![]() Most microscope manufacturers make a concerted effort to make their file types as difficult to open as possible and then thwart the makers of open source analysis software by continually changing formats without notice. One would think that opening images would be the simplest part of routine image analysis. In that way if a command moves to a different folder when Fiji is updated you can always find where it is. I highly recommend using the Command Finder tool (Plugins>Utilities>Find Commands.) to find commands. As a result there are thousands of plugins in ImageJ. Plugin developers like me have been very productive. Once the update is completed, click the Advanced mode menu and select Manage Update Sites and select Stowers Plugins from the menu. If you run FIJI, you can run the updater through Help>Update FIJI. On windows, this is typically c:\Program Files\ImageJ\Plugins. In regular ImageJ, you simply need to copy them to your ImageJ plugins folder. You can install them by downloading them from http://zipped_plugins.html. Though this course will not necessarily rely heavily on my plugins, there are a few chapters that utilize these plugins. FIJI tries to make plugin installation simple by providing a large number of plugins preinstalled and working out dependencies. Plugin installation is another thing that is both an annoyance and an advantage in ImageJ. On almost all versions of ImageJ, the memory can be increased or decreased by running Edit>Options>Memory
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