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How to export imaris image to MATLAB?

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CHUFAN XIAO
CHUFAN XIAO on 23 Jun 2020
Commented: CHUFAN XIAO on 26 Jun 2020
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!

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Answers (1)

Aditya Verma
Aditya Verma on 24 Jun 2020
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

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CHUFAN XIAO
CHUFAN XIAO on 26 Jun 2020
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?

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