Sholl Analysis Plugin Disappears after Updating Fiji

Hey everyone!

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!

Welcome to the forum @ishsethi!

  1. On the “disappearance” of the Sholl Analysis plugin: It is now distributed via the Neuroanatomy update site. See this post for the rationale behind this change. Here are the steps to subscribe to the Neuroanatomy update site:

    1. Run the Fiji Updater (Help → Update…, the penultimate entry in the Help menu)

    2. Click Manage update sites and select the Neuroanatomy checkbox

    3. Click Apply changes and restart Fiji. You will notice that all of neuroanatomy-related plugins are now consolidated under a single menu (Plugins → Neuroanatomy → ). There is also a new tool in the ImageJ toolbar and and Neuroanatomy Shortcuts Window command that are now your entry point for all things neuroanatomy. Note that the Sholl Analysis plugin has now been re-written as an ImageJ2 command (its ImageJ1 counterpart remains available as a legacy plugin). Here is how it looks:

  2. On the column headers not being selected in results tables: If it is an ImageJ1-type of table there is an option in the table’s menu bar under Results → Options… to allow row and column headers to be copied. If it is an ImageJ2-type of table, then unfortunately that option is not (yet) available. You will need to save the table first and then import.

  3. On the “Fiji cannot be opened. 1” error: I have no idea, sorry. Maybe others can chime in. Do you get any errors in the MacOS console when that happens?