orthosliceViewer

Browse orthogonal slices in grayscale or RGB volume

Description

An orthosliceViewer object displays volumetric image data by presenting three orthogonal views of the volume along the x, y, and z dimensions.

Use orthosliceViewer to look at individual slices in a volume. The orthosliceViewer opens, displaying the center slice in each dimension. Each view of the image stack includes a crosshair that you can use to view the different slices of the image stack. The crosshairs are linked so that if you move one, the crosshairs in the related views also move.

The orthosliceViewer object supports properties, object functions, and events that you can use to customize its appearance and functioning. The orthosliceViewer object can send notifications when certain events occur, such as the crosshair moving. For more information, see Events.

Note

By default, clicking and dragging the mouse in the slices displayed interactively changes their brightness and contrast, a technique called window/level. Dragging the mouse horizontally from left to right changes the contrast. Dragging the mouse vertically up and down changes the brightness. Holding down the Ctrl key when clicking and dragging the mouse accelerates changes. Holding down the Shift key while clicking and dragging the mouse slows the rate of change. Press these keys before clicking and dragging. To control this behavior, use the DisplayRangeInteraction property.

Creation

Description

orthosliceViewer(V) displays the volume V in a figure.

orthosliceViewer(___,Name,Value) sets properties using name-value pair arguments. You can specify multiple name-value pairs. Enclose each property name in single quotes.

Example: orthosliceViewer(V,"Colormap",cmap) creates an orthosliceViewer object and specifies the colormap used to display the volume.

s = orthosliceViewer(___) returns an orthosliceViewer object, s, with properties that can be used to control the visualization of the images. Use input arguments from any of the previous syntaxes.

Input Arguments

V — Input volume

numeric array

Input volume, specified as an m-by-n-by-p-by-c numeric array. For grayscale volumes, c is 1. For RGB volumes, c is 3. RGB volumes can only be of class uint8, uint16, single, and double.

Data Types: single | double | int8 | int16 | int32 | uint8 | uint16 | uint32

Properties

General Properties

Colormap — Colormap of image stack

gray(256) (default) | m-by-3 numeric array

Colormap of the image stack, specified as an m-by-3 numeric array with values in the range [0, 1]. The Colormap property has no effect when V is an RGB image stack.

DisplayRange — Display range of grayscale volume

[min(V(:)) max(V(:))] (default) | 2-element vector

Display range of grayscale volume, specified as a 2-element vector of the form [low high]. The value low (and any value less than low) displays as black. The value high (and any value greater than high) displays as white. Values in between are displayed as intermediate shades of gray, using the default number of gray levels. If you specify an empty matrix ([]), orthosliceViewer uses the default value. DisplayRange has no effect when you specify an RGB volume.

DisplayRangeInteraction — Interactive control of display range

"on" | "off"

Interactive control of the display range, specified as one of the following values. This property has no affect when you specify an RGB image stack. For more information about using this capability, see Events.

Value	Description
"on" (default for grayscale intensity volumes)	You can control the display range of a grayscale image stack by left-clicking the mouse and dragging it on the axes.
"off" (default for logical and RGB volumes)	No display range interactivity.

Parent — Parent of orthosliceViewer object

gcf (default) | uipanel | figure

Parent of the orthosliceViewer object, specified as a handle to a uipanel or as a figure created with either the figure or uifigure function. If you do not specify a parent, the parent of the orthosliceViewer object is gcf.

ScaleFactors — Scale factors used to rescale the volume

[1 1 1] (default) | 1-by-3 positive numeric vector

Scale factors used to rescale the volume, specified as a 1-by-3 positive numeric vector. The values in the array correspond to the scale factor applied in the x, y, and z directions.

The orthosliceViewer scales the orthogonal slice views by adjusting the display axes limits. The viewer scales the axes limits relative to each other, such that specifying a ScaleFactors value of [1 1 2] generates the same display as a value of [2 2 4]. The xyz-coordinates in the lower-right corner of the viewer reflect the crosshairs position within the scaled display axes, rather than slice numbers of the input volume V.

SliceNumbers — Indices of image slices to be displayed

center slices in each orthogonal direction | 1-by-3 nonnegative numeric array

Indices of image slices to be displayed, specified as a 1-by-3 nonnegative numeric array. orthosliceViewer displays the corresponding slices at the [x,y,z] indices in the YZ, XZ, and XY views.

Crosshair Properties

CrosshairColor — Crosshair color

[1 1 0] (default) | RGB triplet | color name | short color name

Crosshair color, specified as an RGB triplet, a color name, or a short color name.

You can specify any color using an RGB triplet. An RGB triplet is a 3-element row vector whose elements specify the intensities of the red, green, and blue components of the color. The intensities must be in the range [0, 1].

You can specify some common colors by name as a string scalar or character vector. This table lists the named color options and the equivalent RGB triplets.

Color Name	Short Name	RGB Triplet	Appearance
"red"	"r"	[1 0 0]
"green"	"g"	[0 1 0]
"blue"	"b"	[0 0 1]
"cyan"	"c"	[0 1 1]
"magenta"	"m"	[1 0 1]
"yellow"	"y"	[1 1 0]
"black"	"k"	[0 0 0]
"white"	"w"	[1 1 1]

Here are the RGB triplets for the default colors that MATLAB^® uses in many types of plots.

RGB Triplet	Appearance
[0 0.4470 0.7410]
[0.8500 0.3250 0.0980]
[0.9290 0.6940 0.1250]
[0.4940 0.1840 0.5560]
[0.4660 0.6740 0.1880]
[0.3010 0.7450 0.9330]
[0.6350 0.0780 0.1840]

Example: 'CrosshairColor','r'

Example: 'CrosshairColor','green'

Example: 'CrosshairColor',[0 0.4470 0.7410]

CrosshairEnable — State of linked crosshair objects

'on' (default) | 'inactive' | 'off'

State of the linked crosshair objects, specified as one of the values in this table.

Value	Description
'on'	Crosshair is visible and can be interacted with.
'inactive'	Crosshair is visible but cannot be interacted with
'off'	Crosshair is not visible.

CrosshairLineWidth — Width of crosshair line

number of points per screen pixel (default) | positive numeric scalar

Width of the crosshair line, specified as a positive numeric scalar, measured in points. The default value is the number of points per screen pixel.

CrosshairStripeColor — Color of crosshair stripe

'none' (default) | RGB triplet | color name | short color name

Color of the crosshair stripe, specified as an RGB triplet, a color name, a short color name, or 'none'. If you specify 'none', then the crosshair is a solid color specified by the CrosshairColor property. Otherwise, the crosshair is striped, with colors alternating between the color specified by this property and the color specified by the CrosshairColor property.

You can specify any color using an RGB triplet. An RGB triplet is a 3-element row vector whose elements specify the intensities of the red, green, and blue components of the color. The intensities must be in the range [0, 1].

You can specify some common colors by name as a string scalar or character vector. This table lists the named color options and the equivalent RGB triplets.

Color Name	Short Name	RGB Triplet	Appearance
"red"	"r"	[1 0 0]
"green"	"g"	[0 1 0]
"blue"	"b"	[0 0 1]
"cyan"	"c"	[0 1 1]
"magenta"	"m"	[1 0 1]
"yellow"	"y"	[1 1 0]
"black"	"k"	[0 0 0]
"white"	"w"	[1 1 1]

Here are the RGB triplets for the default colors that MATLAB uses in many types of plots.

RGB Triplet	Appearance
[0 0.4470 0.7410]
[0.8500 0.3250 0.0980]
[0.9290 0.6940 0.1250]
[0.4940 0.1840 0.5560]
[0.4660 0.6740 0.1880]
[0.3010 0.7450 0.9330]
[0.6350 0.0780 0.1840]

Example: 'CrosshairStripeColor','r'

Example: 'CrosshairStripeColor','green'

Example: 'CrosshairStripeColor',[0 0.4470 0.7410]

Object Functions

addlistener	Create event listener bound to event source
getAxesHandles	Get handles to axes in Orthoslice Viewer

Examples

View MRI Data in Orthoslice Viewer

Load an image stack into the workspace.

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

Create a custom Colormap.

cmap = parula(256);

View the MRI data in the Orthoslice Viewer.

s = orthosliceViewer(vol,'Colormap',cmap)

s = 
  orthosliceViewer with properties:

               SliceNumbers: [121 121 78]
             CrosshairColor: [1 1 0]
         CrosshairLineWidth: 1
       CrosshairStripeColor: 'none'
            CrosshairEnable: 'on'
                     Parent: [1×1 Panel]
                   Colormap: [256×3 double]
               DisplayRange: [0 2239]
               ScaleFactors: [1 1 1]
    DisplayRangeInteraction: 'on'

Create GIF of MRI Data Slices using Orthoslice Viewer

Load MRI data and view it in the Orthoslice Viewer.

load(fullfile(toolboxdir('images'),'imdata','BrainMRILabeled','images','vol_001.mat'));
s = orthosliceViewer(vol);

Get the handle of the axes that contains the slice.

[hXYAxes, hYZAxes, hXZAxes] = getAxesHandles(s);

Turn off crosshair for better visibility.

set(s,'CrosshairEnable','off');

Specify the name of the GIF file.

filename = 'animatedYZSlice.gif';

Create an array of slice numbers in the required direction. Consider the YZ direction.

sliceNums = 1:240;

Loop through and create an image at the specified slice position.

for idx = sliceNums
    % Update X slice number to get YZ Slice.
    s.SliceNumbers(1) = idx;
  
    % Use getframe to capture image.
    I = getframe(hYZAxes);
    [indI,cm] = rgb2ind(I.cdata,256);
  
    % Write frame to the GIF File.
    if idx == 1
        imwrite(indI,cm,filename,'gif','Loopcount',inf,'DelayTime',0.05);
    else
        imwrite(indI,cm,filename,'gif','WriteMode','append','DelayTime',0.05);
    end
end

View the animated GIF.

Set Up Listener for Orthoslice Viewer Crosshair Events

Load a stack of images.

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

Create a custom colormap for viewing slices.

cmap = parula(256);

View the image stack in the Orthoslice Viewer.

os = orthosliceViewer(vol,'Colormap',cmap);

Set up listeners for the two Orthoslice Viewer crosshair moving events. When you move the crosshair, the Orthoslice Viewer sends notifications of these events and executes the callback function you specify.

addlistener(os,'CrosshairMoving',@allevents);
addlistener(os,'CrosshairMoved',@allevents);

The allevents callback function displays the name of each event with the previous position and the current position of the crosshair.

function allevents(src,evt)
evname = evt.EventName;
    switch(evname)
        case{'CrosshairMoved'}
            disp(['Crosshair moved previous position: ' mat2str(evt.PreviousPosition)]);
            disp(['Crosshair moved current position: ' mat2str(evt.CurrentPosition)]);
        case{'CrosshairMoving'}
            disp(['Crosshair moving previous position: ' mat2str(evt.PreviousPosition)]);
            disp(['Crosshair moving current position: ' mat2str(evt.CurrentPosition)]);
    end
 end

More About

Events

The orthosliceViewer object can send notifications when the crosshair moves. To receive these notifications, use the addListener function to set up a listener. To set up a listener, specify the name of the event, for example, 'CrosshairMoving', and the function you want executed when the event occurs. The following table lists events supported by the orthosliceViewer object. For an example, see Set Up Listener for Orthoslice Viewer Crosshair Events.

Event Name	Trigger	Event Data	Event Attributes
CrosshairMoving	The crosshair in the orthosliceViewer is moving.	images.stack.browser.CrosshairMovingEventData	NotifyAccess: private ListenAccess: public
CrosshairMoved	The crosshair in the orthosliceViewer has stopped moving.	images.stack.browser.CrosshairMovingEventData	NotifyAccess: private ListenAccess: public

Version History

Introduced in R2019b