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 ViewerView volumetric data and labeled volumetric data
Volume SegmenterSegment 3-D grayscale or RGB volumetric images

Functions

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volshowDisplay volume
labelvolshowDisplay labeled volume
sliceViewerBrowse image slices
orthosliceViewerBrowse orthogonal slices in grayscale or RGB volume
obliquesliceExtract oblique slice from 3-D volumetric data
adaptthreshAdaptive image threshold using local first-order statistics
dicomreadRead DICOM image
dicomreadVolumeConstruct 4-D volume from set of DICOM images
dicomContoursExtract ROI data from DICOM-RT structure set
imbinarizeBinarize 2-D grayscale image or 3-D volume by thresholding
niftiinfoRead metadata from NIfTI file
niftiwriteWrite volume to file using NIfTI format
niftireadRead NIfTI image
tiffreadVolumeRead volume from TIFF file
imabsdiffAbsolute difference of two images
imaddAdd two images or add constant to image
imdivideDivide one image into another or divide image by constant
immultiplyMultiply two images or multiply image by constant
imsubtractSubtract one image from another or subtract constant from image
affine3d 3-D affine geometric transformation
imcrop3Crop 3-D image
imref3dReference 3-D image to world coordinates
imregisterIntensity-based image registration
imregdemonsEstimate displacement field that aligns two 2-D or 3-D images
imresize3Resize 3-D volumetric intensity image
imrotate3Rotate 3-D volumetric grayscale image
imwarpApply geometric transformation to image
fibermetricEnhance elongated or tubular structures in image
fspecial3Create predefined 3-D filter
histeqEnhance contrast using histogram equalization
imadjustnAdjust intensity values in N-D volumetric image
imboxfilt33-D box filtering of 3-D images
imfilterN-D filtering of multidimensional images
imgaussfilt33-D Gaussian filtering of 3-D images
imhistmatchnAdjust histogram of N-D image to match histogram of reference image
imnoiseAdd noise to image
integralBoxFilter33-D box filtering of 3-D integral images
integralImage3Calculate 3-D integral image
medfilt33-D median filtering
bwareaopenRemove small objects from binary image
bwconncompFind connected components in binary image
bwmorph3Morphological operations on binary volume
bwskelReduce all objects to lines in 2-D binary image or 3-D binary volume
imbothatBottom-hat filtering
imcloseMorphologically close image
imdilateDilate image
imerodeErode image
imopenMorphologically open image
imreconstructMorphological reconstruction
imregionalmaxRegional maxima
imregionalminRegional minima
imtophatTop-hat filtering
offsetstrelMorphological offset structuring element
strelMorphological structuring element
watershedWatershed transform
activecontourSegment image into foreground and background using active contours (snakes) region growing technique
bfscoreContour matching score for image segmentation
diceSørensen-Dice similarity coefficient for image segmentation
gradientweightCalculate weights for image pixels based on image gradient
graydiffweightCalculate weights for image pixels based on grayscale intensity difference
imsegfmmBinary image segmentation using fast marching method
imsegkmeans3K-means clustering based volume segmentation
jaccardJaccard similarity coefficient for image segmentation
superpixels33-D superpixel oversegmentation of 3-D image
bwselect3Select objects in binary volume
edge3Find edges in 3-D intensity volume
imgradient3Find gradient magnitude and direction of 3-D image
imgradientxyzFind directional gradients of 3-D image
imhistHistogram of image data
regionprops3Measure properties of 3-D volumetric image regions
randomPatchExtractionDatastoreDatastore for extracting random 2-D or 3-D random patches from images or pixel label images
centerCropWindow3dCreate cuboidal center cropping window
randomCropWindow3dCreate randomized cuboidal cropping window
randomAffine3dCreate randomized 3-D affine transformation
affineOutputViewCreate output view for warping images

Topics

Create Binary Mask Using Volume Segmenter

This example shows how to segment a volume in the Volume Segmenter app.

Compute 3-D Superpixels of Input Volumetric Intensity Image

This example shows how to convert 3-D MRI data into a grayscale intensity image of superpixels.

Explore 3-D Volumetric Data with Volume Viewer App

You can view perpendicular cross-sections of 3-D volumetric data using the Volume Viewer app. Adjust the rendering to reveal structures within the volume.

Explore 3-D Labeled Volumetric Data with Volume Viewer App

You can view 3-D labeled volumetric data using the Volume Viewer app. You can view the volume and the labeled volume simultaneously and change the opacity and color map.

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

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

Segment Lungs from 3-D Chest Scan

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

Open Live Script
3-D Brain Tumor Segmentation Using Deep Learning

3-D Brain Tumor Segmentation Using Deep Learning

Train a 3-D U-Net neural network and perform semantic segmentation of brain tumors from 3-D medical images. The example shows how to train a 3-D U-Net network and also provides a pretrained network. Use of a CUDA-capable NVIDIA™ GPU with compute capability 3.0 or higher is highly recommended for 3-D semantic segmentation (requires Parallel Computing Toolbox™).

Open Live Script

Image Processing Toolbox Documentation

Support