Opening TIFF images using ITK-SNAP

Does anyone know how to open .tiff images with ITK-SNAP and export the annotated images in .tiff? I do not find the support of .tiff images in ITK-SNAP and do not know how to open .tiff images.

Hi @pmcesky,

  • From the File menu , select “Open Main Image”

  • You select your tif file and for the file format you select Generic ITK format
    image

  • After clicking next you should arrive on something like this , just click Finish !

Cheers,

Romain

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By request from @romainGuiet, thiis post has been moved to its own topic, thus removing it from Comparaison of some tools for 3D dense ground truth annotations

Thanks very much!
Yeah, this is a way to open tif images with ITK-SANP. But the problem is that, if the voxel scale is different in x,y,z, that means the voxel is anisotropic, then ITK-SNAP can not display the image properly as the original one, since it treat x,y,z isotropicaly. I tried to open binary format by setting some parameters but failed.
Anyway, I was trying to annotate 3D voxels, so I tried ITK-SNAP as the comparison shows it maybe the best one to do this. But after encountering this problem, I’ve turned to LabKit with Fiji, which works well for my task.
Thanks!

I encountered the same problem and found a solution, so in case you want to go back to ITK-SNAP: for anisotropic stacks, you can adjust the voxel size in Fiji (Image-> Properties) and then save it in the MHD/MHA format. When you import that image into ITK-Snap the correct voxel size is used.

Oh, thanks! That is a good solution. I’ll try this sometime later to see if ITK-SNAP is better than LabKit for voxel annotation.
Thanks!