Unable to open .lif files on Mac

[mbusi]

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

[wmoore]

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.

[mbusi]

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