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version (1.07 MB) by Peter Beemiller
Read image and segmentation object data stored in ims files.

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Updated 29 May 2016

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ImarisReader is a set of classes for reading the data stored in ims files. ImarisReader can read the primary image data, as well as the data for segmented objects: Cells, Filaments, Spots and Surfaces.

Cite As

Peter Beemiller (2020). PeterBeemiller/ImarisReader (, GitHub. Retrieved .

Comments and Ratings (4)

Caleb Stoltzfus

Jonny Cheng

I have some problem with reading the ims format file from Lavision Davis 10. I tried with this code, but it doesn't work. The full error :
Warning: The following error was caught while executing 'ImarisReader' class destructor:
Error using hdf5lib2
The HDF5 library encountered an error and produced the following stack trace information:

H5Fclose not a file ID

Error in H5F.close (line 16)
H5ML.hdf5lib2('H5Fclose', id);

Error in ImarisReader/delete (line 180)

Error in ImarisReader (line 36)
function obj = ImarisReader(imsFile)

Error in ReadIMS (line 12)
imsObj = ImarisReader(xPath);
> In ImarisReader (line 36)
In ReadIMS (line 12)
Error using hdf5lib2
The filename specified was either not found on the MATLAB path or it contains unsupported characters.

Error in (line 60)
file_id = H5ML.hdf5lib2('H5Fopen', filename, flags, fapl);

Error in ImarisReader (line 53)
obj.FID =, ...

Error in ReadIMS (line 12)
imsObj = ImarisReader(xPath);

Thanks in advance. Please let me know if you have any idea about that and send me email:

Best Regards,

Vassilis Papaioannou

Thank you very much! Apart from solving my problem, you also taught me about HDF5 and what I need to do in case that I want something else.

Jon Wieser

MATLAB Release Compatibility
Created with R2009b
Compatible with any release
Platform Compatibility
Windows macOS Linux

Inspired: CytoMAP

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