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Matlab R2017b and bfopen exception

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Historical discussions about the Bio-Formats library. Please look for and ask new questions at https://forum.image.sc/tags/bio-formats

If you are having trouble with image files, there is information about reporting bugs in the Bio-Formats documentation. Please send us the data and let us know what version of Bio-Formats you are using. For issues with your code, please provide a link to a public repository, ideally GitHub.

Matlab R2017b and bfopen exception

Postby tinttana » Mon Feb 26, 2018 2:11 pm

Hi

I'm new to both Matlab and Bioformats: I'm getting to know the first basic commands for image reading and opening.
I just installed Bioformats and I added my bfmatlab directory to the MATLAB path. I put loci_tools.jar in MATLAB/R2017b/bin and added the directory to the MATLAB path.

I'm trying to open a .lif frame serie with 3 channels using bfopen. This is the exception I get and I haven't found any similar issue on other Matlab discussions.

Do some of you know how to fix this?

Thanks :)
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Re: Matlab R2017b and bfopen exception

Postby dgault » Tue Feb 27, 2018 11:39 am

Hi,

If possible would you be able to upload a sample file showing this issue to help us reproduce the problem. You can upload a sample file to https://www.openmicroscopy.org/qa2/qa/upload/

David Gault
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Re: Matlab R2017b and bfopen exception

Postby tinttana » Tue Feb 27, 2018 2:34 pm

dgault wrote:Hi,

If possible would you be able to upload a sample file showing this issue to help us reproduce the problem. You can upload a sample file to https://www.openmicroscopy.org/qa2/qa/upload/

David Gault


Just uploaded a 10-frame example on the link you gave me ('multipage_tiff_example.tif').
I of course tried bfopen with it and the result was the same as with the original file.

Code is just:

prova = bfopen('file_path')

Thanks,

Elsi
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Re: Matlab R2017b and bfopen exception

Postby dgault » Wed Feb 28, 2018 4:41 pm

Thank you Elsi,

We received the uploaded sample file and I was able to test it and reproduce the problem you were seeing. I have not yet been able to solve the issue but I will continue to test it and keep this thread updated when I make further progress. Thank you for your patience.

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Re: Matlab R2017b and bfopen exception

Postby dgault » Thu Mar 01, 2018 12:02 pm

Following up on this issue, the bfopen command is completing as expected, it appears though that the pixel data is too large to be printed out in one go when using the command as below:
Code: Select all
data =  bfopen('file_path')


However you can still store and access the data when using the command with a semicolon afterwards:
Code: Select all
data =  bfopen('file_path');


The data can then be accessed as in the examples on https://docs.openmicroscopy.org/bio-for ... b-dev.html
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Re: Matlab R2017b and bfopen exception

Postby tinttana » Thu Mar 15, 2018 2:11 pm

Thanks a lot, your reply was very helpful.
The code now works perfectly.

Thank you

Elsi
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