NOTE: `ijmshow` is not recommended any more because of its dependency on `IJM`. Consider using `copytoImagePlus` instead.

ijmshow

A MATLAB function. A wrapper of net.imagej.matlab.ImageJMATLABCommands.show() (or IJM.show()) to support opening a MATLAB array as 5D hyperstack in ImageJ

copytoImagePlus does the same job without requiring the Java object IJM
copytoImg and copytoImgPlus are bundled with Fiji and work in a similar way but using ImageJ2 API and objects.

Opening an image in ImageJ from within MATLAB

https://imagej.net/MATLAB_Scripting#Running_ImageJ_within_MATLAB

ImageJ-MATLAB as part of Fiji installation allows us to open an ImageJ instance from within MATLAB and we can transfer an array of data using IJM.show('name') (from MATLAB to ImageJ) and IJM.getDataset() and IJM.getDatasetAs('name')(from ImageJ to MATLAB).

Although these are useful, the current version of ImageJ-MATLAB's IJM.show('name') has the following limitations:

IJM.show('name') will flip over the X and Y axes of array between MATLAB and ImageJ
IJM.show('name') cannot handle multidimensional (>2D) images properly; All the third and higher dimensions are piled as the fifth dimension of a 5D hyperstack. This is a real pain if you are handling more than one channel, one slice, or one frame of images, as is often the case.
No matter what data type the original MATLAB array is, it is shown in ImageJ as int32 data type. Conversion of the datatype to bytes (uint8) or short ( uint16) in ImageJ can involve scaling of numeric values, resulting in unexpected changes of pixel values, unless carefully avoided.

ijmshow is a wrapper of net.imagej.matlab.ImageJMATLABCommands.show() (or IJM.show()) and offers solutions to the above issues. Until someone can fix the IJM.show() properly some day, ijmshow will be useful for interaction between MATLAB and ImageJ.

X and Y axes can be corrected (eg, using YXCZT by default) or left as default behaviour (eg. XYCZT)
Thedimorder input argument can specify the dimensions for channels (C), slices (Z), and frames (T) (by default YXCZT)
Numeric values of pixel data are maintained while the image type is converted to 16 bit or 8 bit depending on the data type of the original MATLAB array.
You can access IJM in the base Workspace from within a MATLAN function. You can open a MATLAB array in a function with ImageJ.

Syntax

imp = ijmshow(I)
imp = ijmshow(I,dimorder)
imp = ijmshow(____,'Param',value)

% Param can be 'NewName' or 'FrameInterval'

MATLAB code examples

RGB image

>> addpath '/Applications/Fiji.app/scripts'
>> ImageJ

>> I = imread('peppers.png') % the size of I is 384 x 512 x 3 in MATLAB

>> IJM.show('I')

This will end up X and Y flipped over, and channels are not recognized as channels (instead, it is interpreted as time frames).

>> imp = ijmshow(I)
>> imp = ijmshow(I,'YXC') % equivalent as above
>> imp = ijmshow(I,'YXCZT') % equivalent as above

>> imp = ijmshow(I,'XYC') % X an Y flipped over

5D hyperstack

>> imp = IJ.openImage("http://imagej.nih.gov/ij/images/Spindly-GFP.zip");
>> imp.show();
>> imp

imp =
img["mitosis.tif" (-1132), 16-bit, 171x196x2x5x51]

The image has 171 X, 196 Y, 2 channels (C), 5 slices (Z), and 51 frames (T).

>> IJM.getDatasetAs('I');

>> size(I)

ans =
   171   196     2     5    51

Note that X and Y have already been flipped over by IJM.getDatasetAs('I')

>> class(I)

ans =
    'double'

Note that the data type is double rather than uint16.

>> I16 = uint16(I); % convert to uint16
>> IJM.show('I16') 
>> imp2 = ij.IJ.getImage()

imp2 =
img["" (-1136), 32-bit, 171x196x1x1x510]

IJM.show() will flip X and Y again, so back to normal X and Y. However, the third to fifth dimensions of the image are all piled in the fifth dimension as 510 time frames (T). The image is in 32 bit type.

>> imp3 = ijmshow(I,'XYCZT')

imp3 =
img["" (-1180), 16-bit, 171x196x2x5x51]

'XYCZT' will accept the flipped over X and Y as input. Now it is shown as 2 channels (C), 5 slices (Z) and 51 frames (T) as expected. Image type is 16bit. The image looks brighter because of the difference in DisplayRange setting, but the numeric values were identical to the original.

`ijmshow_test`

This is a matlab.unittest.TestCase subclass and verify the numeric values and dimensions of the ImagePlus objects in ImageJ opened by ijmshow.

Issues

12bit data is not well supported or tested
FrameInterval may not be properly set, because File Info... does not show the Frame Interval.
Display Ranges needs to be set separately. It's possible to implement an option to automatically set Display Ranges from the min to the max of each channel. It's not clear what CompositeImage.resetDisplayRanges() does.
IJM.show(name) appear to have a problem with handling large image data.
copytoImagePlus does the same job without requiring the Java object IJM
copytoImg and copytoImgPlus are bundled with Fiji and work in a similar way but using ImageJ2 API and objects.

Contacts

Kouichi C. Nakamura, Ph.D.

kouichi.c.nakamura@gmail.com

MRC Brain Network Dynamics Unit, Department of Pharmacology, University of Oxford

kouichi-c-nakamura/ijmshow

NOTE: ijmshow is not recommended any more because of its dependency on IJM. Consider using copytoImagePlus instead.