I have been encountering a few troubles with the Sholl Analysis plugin on Fiji over the last few days and would appreciate any help. For reference, I am on macOS 11.2.3 running Java 8 Update 291.
First, after I get the summary and detailed table of results, I am unable to copy them into an excel spreadsheet with their headers. Is there a way to do this?
A bigger issue comes when I go to the Java-8 update site. When I go to Help —> Update, I get an error saying “There are locally modified files!” (as shown in the following image).
After I click OK, and make sure that Java-8 is checked in the “Manage update sites” section, I click “Apply changes” on the ImageJ Updater. Of note, I do see Sholl_Analysis.jar at the very top of my list of files. Once I have clicked Apply Changes, I get a second error message as shown here:
After this it doesn’t matter if I click “keep the local version” or “update jars/ij-1.53c.jar”. I click “OK” and the updater does its thing and eventually tells me “Updated successfully! Please restart ImageJ!” Upon restarting Fiji, I do not see Sholl anymore in the analysis menu. I also cannot find it in any subheading in the analysis menu, and when I search for it in the search function of the application no results come up.
I also have another issue that sometimes arises when I re-install Fiji. When I update to v1.53i from v1.53c, occasionally I get an error message from my mac saying “Fiji cannot be opened. 1”. This error does not always happen, but when it does happen I have to reinstall Fiji again, as it cannot be opened at all.
Thank you so much for your help!