Installation

[tischi]

@Mava04, I think I have a running version now, could you please try to install and run it accord to these instructions? https://github.com/tischi/fiji-plugin-FISH/blob/master/README.md#installation

[Mava04]

@tischi, I followed your instructions. However, I cannot install the plugin, and I am not getting any error message. What might have gone wrong?

[Mava04]

@tischi The plugin is not listed in the window with the plugins that may be installed or updated

[tischi]

OK! Let's try to figure it out:

1. are you sure you checked the update site EMBL-CBA ?
2. can you check whether the plugin is within your jars folder? For me it looks like this:

   tischer@Christians-MBP ~ $ ls /Applications/Fiji.app/jars/fiji-plugin-*
   -rw-r--r--  1 tischer  staff    39K Apr  9 16:00 /Applications/Fiji.app/jars/fiji-plugin-FISH-0.1.0.jar
   -rw-r--r--  1 tischer  staff   559K Mar 25 08:35 /Applications/Fiji.app/jars/fiji-plugin-bigDataProcessor2-0.3.10.jar
   -rw-r--r--  1 tischer  staff   269K Apr  4 16:12 /Applications/Fiji.app/jars/fiji-plugin-cats-0.7.3.jar
   -rw-r--r--  1 tischer  staff    50K Apr  3 10:04 /Applications/Fiji.app/jars/fiji-plugin-elastixWrapper-0.4.3.jar
   -rw-r--r--  1 tischer  staff    12K Oct 29 07:44 /Applications/Fiji.app/jars/fiji-plugin-granulometry-0.1.0.jar
   -rw-r--r--  1 tischer  staff    84K Oct 29 07:44 /Applications/Fiji.app/jars/fiji-plugin-illuminationCorrection-0.1.03.jar
   -rw-r--r--  1 tischer  staff   118K Oct 29 07:44 /Applications/Fiji.app/jars/fiji-plugin-imageRegistration-0.5.14.jar
   -rw-r--r--  1 tischer  staff   8.8K Oct 29 07:44 /Applications/Fiji.app/jars/fiji-plugin-lazyRatioViewer-0.1.0.jar
   -rw-r--r--  1 tischer  staff   240K Apr  4 15:41 /Applications/Fiji.app/jars/fiji-plugin-morphometry-0.5.2.jar
   -rw-r--r--  1 tischer  staff    76K Oct 29 07:45 /Applications/Fiji.app/jars/fiji-plugin-multiTemplateMatching-0.4.0.jar
   -rw-r--r--  1 tischer  staff    96K Oct 29 07:44 /Applications/Fiji.app/jars/fiji-plugin-plateViewer-0.2.23.jar
   -rw-r--r--  1 tischer  staff    85K Mar  1 12:45 /Applications/Fiji.app/jars/fiji-plugin-platynereisViewer-0.5.8.jar
   -rw-r--r--  1 tischer  staff    12K Oct 29 07:44 /Applications/Fiji.app/jars/fiji-plugin-yamlMetadataCreator-0.1.07.jar

with fiji-plugin-FISH-0.1.0.jar present.

[Mava04]

@tischi, Yes, EMBL-CBA is ticked and the jar file is there. There was also an update today. However, I still cannot find the plugin when I open ImageJ.

[tischi]

Are you sure you are looking in the right place? I moved it from EMBL to Analyze: [ Plugins > Analyze > FISH Spots ]

[Mava04]

I checked basically everywhere, and first of all in Analyze. It's strange. Might it be that there are some issues with other packages, apart from the open-stacks-as-virtualstacks? Anyway, I'll check again when I'm back home, just to be totally sure...

[tischi]

ok. let me know. if it does not work like this, I can try something else.

[Mava04]

@tischi Bad news, I still cannot see the plugin. It's in the jar folder, but I cannot find it anywhere in ImageJ. Re-installing Fiji did not solve the issue.

[tischi]

seems to work now.