Can not open .jp2 image

[franfcunha]

Hi everyone,
@petebankhead first of all congratulations for this amazing work!

I was wondering to use QU Path in order to perform image registration of consecutive sections. My images are .jp2 format. I already added both JARs related to bio formats to the default plugins folder.
Still not being able to open my image, it throws me error.

What can I do?

Thank you very much

[petebankhead]

Thanks @franfcunha !

I recently opened a (very small, single-channel) .jp2 image in QuPath with the help of Bio-Formats, but I do not have a whole slide image in that format to test. JPEG2000 does currently appear on the Bio-Formats list of supported formats with a tick in the 'pyramid' column... but I am not sure whether that should be interpreted as meaning pyramidal .jp2 whole slide images are supported, or if it is simply a comment on the capabilities of the format.

I would suggest asking the OME team about this through their mailing list - they are the experts.

Apart from that, in QuPath under View → Show log you may get more useful information to help track down the source of any error. Where Bio-Formats is involved, I would also recommend trying to open a cropped/lower resolution part of any problematic image with Fiji as well, since the Bio-Formats plugin for Fiji is much more established. This can helps to track down whether the problem is most likely to be with the file itself, the file reader, or the QuPath extension.

[petebankhead]

Closing this as it is really a file format issue, best taken care of through OpenSlide, Bio-Formats or another extension.

Speaking of which, this may be worth investigating: https://github.com/STTARR/qupath-extension-gdal