Learning Shape Reconstruction from Sparse Measurements with Neural Implicit Functions

Tamaz Amiranashvili, David Lüdke, Hongwei Bran Li, Bjoern Menze, Stefan Zachow

Research output: Contribution to journalConference articlepeer-review

10 Scopus citations


Reconstructing anatomical shapes from sparse or partial measurements relies on prior knowledge of shape variations that occur within a given population. Such shape priors are learned from example shapes, obtained by segmenting volumetric medical images. For existing models, the resolution of a learned shape prior is limited to the resolution of the training data. However, in clinical practice, volumetric images are often acquired with highly anisotropic voxel sizes, e.g. to reduce image acquisition time in MRI or radiation exposure in CT imaging. The missing shape information between the slices prohibits existing methods to learn a high-resolution shape prior. We introduce a method for high-resolution shape reconstruction from sparse measurements without relying on high-resolution ground truth for training. Our method is based on neural implicit shape representations and learns a continuous shape prior only from highly anisotropic segmentations. Furthermore, it is able to learn from shapes with a varying field of view and can reconstruct from various sparse input configurations. We demonstrate its effectiveness on two anatomical structures: vertebra and distal femur, and successfully reconstruct high-resolution shapes from sparse segmentations, using as few as three orthogonal slices.

Original languageEnglish
Pages (from-to)22-34
Number of pages13
JournalProceedings of Machine Learning Research
StatePublished - 2022
Event5th International Conference on Medical Imaging with Deep Learning, MIDL 2022 - Zurich, Switzerland
Duration: 6 Jul 20228 Jul 2022


  • neural implicit shape representations
  • shape priors
  • shape reconstruction


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