Open Microscopy Environment

Hello all,

Thanks in advance for any help...!

I have recently (like last week) purchased a brand new MacBook Pro running Mac OS 10.9. I downloaed ImageJ (v1.48p) and added the "loci_tools.jar" from this website to the plugins folder so that I could look at my .lif files. I am unable to open up my .lif files which previously, on the Windows laptop that I was using before, that I could open no problems.

I'm having several seemingly inter-related problems:
(a) if I only copy "loci_tools.jar" into the plugins folder as instructed on the website, then the Bio-Formats LOCI menu does not show up at all. Only if I also place the "loci_plugins.jar" file in the Plugins folder does LOCI show up under the Plugins menu.
(b) If I get LOCI to show up under the Plugins menu, when I try to select "Bio-formats Importer", then no window/menu pops up. The computer just sits there.
(c) If I try to double-click on a .lif file [which I know is not corrupted, 'cause it opens up just fine with a Windows machine], then I get the error message "File is not in a supported format, a reader plugin is not available, or it was not found."

It seems to me that the problem is with ImageJ and the loci plugin -- but these are fresh downloads and newly installed so that doesn't seem right.

Is there a bug with ImageJ and the Mac OS that anyone knows about? Is there some setting that I need to activate or de-activate? Any advice welcome.

Thanks for any help.
--Nick

Here's a couple of guesses (I'm no ImageJ expert, but there's certainly no issue with IJ on Mac that we're aware of):

Are you using the LOCI plugin to open the image? Do you go to Plugin > LOCI > Bio-Formats Importer? If you're simply double-clicking the .lif file it might be using some other code to open it.

Another thing you could try is to use Fiji - which is an ImageJ package that has all the Bio-Formats jars installed and an updater for keeping them all in sync. http://fiji.sc/Downloads

To get the latest version of Bio-Formats (this will have a few more bug-fixes etc) follow instructions at http://fiji.sc/Bio-Formats#Daily_builds to update to BF-5.

Hope that helps, let us know if theres any more problems,

Will.

Thanks Will for all the suggestions!

Somehow things are fixed....I'm not clear what I'm doing differently but now this week the menu appears appropriately and the plug-in seems to be working as it supposed to....beats me.

Maybe it just needed time to percolate in my new Mac....

Thanks for the help!
--N