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bonej-org / BoneJ2

Plugins for bone image analysis
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Anisotropy does not recognize image stack as 3D image #248

Closed SebastienCallens closed 4 years ago

SebastienCallens commented 4 years ago

Hello, I have an issue with some of the tools in BoneJ2, including the anisotropy tool. Whenever I try to run it on a stack of binarized images (see attached file), I get the error message that a "3D image" is required. This also happens when I try the anisotropy tool on the EF test images.

Do you know how I should convert the image stack into a suitable 3D image for the anistropy calculation? I don't understand why it is not accepted in its current format.

Thanks a lot in advance!

testAnisotropy.zip

alessandrofelder commented 4 years ago

Hello, Thanks for getting in touch! The issue with the test image you have provided is that the third dimension is temporal, not spatial. You can change this in ImageJ via Image>Properties. Can I ask you to post future questions on the ImageJ forum with a BoneJ tag, so that they will be easier to find in the future, please?

Hope this helps!

@mdoube @rimadoma we might want to specify the fact that we expect 3 spatial dimensions in the error message? Just a thought...

rimadoma commented 4 years ago

we expect 3 spatial dimensions in the error message?

Not a bad idea. Do you have time to look at the EF test images?

alessandrofelder commented 4 years ago

I am not sure which EF test images @SebastienCallens refers too? Just tested that Anisotropy works on shrew.tif now, which is an EF test image givee on bonej.org, and it does :)

rimadoma commented 4 years ago

I am not sure which EF test images @SebastienCallens refers too?

I think images from Plugins>BoneJ>Test images>Create EF test images

alessandrofelder commented 4 years ago

Ooo yes, that is a 🐛 ! Thanks for spotting that, @SebastienCallens and @rimadoma !

Slightly different to @SebastienCallens's problem (but same outcome) because that command creates extra channel dimensions (which used to be OK for EF), not extra temporal dimensions, instead of z spatial dimensions. Will fix now.

SebastienCallens commented 4 years ago

Thanks a lot for getting back so quickly and for clarifying this issue! Regarding the EF images, I was indeed referring to the ones that @rimadoma mentioned. Just so you know, I could run my file without problems in BoneJ1.

I will also make sure to post future questions in the forum. Thanks again!