How do I use menu item x?
Check out the User Guide, on the left menu of this website. Hitting the Help button in most commands' options dialog will take you straight there. If that doesn't answer your question, post a question on the support page.
I'm new to ImageJ. Where can I get started with tutorials and How-Tos?
Have a look at the ImageJ User Guide, the ImageJ Wiki and the Fiji documentation. If you get stuck, having read these resources and searched the web, consider posting an item on the ImageJ Forum.
BoneJ complains that my ImageJ version is too old
Do what it says: update ImageJ by running Help > Update ImageJ. This is a feature that stops you from getting wrong results due to bugs or missing features in old versions of ImageJ.
Nothing happens when I select a BoneJ menu item. What's wrong?
This is usually a configuration issue. BoneJ looks for all the required libraries and dies quietly if it doesn't find them. Make sure you have followed the installation instructions carefully.
I tried to install the 3D libraries but it didn't work
You might be behind a proxy server. Try changing these to your the appropriate values in Edit > Options > Proxy settings. Alternatively, you might need Administrator (root / sudo) permissions to alter your Java installation, in which case you must run ImageJ as Administrator, root or sudo, so that the 3D viewer has permission to copy the 3D libraries to the correct place.
How do I cite BoneJ?
Please cite the BONE manuscript that describes BoneJ:

Doube M, Kłosowski MM, Arganda-Carreras I, Cordeliéres F, Dougherty RP, Jackson J, Schmid B, Hutchinson JR, Shefelbine SJ. BoneJ: free and extensible bone image analysis in ImageJ. Bone 47 1076-1079 (2010). doi: 10.1016/j.bone.2010.08.023

Remember to list the version numbers of BoneJ (Help > About Plugins... > BoneJ) and ImageJ (Help > About ImageJ) because these represent defined states of the programs, which can be looked up and examined thanks to Git tagging.

If you used a single plugin heavily, check the user guide where the papers used for each plugin's development are listed. BoneJ is nothing without ImageJ, so you should cite ImageJ too.
ImageJ keeps on crashing with an out of memory error
First, try increasing the amount of memory available: Edit > Options > Memory & Threads. Have a look at these more detailed instructions too. Second, install some more RAM. Some of the algorithms in BoneJ are very memory hungry, and the only way to get them to run on your big datasets is to install more memory.

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