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copytoImagePlus

copytoImagePlus is a MATLAB function. Assuming you have communication between ImageJ and MATLAB via ImageJ-MATLAB, copytoImagePlus allows you to turn a MATLAB array into ImageJ1 ImagePlus object (a hyperstack).

  • This function is similar to ijmshow, but unlike ijmshow, copytoImagePlus does not require net.imagej.matlab.ImageJMATLABCommands object IJM in base MATLAB Workspace. Therefore, copytoImagePlus can be used both when you launch an instance of ImageJ from within MATLAB (like ijmshow) and when you launch an instance of MATLAB from ImageJ.

  • copytoImg and copytoImgPlus are bundled with Fiji and work in a similar way but using ImageJ2 API and objects, instead of ImageJ1 ImagePlus object.

Syntax

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

Optional Parameter/Value pairs

'NewName'        char row vector | 'new' (default)
	               The window title of the new image in ImageJ

'FrameInterval'  scalar
                 Time frame sampling interval in seconds

MATLAB code examples

Launching ImageJ form within MATLAB

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

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

Image004.png

>> imp = copytoImagePlus(I,'XYC')
>> imp.show();

Image005.png

5D hyperstack

Open a sample hyperstack image in ImageJ.

>> imp = ij.IJ.openImage("http://imagej.nih.gov/ij/images/Spindly-GFP.zip");
>> imp.show();
>> imp.setZ(3);

Image006.png

Retrieve the array of image data to MATLAB. Note that X and Y axes are flipped over.

>> IJM.getDatasetAs('I');
>> size(I) 
ans =
   171   196     2     5    51

Data is in double type, although they are better in uint16 type.

>> class(I)
ans =
    'double'

>> I16 = uint16(I); % convert to uint16
>> imp2 = copytoImagePlus(I16,'XYCZT') % flip the X and Y axes back 
>> imp2.show()

Image007.png

Launching MATLAB from ImageJ

Execute a MATLAB script from Fiji's Macro Editor. File > New > Script and select Language > MATLAB

addpath('scripts')
Miji(false) % add Fiji to Jave class path
I = imread('corn.tif',3);
imp = copytoImagePlus(I) % the function needs to be in MATLAB search path
imp.show();

Image008.png

copytoImagePlus_test

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

Issues

  • 12bit data is not well supported or tested
  • FrameInterval may not be properly set, because File Info... does not show the Frame Interval.
  • 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.

[email protected]

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