Conunetr: A Conditional Transformer Network for 3D Micro-Ct Embryonic Cartilage Segmentation

Nishchal Sapkota, Yejia Zhang, Susan M. Motch Perrine, Yuhan Hsi, Sirui Li, Meng Wu, Greg Holmes, Abdul R. Abdulai, Ethylin W. Jabs, Joan T. Richtsmeier, Danny Z. Chen

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

Abstract

Studying the morphological development of cartilaginous and osseous structures is critical to the early detection of life-threatening skeletal dysmorphology. Embryonic cartilage undergoes rapid structural changes within hours, introducing biological variations and morphological shifts that limit the generalization of deep learning-based segmentation models that infer across multiple embryonic age groups. Obtaining individual models for each age group is expensive and less effective, while direct transfer (predicting an age unseen during training) suffers a potential performance drop due to morphological shifts. We propose a novel Transformer-based segmentation model with improved biological priors that better distills morphologically diverse information through conditional mechanisms. This enables a single model to accurately predict cartilage across multiple age groups. Experiments on the mice cartilage dataset show the superiority of our new model compared to other competitive segmentation models. Additional studies on a separate mice cartilage dataset with a distinct mutation show that our model generalizes well and effectively captures age-based cartilage morphology patterns. Code is available in GitHub.

Original languageEnglish
Title of host publicationIEEE International Symposium on Biomedical Imaging, ISBI 2024 - Conference Proceedings
PublisherIEEE Computer Society
ISBN (Electronic)9798350313338
DOIs
StatePublished - 2024
Event21st IEEE International Symposium on Biomedical Imaging, ISBI 2024 - Athens, Greece
Duration: 27 May 202430 May 2024

Publication series

NameProceedings - International Symposium on Biomedical Imaging
ISSN (Print)1945-7928
ISSN (Electronic)1945-8452

Conference

Conference21st IEEE International Symposium on Biomedical Imaging, ISBI 2024
Country/TerritoryGreece
CityAthens
Period27/05/2430/05/24

Keywords

  • Cartilage Segmentation
  • Conditional Model
  • Cranial Dysmorphology
  • Transformers

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