Import and Spatial Referencing

Read images and spatial metadata from medical imaging file formats

Medical Imaging Toolbox™ supports specialized file formats that store medical image data and metadata that describes the patient, imaging procedure, and spatial referencing. Spatial referencing specifies the location of an image in the patient coordinate system, which is defined relative to the anatomical axes of the patient. The medicalVolume and medicalImage objects automatically parse metadata to import and store image data and spatial information from DICOM, NIfTI, and NRRD files. You can also read the image and metadata separately using functions for each file format.

You can also read large microscopy images using the OpenSlide and Bio-Formats libraries by using the Medical Imaging Toolbox Interface for Whole Slide Imaging File Reader. You can install the support package from the Add-On Explorer. For more information about installing add-ons, see Get and Manage Add-Ons.

Functions

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Import and Work with Medical Images

`medicalImage`	2-D medical image pixel data and file metadata (Since R2022b)
`extractFrame`	Extract pixel data for one frame of 2-D medical image series (Since R2022b)
`montage`	Display medical image slices or frames as montage in patient coordinates (Since R2023a)
`implay`	View 2-D medical image series in Video Viewer app (Since R2023a)

Import and Work with Medical Volumes

`medicalVolume`	3-D medical image voxel data and spatial referencing information (Since R2022b)
`extractSlice`	Extract voxels and spatial details for one slice of medical volume (Since R2022b)
`montage`	Display medical image slices or frames as montage in patient coordinates (Since R2023a)
`replaceSlice`	Replace voxel values for one slice of medical volume (Since R2022b)
`resample`	Resample medical image volume in different patient coordinate system (Since R2022b)
`reposition`	Update position of medical volume in patient coordinates (Since R2025a)
`sliceCorners`	Extract coordinates of corner voxels for one slice of medical volume (Since R2022b)
`sliceLimits`	Extract X-, Y-, Z-limits for one slice of medical volume (Since R2022b)
`sliceViewer`	Browse slices of medical image volume in patient coordinates (Since R2023a)
`updateOrientation`	Update slice orientation of medical volume voxels (Since R2025a)
`volshow`	Display medical volume in patient coordinates (Since R2023a)
`write`	Write affine medical volume data to NIfTI file (Since R2022b)

Spatial Referencing for Medical Volumes

`medicalref3d`	Spatial referencing information for 3-D medical image volumes (Since R2022b)
`intrinsicToWorldMapping`	Geometric transform between intrinsic and patient coordinates of medical image volume (Since R2022b)
`contains`	Determine if affine image volume contains points specified in patient coordinate system (Since R2022b)
`intrinsicToWorld`	Map points from intrinsic coordinates to patient coordinates (Since R2022b)
`oneSliceIntrinsicToWorldMapping`	Geometric transform between intrinsic and patient coordinates of medical image volume slice (Since R2022b)
`updatePatientCoordinateSystem`	Update patient coordinate system convention (Since R2022b)
`reposition`	Update intrinsic-to-world mapping of spatial referencing object (Since R2025a)
`sliceCorners`	Extract patient coordinates of corner voxels for one slice (Since R2022b)
`worldToIntrinsic`	Map points from patient coordinates to intrinsic coordinates (Since R2022b)
`worldToSubscript`	Convert from patient coordinates to row and column subscripts (Since R2022b)

Import Whole Slide Microscopy Images

`openslideinfo`	Read whole slide image file metadata using OpenSlide library (Since R2026a)
`openslideread`	Read whole slide image data using OpenSlide library (Since R2026a)
`bioformatsinfo`	Read whole slide image file metadata using Bio-Formats library (Since R2026a)
`bioformatsread`	Read whole slide image data using Bio-Formats library (Since R2026a)

Read Image Data and Metadata from Specific File Formats

Work with DICOM Files

`dicominfo`	Read metadata from DICOM message
`dicomread`	Read DICOM image
`dicomwrite`	Write images as DICOM files
`dicomCollection`	Gather details about related series of DICOM files
`dicomFile`	Process DICOM file (Since R2023a)
`isAttribute`	Check if specified attribute is present in DICOM file (Since R2023a)
`getAttribute`	Get value of specified top level DICOM attribute (Since R2023a)
`findAttribute`	Find location and value of specified DICOM attribute (Since R2023b)
`updateAttribute`	Update value of specified DICOM attribute (Since R2023b)
`getPixelData`	Get pixel data of DICOM file (Since R2023a)
`write`	Create selectively modified copy of DICOM file (Since R2023a)
`dicomConnection`	Establish connection with PACS server (Since R2024b)
`testConnection`	Test connection with PACS server (Since R2024b)
`dicomstore`	Store DICOM files to PACS server (Since R2024b)
`dicomquery`	Query PACS server for DICOM metadata (Since R2024b)
`dicomget`	Retrieve DICOM files from PACS server (Since R2024b)

Work with NRRD Files

`isnrrd`	Check if file is valid NRRD file (Since R2022b)
`nrrdinfo`	Read metadata from NRRD file (Since R2022b)
`nrrdread`	Read NRRD image (Since R2022b)

Work with NIfTI Files

`niftiinfo`	Read metadata from NIfTI file
`niftiread`	Read NIfTI image
`niftiwrite`	Write volume to file using NIfTI format

Work with Analyze 7.5 Files

`analyze75info`	Read metadata from header file of Analyze 7.5 data set
`analyze75read`	Read image data from image file of Analyze 7.5 data set

Work with Interfile Files

`interfileinfo`	Read metadata from Interfile file
`interfileread`	Read images in Interfile format

Topics

Medical Image Coordinate Systems
Learn how image locations are defined in the intrinsic and patient coordinate systems.
Working with PACS Server for DICOM Image Retrieval
This example shows you how to establish a connection with a Picture Archiving and Communication System (PACS) server and retrieve DICOM images from the PACS server. (Since R2024b)
DICOM Support in Image Processing Toolbox
The Digital Imaging and Communications in Medicine (DICOM) Standard facilitates access to image data and files across medical imaging equipment.
Mayo Analyze 7.5 Files
Analyze 7.5 is a file format, developed by the Mayo Clinic, for storing MRI data.
Interfile Files
Interfile is a file format that was developed for the exchange of nuclear medicine image data.
Work with Whole Slide Images Using OpenSlide and Bio-Formats
Read metadata and images from WSI file formats using the OpenSlide and Bio-Formats libraries.

Featured Examples

Read, Process, and Write 3-D Medical Images

Import and display a medical image volume in patient coordinates, apply a smoothing filter.

Open Live Script

Read, Process, and View Ultrasound Data

Import and display a 2-D multiframe ultrasound series, and apply a denoising filter to each frame.

Open Live Script