results using the Volume Viewer app.

Open Live Script

3-D Brain Tumor Segmentation Using Deep Learning

Perform semantic segmentation of brain tumors from 3-D medical images.

Open Live Script