Bio-Formats in open source digital pathology software

[pbankhead]

Hi,

I’ve recently released new open source (GPL v3+) digital pathology software, QuPath: http://qupath.github.io

Currently, QuPath primarily uses OpenSlide to handle images - but it would be fantastic to be able to offer Bio-Formats support as well.

In the short term, I'd ideally like to do so by providing an optional Bio-Formats extension, and requiring any user who installs it to also go and download bioformats_package.jar separately.

I've coded up something that basically works (at least for some formats) here:
https://github.com/petebankhead/qupath- ... -extension

Certainly this code needs to be improved (I have only just found this forum, and still need to read it more!), but my most immediate question is about distribution and licensing.

My understanding is that Bio-Formats is licensed under GPL v2, so it would be compatible with QuPath (GPL v3+). However, I would like to keep things simple for now, and avoid any requirement to manage more dependencies and licenses directly within QuPath. Therefore I hoped that the approach I’ve been exploring (i.e. offering an extension, but requiring users to download Bio-Formats separately to use it) would help maintain a clear separation.

Have I got this right, and does this approach seems fair and proper from a Bio-Formats/GPL point of view? Or would there be a better way?

Any advice would be much appreciated.

Thanks!

Pete

[rleigh]

Dear Pete,

What you are doing looks absolutely fine and is entirely within the spirit and letter of the GPL licensing.

I double-checked our licensing and there's a slight discrepancy in that all the main licence text files are GPL v2 while the source files have GPL v2+ header text. We'll look at clarifying that if needed, but your project being GPL 3+ is entirely compatible with the GPL v2+ licence from the source files.

Regarding separation, you're entirely within your rights under the GPL to embed Bio-Formats since the work as a whole would be GPL 3+ which is also compatible with the GPL v2+ licensing of Bio-Formats. Since the base QuPath is GPL 3+, adding Bio-Formats using the appropriate maven dependencies would be fine.


Kind regards,
Roger

[pbankhead]

That's great - thanks Roger!

Best wishes,

Pete