CutNII provides visualization and slicing of 3D isotropic image data (e.g. MRI) and atlases. The software features orthogonal views of the three standard planes (coronal, sagittal, horizontal) and a custom-angle slice cut through the volume. Slicing generates an arbitrarily positioned, oriented and sized rectangular sample from the dataset.

The main use of CutNII is to produce custom-angle atlas slices that match histological sections with non-standard cutting angles. In addition, custom slices allow inspection of anatomical features from non-conventional angles.

Multi-modality atlasing datasets to be provided with CutNII:

- Waxholm Space Atlas of the Sprague Dawley rat brain (T2* MRI, DTI, and delineations)
- Allen Mouse Brain Atlas reference atlas (grayscale Nissl volume reconstruction and delineations)