Help installing Bio-Formats

I want to use Bio-Formats to directly work with .nd2 files. As the website instructs https://docs.openmicroscopy.org/bio-formats/5.8.2/users/matlab/index.html, I downloaded and unzipped the folder. I then added the .m files to my Matlab path, including the .jar file 'bioformats_package.jar'. However, I can't use any of the functions due to this error:

 Error using bfopen (line 100)
 Missing Bio-Formats library. Either add bioformats_package.jar to the static Java 
 path or add it to the Matlab path.

I tried a few things, eg adding 'bioformats_package.jar' to the static Java path. I am inexperienced when it comes to working with libraries etc, so I may be missing something simple.

For reference, all of my work/files are in '\Users\user_name\Documents\MATLAB\Image Analysis'

I pasted all of the files from the Bio-Formats website directly in this 'Image Analysis' folder, along with the rest of my .m files. Yet I can't use Bio-Formats.

Answer 1

[Paul Stroe]

Hi, I am using MATLAB R2018b and I also had this issue, I think that Bioformats did not catch up with the new Matlab release.

The issue is the is_octave(), you just have to comment everything out, since you know you are using Matlab.

In bfCheckJavaPath

%    if is_octave()
%        version = char(java_get('loci.formats.FormatTools', 'VERSION'));
%    else
        version = char(loci.formats.FormatTools.VERSION);
%    end

Also in createMinimalOMEXMLMetadata.m, as bfsave will not work as well

% if is_octave()
%     java_true = java_get('java.lang.Boolean', 'TRUE');
% else
    java_true = java.lang.Boolean.TRUE;
% end