Learning Shape Reconstruction from Sparse Measurements with Neural Implicit FunctionsDownload PDF

Dec 09, 2021 (edited Apr 04, 2022)MIDL 2022Readers: Everyone
  • Keywords: shape reconstruction, shape priors, neural implicit shape representations
  • TL;DR: We build a high-resolution shape prior from sparse, anisotropic data and apply it to various shape reconstruction tasks.
  • Abstract: 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.
  • Registration: I acknowledge that publication of this at MIDL and in the proceedings requires at least one of the authors to register and present the work during the conference.
  • Authorship: I confirm that I am the author of this work and that it has not been submitted to another publication before.
  • Paper Type: methodological development
  • Primary Subject Area: Segmentation
  • Secondary Subject Area: Learning with Noisy Labels and Limited Data
  • Confidentiality And Author Instructions: I read the call for papers and author instructions. I acknowledge that exceeding the page limit and/or altering the latex template can result in desk rejection.
  • Code And Data: Code: https://github.com/menzelab/implicit-shape-reconstruction Lumbar vertebra dataset (Verse19): https://github.com/anjany/verse Distal Femur dataset (OAI-ZIB): https://pubdata.zib.de
6 Replies