Display 2-D blockedImage
object
A bigimageshow
object displays data from a
blockedImage
object. The bigimageshow
object
progressively loads image data based on image extents and screen resolution.
bigimageshow(
displays the 2-D blocked
image bim
)bim
.
For categorical data, bigimageshow
sets the axis colormap to
parula
. For numeric data, gray
is the default
colormap.
b = bigimageshow(___)
returns the
bigimageshow
object b
. Use b
to
modify the display settings after you display the blocked image.
sets initial display properties using name-value
pairs. You can specify multiple name-value pairs. Enclose each argument or property name
in quotes.b
= bigimageshow(___,Name,Value
)
For example,
bigimageshow(bim,'GridVisible','on','GridLineStyle',':')
displays the
blocked image, bim
, and overlays dotted grid lines.
bim
— Blocked imageblockedImage
objectBlocked image, specified as a blockedImage
object.
hax
— Parent axesParent axes of bigimageshow
object, specified as an axes
object.
Parent
— Parent axes of bigimageshow
objectgca
(default) | axes
objectParent axes of the bigimageshow
object, specified as an
axes
object. If you do not specify a parent,
bigimageshow
uses the handle to the current figure,
gca
. If a figure does not exist, bigimageshow
creates a new figure.
CData
— 2-D blockedImage
object to displayblockedImage
object2-D blockedImage
object to display, specified as a blockedImage
object.
CDataMapping
— Color data mapping method'direct'
(default) | 'scaled'
Color data mapping method, specified as 'direct'
or
'scaled'
. Use this property to control the mapping of color data
values in CData
into the colormap. CData
must be
a vector or a matrix defining indexed colors. This property has no effect if
CData
is a 3-D array defining RGB colors.
The methods have these effects:
'direct'
— Interpret the values as indices into the
current colormap. Values with a decimal portion are fixed to the nearest lower
integer.
If the values are of type double
or
single
, values of 1
or less map to
the first color in the colormap. Values equal to or greater than the length
of the colormap map to the last color in the colormap.
If the values are of type uint8
,
uint16
, uint32
,
uint64
, int8
,
int16
, int32
, or
int64
, values of 0
or less map to
the first color in the colormap. Values equal to or greater than the length
of the colormap map to the last color in the colormap (or up to the range
limits of the type).
If the values are of type logical
, values of
0
map to the first color in the colormap and values of
1
map to the second color in the colormap.
'scaled'
— Scale the values to range between the
minimum and maximum color limits. The CLim
property of the axes
contains the color limits.
AlphaData
— Transparency data1
(default) | numeric scalar |
blockedImage
objectTransparency data, specified in one of these forms:
Numeric scalar — Use a consistent transparency across the entire image.
2-D blockedImage
object — Transparency data must
have the same rows and columns extent as the CData
2-D
blockedImage
object. The blocked image can have multiple
resolution levels, in which case, bigimageshow
selects the
level closest to the current ResolutionLevel
for
display.
The AlphaDataMapping
property controls how MATLAB® interprets the alpha data transparency values.
Example: 0.5
Data Types: single
| double
| int8
| int16
| int32
| int64
| uint8
| uint16
| uint32
| uint64
| logical
AlphaDataMapping
— Interpretation of AlphaData
values 'none'
(default) | 'scaled'
| 'direct'
Interpretation of AlphaData
values, specified as one of these
values:
'none'
— Interpret the values as transparency values.
A value of 1 or greater is completely opaque, a value of 0 or less is completely
transparent, and a value between 0 and 1 is semitransparent.
'scaled'
— Map the values into the figure’s alphamap.
The minimum and maximum alpha limits of the axes determine the alpha data values
that map to the first and last elements in the alphamap, respectively. For example,
if the alpha limits are [3 5]
, alpha data values less than or
equal to 3
map to the first element in the alphamap. Alpha data
values greater than or equal to 5
map to the last element in the
alphamap. The ALim
property of the axes contains
the alpha limits. The Alphamap
property of the
figure contains the alphamap.
'direct'
— Interpret the values as indices into the
figure’s alphamap. Values with a decimal portion are fixed to the nearest lower
integer:
If the values are of type double
or
single
, values of 1 or less map to the first element in the
alphamap. Values equal to or greater than the length of the alphamap map to the
last element in the alphamap.
If the values are of type integer, then values of 0 or less map to the first
element in the alphamap. Values equal to or greater than the length of the
alphamap map to the last element in the alphamap (or up to the range limits of
the type). The integer types are uint8
,
uint16
, uint32
,
uint64
, int8
, int16
,
int32
, and int64
.
If the values are of type logical
, values of
0
map to the first element in the alphamap and values of
1
map to the second element in the alphamap.
ResolutionLevel
— Resolution level'fine'
| 'coarse'
Resolution level of the 2-D blockedImage
object to display,
specified as a positive integer that identifies a resolution level of the 2-D
blockedImage
object in the CData property. Resolution level can
also be specified as 'fine'
or 'coarse'
corresponding to these two limits. The default value is computed based on available
screen space and resolution.
ResolutionLevelMode
— Selection mode for resolution level'auto'
(default) | 'manual'
Selection mode for resolution level, specified as one of these values:
'auto'
— Automatically select resolution level based
on parent axes and available screen size.
'manual'
— Manually specify resolution level by
setting the ResolutionLevel
property.
GridVisible
— Grid visibility'off'
(default) | 'on'
Grid visibility, specified as 'off'
or 'on'
.
bigimageshow
spaces the grid in world units to include as many
pixels as specified by CData
.BlockSize
at the
current GridResolutionLevel
.
GridLevel
— Resolution level of blocked image at which to show grid'fine'
| 'coarse'
Resolution level of blocked image at which to show grid, specified as one of these values:
positive integer — Display the grid specified as a numeric scalar that
identifies a resolution level of the 2-D blockedImage
object in
CData property. Value is between 1 and the value of the
NumLevels
property of the blocked image in the
bigimageshow
CData
property.
'fine'
— Display the grid at the finest resolution
level.
'coarse'
— Display the grid at the coarsest
resolution level.
By default, GridLevel
has the same value as
ResolutionLevel
property.
GridLevelMode
— Selection mode for grid level'auto'
(default) | 'manual'
Selection mode for grid level, specified as one of these values:
'auto'
— Select the grid resolution level to match
the image data resolution level ResolutionLevel
.
'manual'
— Manually specify the grid resolution
level by setting the GridLevel
property.
GridColor
— Grid line color'blue'
(default) | RGB triplet | hexadecimal color code | color name | short color nameGrid line color, specified as an RGB triplet, a hexadecimal color code, a color
name, or a short color name. To display the grid lines, set the
GridVisible
property to 'on'
.
For a custom color, specify an RGB triplet or a hexadecimal color code.
An RGB triplet is a three-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]
; for example, [0.4
0.6 0.7]
.
A hexadecimal color code is a character vector or a string
scalar that starts with a hash symbol (#
)
followed by three or six hexadecimal digits, which can range
from 0
to F
. The
values are not case sensitive. Thus, the color codes
'#FF8800'
,
'#ff8800'
,
'#F80'
, and
'#f80'
are equivalent.
Alternatively, you can specify some common colors by name. This table lists the named color options, the equivalent RGB triplets, and hexadecimal color codes.
Color Name | Short Name | RGB Triplet | Hexadecimal Color Code | Appearance |
---|---|---|---|---|
'red' | 'r' | [1 0 0] | '#FF0000' | |
'green' | 'g' | [0 1 0] | '#00FF00' | |
'blue' | 'b' | [0 0 1] | '#0000FF' | |
'cyan' | 'c' | [0 1 1] | '#00FFFF' | |
'magenta' | 'm' | [1 0 1] | '#FF00FF' | |
'yellow' | 'y' | [1 1 0] | '#FFFF00' | |
'black' | 'k' | [0 0 0] | '#000000' | |
'white' | 'w' | [1 1 1] | '#FFFFFF' |
Here are the RGB triplets and hexadecimal color codes for the default colors MATLAB uses in many types of plots.
RGB Triplet | Hexadecimal Color Code | Appearance |
---|---|---|
[0 0.4470 0.7410] | '#0072BD' | |
[0.8500 0.3250 0.0980] | '#D95319' | |
[0.9290 0.6940 0.1250] | '#EDB120' | |
[0.4940 0.1840 0.5560] | '#7E2F8E' | |
[0.4660 0.6740 0.1880] | '#77AC30' | |
[0.3010 0.7450 0.9330] | '#4DBEEE' | |
[0.6350 0.0780 0.1840] | '#A2142F' |
Example: b.GridColor = [1 0 0]
Example: b.GridColor = 'r'
Example: b.GridColor = 'red'
Example: b.GridColor = '#FF0000'
GridAlpha
— Grid line transparency0.8
(default) | value in the range [0,1]
Grid line transparency, specified as a value in the range [0, 1]. A value of
1
means completely opaque and a value of 0
means
completely transparent. To display the grid lines, set the
GridVisible
property to 'on'
.
Example: b.GridAlpha = 0.5
GridLineWidth
— Grid line width1
(default) | positive numeric valueGrid line width, specified as a positive numeric value, measured in points. To
display the grid lines, set the GridVisible
property to
'on'
.
GridLineStyle
— Grid line style'-'
(default) | '--'
| ':'
| '-.'
Grid line style, specified as one of the line styles in this table.
Line Style | Description | Resulting Line |
---|---|---|
'-' | Solid line |
|
'--' | Dashed line |
|
':' | Dotted line |
|
'-.' | Dash-dot line |
|
To display the grid lines, set the GridVisible
property to 'on'
.
Example: b.GridLineStyle = '--'
Interpolation
— Interpolation method'linear'
(default) | 'nearest'
Interpolation method used to resample pixels, specified as
'linear'
for bilinear interpolation, or
'nearest'
for nearest neighbor interpolation.
For categorical data, bigimageshow
supports only nearest neighbor
interpolation. For logical data, the default value is
'nearest'
.
On Windows systems with a software version of OpenGL, the only supported
interpolation option is 'nearest'
.
Visible
— Control image visibility'on'
(default) | 'off'
Control image visibility, specified as one of these values:
'on'
— Display the bigimageshow
object.
'off'
— Hide the object without deleting it. You
still can access the properties of an invisible object.
Create a blocked image using a modified version of the image "tumor_091.tif" from the CAMELYON16 data set. The original image is a training image of a lymph node containing tumor tissue. The original image has eight resolution levels, and the finest level has resolution 53760-by-61440. The modified image has only three coarse resolution levels. The spatial referencing of the modified image has been adjusted to enforce a consistent aspect ratio and to register features at each level.
bim = blockedImage('tumor_091R.tif');
Display the blocked image.
h = bigimageshow(bim);
Zoom in on a region in the image.
xlim([2100, 2600]) ylim([1800 2300])
To view the image at various resolution levels, specify a new value for the ResolutionLevel property. The axis limits remain the same, but bigimageshow
ensures that the images from other levels are correctly sized. When you set ResolutionLevel
, the ResolutionLevelMode
value changes to 'manual'
automatically.
h.ResolutionLevel = 3; pause(1); h.ResolutionLevel = 2; pause(1); h.ResolutionLevel = 1; pause(1);
Create a blocked image from a sample image included with the toolbox.
bim = blockedImage('tumor_091R.tif','BlockSize', [128 128]);
Display the blocked image with bigimageshow, specifying that you want the grid to be visible, on the finest resolution level. Also specify the color, width, and transparency.
h = bigimageshow(bim,... 'GridVisible','on', 'GridLevel', 1,... 'GridLineWidth', 2, 'GridColor','k','GridAlpha',0.3);
bim = blockedImage('tumor_091R.tif');
Create a coarse mask.
bmask = apply(bim, @(im)im2gray(im.Data)<120, "Level", 3);
Overlay the mask as an alpha layer.
ha1 = subplot(1,2,1); h = bigimageshow(bim); h.AlphaData = bmask; h.AlphaDataMapping = 'direct'; alphamap([0.4 1]) h.Parent.Color = 'r';
Independently visualize the mask.
ha2 = subplot(1,2,2); bigimageshow(bmask); linkaxes([ha1, ha2]);
Create a blocked image using a modified version of image "tumor_091.tif" from the CAMELYON16 data set. The original image is a training image of a lymph node containing tumor tissue. The original image has eight resolution levels, and the finest level has resolution 53760-by-61440. The modified image has only three coarse resolution levels. The spatial referencing of the modified image has been adjusted to enforce a consistent aspect ratio and to register features at each level.
bim = blockedImage('tumor_091R.tif');
Create a mask using the coarsest resolution level of the blocked image.
bmask = apply(bim, @(im)im2gray(im.Data)<120, "Level", 3);
Display the blocked image with the mask.
h = bigimageshow(bim); showmask(h, bmask);
Experiment with different inclusion thresholds and block sizes to get a better fit of the mask over the stained area. By default, the inclusion threshold is 0.5.
showmask(h, bmask, 'InclusionThreshold', 0.2); showmask(h, bmask, 'InclusionThreshold', 0); showmask(h, bmask, 'InclusionThreshold', 0.06);
Change the block size to get a tighter fit.
showmask(h, bmask, 'InclusionThreshold', 0.06, 'BlockSize', [256 256]); showmask(h, bmask, 'InclusionThreshold', 0.14, 'BlockSize', [256 256]);
When you are satisfied with the mask, use it to segment the lymph node.
bls = selectBlockLocations(bim,'BlockSize', [256 256],... 'Mask', bmask, 'InclusionThreshold', 0.14); bregion = apply(bim, @(im)im.Data, 'BlockLocationSet', bls); figure bigimageshow(bregion);
Create a blocked image using a modified version of the image "tumor_091.tif" from the CAMELYON16 data set. The original image is a training image of a lymph node containing tumor tissue. The original image has eight resolution levels, and the finest level has resolution 53760-by-61440. The modified image has only three coarse resolution levels. The spatial referencing of the modified image has been adjusted to enforce a consistent aspect ratio and to register features at each level.
bim = blockedImage('tumor_091R.tif');
Create a label image at a coarse level.
cim = gather(bim); cgim = im2gray(cim); numClasses = 4; thresh = multithresh(cgim, numClasses-1); labels = imquantize(cgim, thresh); imagesc(labels) axis square title('Coarse label image');
Convert the labels image back to a blockedImage, using the same spatial referencing as the original image.
blabels = blockedImage(labels,'WorldStart',bim.WorldStart(3,1:2),... 'WorldEnd', bim.WorldEnd(3,1:2));
Display the original blockedImage.
figure hB = bigimageshow(bim);
Overlay the labels image on the original blocked image in a new axis. Use interpolation to ensure labels have crisp boundaries and the AlphaData property to control the transparency of the label layer. Turn off the axes visibility so the underlying image shows through. Specify unique colors for each label.
hLa = axes; hL = bigimageshow(blabels, 'Parent', hLa); hL.Interpolation = 'nearest'; hL.AlphaData = 0.3; hLa.Visible = 'off'; hLa.CLim = [1 numClasses]; colormap(hLa,hsv(numClasses));
[1] Bejnordi, Babak Ehteshami, Mitko Veta, Paul Johannes van Diest, Bram van Ginneken, Nico Karssemeijer, Geert Litjens, Jeroen A. W. M. van der Laak, et al. “Diagnostic Assessment of Deep Learning Algorithms for Detection of Lymph Node Metastases in Women With Breast Cancer.” JAMA 318, no. 22 (December 12, 2017): 2199–2210. https://doi.org/10.1001/jama.2017.14585.
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