We’ve had some requests for an update of ImageJ in CellProfiler to version 1.46 (see https://github.com/CellProfiler/CellProfiler/issues/418. The support for this is somewhat informal, but if you need an updated version of ImageJ, you’ll need our modified version which includes a few extra classes. You can download the .jar file from http://www.broadinstitute.org/~leek/ij-1.46r/ij.jar. ij.jar resides in the imagej directory in the installed version; this is usually c:\Program Files\CellProfiler\imagej directory. You should copy the existing ij.jar to some place safe and replace it with the downloaded one.
I’d recommend only doing this if you need the functionality in 1.46.
Our next release will use ImageJ 2.0 and will work on both the Mac and PC. The command menu system will be improved and the standard commands will have settings that correspond to those you see in the command’s dialog box in ImageJ. The functionality is still in an alpha stage and some ImageJ interoperability still remains to be completed.