Need help with bonej plugin

Tags: #<Tag:0x00007fb88680ef08> #<Tag:0x00007fb88680edc8>


Hi, hope you are all doing well.

I have recently installed Fiji on my laptop with bonej plugin. I have difficulty in measuring the thickness of a bone, whenever I click on thickness link, it gets stuck on “EDT transformation 1/3…”. Apart from my supervisor’s computer, it doesn’t work on any other device (I have tried it on mac laptop and windows). Can anyone help me with this please?

Many thanks


Hello Aman,

Depending on the image LocalThickness_ can involve some pretty heavy calculations, and take considerable time. It may be just a case of your supervisor’s computer being more powerful. The LocalThickness_ plugin comes with Fiji by default, so you don’t need to install BoneJ just for that. Have you tried running the stand alone version from the menu path Analyze > Local Thickness? The Local Thickness (masked, calibrated, silent) option in this sub-menu is a tiny bit faster, because it doesn’t display the intermediate steps in the process.

Best Regards,


Hello Richard,

Thank you for replying. I have an account on my supervisor’s computer as well but bonej plugin didn’t work. I have tried a lot of different computers and i get the same result. I have also tried the stand alone version from the menu path, it didn’t work. I am new to imageJ so I am not sure what the problem is.

This is the image I am working with, I am trying to calculate trabecular thickness. I was told to use the following method: select the area I want to measure, then click clear outside > fill > deselect > invert > convert to 8-bit > bonej > thickness. Would the same method work for stand alone Fiji path as well?
Sorry for so many questions, I have been trying to make it work for ages now.


Note that LocalThickness_ expects a binary image. Thus after Invert call Process > Binary > Make binary. Binarization also makes the image 8-bit, so you can drop that step from your workflow. The plugin ran successfully on my computer after binarization, but took a little while despite my workstation being quite powerful. The same method will work with the stand-alone plugin. I need to add more documentation to the wiki page of LocalThickness_, thank you for pointing out this omission.

Best regards,

Edit: LocalThickness_ doesn’t actually expect a binary image, it works with any 8-bit grey-scale. Processing a grey-scale image takes a lot longer than binary (10+ minutes), and the results make more sense in the latter case at least to my untrained eye. Also at the moment the plugin accepts an 8-bit colour image, which it shouldn’t. I’m afraid this bug is my handiwork.