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

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



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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.

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.