Computational Study of the Chitin Secreting Gland of Riftia pachyptila. - Thomas Boudier; Francoise Gaill; Anne Strauss (BCEC, 1997)

Organising multi-dimensional biological image information: the BioImage Database. - José María Carazo; Ernst H. K. Stelzer; A. Engel; I. Fita; C. Henn; J. Machtynger; P. McNeil; David M. Shotton; Monica Chagoyen; Pedro A. de Alarcón; R. Fritsch; J. B. Heymann; et al. (Nucleic Acids Res., 1999)

VIDOS, a system for video editing and format conversion over the Internet. - Thomas Boudier; David M. Shotton (Comput. Networks, 2000)

TomoJ: tomography software for three-dimensional reconstruction in transmission electron microscopy. - Cédric Messaoudi; Thomas Boudier; Carlos Oscar Sánchez Sorzano; Sergio Marco (BMC Bioinform., 2007)

NEMO: a tool for analyzing gene and chromosome territory distributions from 3D-FISH experiments. - E. Iannuccelli; F. Mompart; Joël Gellin; Yvette Lahbib-Mansais; Martine Yerle; Thomas Boudier (Bioinform., 2010)

TANGO: a generic tool for high-throughput 3D image analysis for studying nuclear organization. - Jean Ollion; Julien Cochennec; François Loll; Christophe Escudé; Thomas Boudier (Bioinform., 2013)

Classified region growing for 3D segmentation of packed nuclei. - Jaza Gul-Mohammed; Thomas Boudier (ISBI, 2014)

A generic classification-based method for segmentation of nuclei in 3D images of early embryos. - Jaza Gul-Mohammed; Ignacio Arganda-Carreras; Philippe Andrey; Vincent Galy; Thomas Boudier (BMC Bioinform., 2014)

Detection of high-grade atypia nuclei in breast cancer imaging. - Henri Noël; Ludovic Roux; Shijian Lu; Thomas Boudier (Digital Pathology, 2015)

OpenSegSPIM: a user-friendly segmentation tool for SPIM data. - Laurent Gole; Kok Haur Ong; Thomas Boudier; Weimiao Yu; Sohail Ahmed (Bioinform., 2016)

NucleiNet: A convolutional encoder-decoder network for bio-image denoising. - Zichuan Liu; Yifei Hu; Hang Xu 001; Lamees Nasser; Philippe Coquet; Thomas Boudier; Hao Yu 001 (EMBC, 2017)

Persistent homology for object segmentation in multidimensional grayscale images. - Rabih Assaf; Alban Goupil; Valeriu Vrabie; Thomas Boudier; Mohammad Kacim (Pattern Recognit. Lett., 2018)

EM-net: Deep learning for electron microscopy image segmentation. - Afshin Khadangi; Thomas Boudier; Vijay Rajagopal (ICPR, 2020)

EM-stellar: benchmarking deep learning for electron microscopy image segmentation. - Afshin Khadangi; Thomas Boudier; Vijay Rajagopal (Bioinform., 2021)

Tight Lower Bounds in the Supported LOCAL Model. - Alkida Balliu; Thomas Boudier; Sebastian Brandt 002; Dennis Olivetti (PODC, 2024)

Distributed Algorithms for Potential Problems. - Alkida Balliu; Thomas Boudier; Francesco D'Amore 001; Dennis Olivetti; Gustav Schmid; Jukka Suomela (CoRR, 2025)