Fiji now ships Bio-Formats dev_4_4 stable builds

[Curtis Rueden]

Hi everyone,

For some time, Fiji has been shipping Bio-Formats builds from the develop branch of Bio-Formats (i.e., 4.5.x), rather than from the dev_4_4 branch (i.e., 4.4.x). There were several reasons for this:

1) There is still work on develop that is not part of dev_4_4 and hence not part of any released version of Bio-Formats. In particular, I made major improvements to the Prairie format reader a few months ago, which became part of develop but not yet dev_4_4.

2) There was a technical issue with the ImageJ updater which prevented us from switching back to 4.4.x releases or builds.

The Prairie work is now pending inclusion in dev_4_4:

https://github.com/openmicroscopy/bioformats/pull/508

And the ImageJ updater issue has now been fixed:

http://trac.imagej.net/ticket/1603

So I have now uploaded Fiji to use dev_4_4 again. As documented on the Fiji wiki (http://fiji.sc/Bio-Formats#Source_code), Fiji's fiji branch (http://github.com/fiji/bioformats/tree/fiji) reflects the version of Bio-Formats currently available from the Fiji updater. At the moment, that is dev_4_4 with PR #508 merged in, to ensure the Prairie fixes remain available to end users.

Unfortunately, reverting Fiji to dev_4_4 served as a forcible reminder that I forgot a critically important reason why we were using develop builds:

3) ImgLib2 and ImageJ2 depend on develop. And Fiji inherits the ImageJ update site, which is what ImageJ2 uses. So now, there is an impending issue with the ImageJ 2.0.0-beta-7 release: the ImageJ update site will need to switch back to develop builds again for beta7.

Switching back to dev_4_4 has also very likely broken any existing ImageJ2 beta installations that update to the latest code. (Since ImageJ2 is still in beta, I am less concerned about that, though it is still not ideal.)

Moving forward, ImageJ will increasingly depend on the SCIFIO refactoring work, which is all based on develop. If we want to also provide a stable Bio-Formats update site for ImageJ from openmicroscopy.org (which was the tentative eventual plan), we will need to carefully consider how to accomplish that. It can probably be done but may require shipping 4.4.x and 4.5.x side by side, which would be rather unfortunate.

Regards,

Curtis

[Johannes Schindelin]

Hi,

On Tue, 7 May 2013, Curtis Rueden wrote:

> Switching back to *dev_4_4* has also very likely broken any existing

> ImageJ2 beta installations that update to the latest code.

Yes, ImageJ2 is broken due to the downgrade of Bio-Formats.

Ciao,
Dscho