Bioformats version in bleeding-edge CP

Hi,
We’re using the bleeding edge version of CP on both Linux and MacOS to take advantage of its support for the more recent version of Bioformats (5.1.1) in there. However, even 5.1.1 has a few shortcomings that have been fixed in later release of Bioformats. Can I just replace the various bioformats jars in the src/CellProfiler/imagej/jars directory with the equivalent newer jars? And if yes, which jars should I replace with the more recent ones?
Thanks,

  • Damir

Hi all,

I just installed the 2.2.0rc2 beta on both Windoze and Ubuntu 14.04 and am still trying to find out which version of the bioformats library is in this version of CP. And more importantly, whether and how I can update to the most recent 5.1.8 in order to take advantage of some important fixes that are in 5.1.8 (related to nd2 and czi handling).

On Ubuntu I noticed a loci_tools.jar in the python-bioformats 1.0.5 package. Is that the one in use? It appears to be pretty old. On Windoze I can’t even find a loci_tools.jar. Where does it hide its bioformats library?

Thanks,

  • Damir

Comments @LeeKamentsky?

The bioformats library in CellProfiler is now packages within the file, prokaryote.jar and the Python prokaryote package handles installing CellProfiler’s Java dependencies into the Python site-packages.

There are two ways to update bioformats informally. You can set your Java CLASSPATH to point to the latest bioformats-package.jar file or you can clone the prokaryote GIT repository (https://github.com/CellProfiler/prokaryote), and edit pom.xml to upgrade bioformats. After that, you can run Maven to build it and substitute the result for your old prokaryote.jar.