Detection of Deformable Objects in 3D Images Using Markov-Chain Monte Carlo and Spherical Harmonics. - Khaled Khairy; Emmanuel Reynaud; Ernst Stelzer (MICCAI (2), 2008)

Spherical harmonics-based parametric deconvolution of 3D surface images using bending energy minimization. - Khaled Khairy; Jonathon Howard (Medical Image Anal., 2008)

Joint Deformable Registration of Large EM Image Volumes: A Matrix Solver Approach. - Khaled Khairy; Gennady Denisov; Stephan Saalfeld (CoRR, 2018)

Deformable Registration of Whole Brain Zebrafish Microscopy Using an Implementation of the Flash Algorithm Within Ants. - Greg M. Fleishman; Miaomiao Zhang; Nicholas J. Tustison; Isabel Espinosa-Medina; Yu Mu; Khaled Khairy; Misha B. Ahrens (ISBI, 2019)

An End-To-End Pipeline for Fully Automatic Morphological Quantification of Mouse Brain Structures From MRI Imagery. - Shahinur Alam; Tae-Yeon Eom; Jeffrey Steinberg; David Ackerman; J. Eric Schmitt; Walter J. Akers; Stanislav S. Zakharenko; Khaled Khairy (Frontiers Bioinform., 2022)

An Image Analysis Pipeline for Quantifying the Features of Fluorescently-Labeled Biomolecular Condensates in Cells. - David W. Baggett; Anna Medyukhina; Swarnendu Tripathi; Hazheen K. Shirnekhi; Huiyun Wu; Stanley B. Pounds; Khaled Khairy; Richard W. Kriwacki (Frontiers Bioinform., 2022)

Deep-learning-based acceleration of MRI for radiotherapy planning of pediatric patients with brain tumors. - Shahinur Alam; Jinsoo Uh; Alexander Dresner; Chiaho Hua; Khaled Khairy (CoRR, 2023)

Z-UPSCALING: Optical Flow Guided Frame Interpolation for Isotropic Reconstruction of 3D EM Volumes. - Fisseha A. Ferede; Ali Khalighifar; Jaison John; Krishnan Venkataraman; Khaled Khairy (ISBI, 2025)