Open Microscopy Environment

Hello,
I haven't found any documentation about it, and I am quite new to bioformats and also to openCV. But I'd guess that it is possible and maybe you can help me here. I would like to avoid Matlab.
Can I use bioformats (with the proper c++ bindings libraries) to read images into openCV compatible format?
I have seen that ITK is a supported option, maybe I can use the itk-opencv bridge? Do you know if there is a direct way from bioformat to opencv?
Thanks in advance.

Hi,

I'm unaware of any "direct" way to use bioformats with opencv.

If you are using C++, then one possibility would be to build the Jace C++ wrappers (https://www.openmicroscopy.org/site/support/bio-formats4/developers/non-java-code.html). The bioformats itk bridge plus the itk opencv bridge might work, but I'm unaware of anyone trying this out, so can't make any particular recommendations here.

It looks like OpenCV can read standard TIFF files, so you could use bioformats to write out OME-TIFF and then read this with OpenCV. But that would be external to any C++ code unless you did it using the Jace wrappers (which can be done, but the bfconvert tool could do it directly).

Regards,
Roger

That's a nice recommendation, I didn't realized that OpenCV could read OME-TIFF. I'll do that. Thanks for it.
Best regards,
PHC