How to export imaris image to MATLAB?

I'm trying to export 3D images from imaris to MATLAB，and get the matrix in MATLAB. Do the plug in imaris can help? Or can I just read .ims format in MATLAB? Hoping to get answers soon. Thanks!

Answer 1

[Aditya Verma]

Hi!

While MATLAB doesn't support imaris file format out of the box (which can be check from here), you can use the implementation provided in the File Exchange by Peter Beemiller: https://www.mathworks.com/matlabcentral/fileexchange/56534-peterbeemiller-imarisreader.

The instructions to use it are specified in the github repository: https://github.com/PeterBeemiller/ImarisReader

Thanks

[CHUFAN XIAO]

Thanks for your help! I've tried but there's running some bugs like

Error using hdf5lib2
The HDF5 library encountered an error and produced the following stack trace information: 
  H5Gclose    not a group
warning H5G.close (line 16)
H5ML.hdf5lib2('H5Gclose', id);
warning SurpassObjectReader/delete (line 117)
            H5G.close(obj.GIDS8)

warning SpotsReader (line 16)
        function obj = SpotsReader(GID)

warning ImarisReader (line 137)
                        cSpots = SpotsReader(cGID);

I don't know how to do with it. And "hdf5lib2" cannot find files, so is it the problem of hdf5?

[Shubham]

@CHUFAN XIAO Did you solve it? I am also getting the same error.