Open Microscopy Environment

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

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

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

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.

David Gault

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

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

Thank you

Elsi