Bead-based mosaicing of single plane illumination microscopy images using geometric local descriptor matching. - Stephan Preibisch; Stephan Saalfeld; Torsten Rohlfing; Pavel Tomancak (Image Processing, 2009)

Globally optimal stitching of tiled 3D microscopic image acquisitions. - Stephan Preibisch; Stephan Saalfeld; Pavel Tomancak (Bioinform., 2009)

CATMAID: collaborative annotation toolkit for massive amounts of image data. - Stephan Saalfeld; Albert Cardona; Volker Hartenstein; Pavel Tomancak (Bioinform., 2009)

As-rigid-as-possible mosaicking and serial section registration of large ssTEM datasets. - Stephan Saalfeld; Albert Cardona; Volker Hartenstein; Pavel Tomancak (Bioinform., 2010)

ImgLib2 - generic image processing in Java. - Tobias Pietzsch; Stephan Preibisch; Pavel Tomancak; Stephan Saalfeld (Bioinform., 2012)

BigDataViewer: Interactive Visualization and Image Processing for Terabyte Data Sets. - Tobias Pietzsch; Stephan Saalfeld; Stephan Preibisch; Pavel Tomancak (CoRR, 2014)

Post-acquisition image based compensation for thickness variation in microscopy section series. - Philipp Hanslovsky; John A. Bogovic; Stephan Saalfeld (ISBI, 2015)

Image based compensation for thickness variation in microscopy section series. - Philipp Hanslovsky; John A. Bogovic; C. Shan Xu; Kenneth J. Hayworth; Zhiyuan Lu; Harald F. Hess; Stephan Saalfeld (CoRR, 2015)

Robust registration of calcium images by learned contrast synthesis. - John A. Bogovic; Philipp Hanslovsky; Allan Wong; Stephan Saalfeld (ISBI, 2016)

Deep Learning for Isotropic Super-Resolution from Non-isotropic 3D Electron Microscopy. - Larissa Heinrich; John A. Bogovic; Stephan Saalfeld (MICCAI (2), 2017)

PreMosa: extracting 2D surfaces from 3D microscopy mosaics. - Corinna Blasse; Stephan Saalfeld; Raphaël Etournay; Andreas Sagner; Suzanne Eaton; Eugene W. Myers (Bioinform., 2017)

Image-based correction of continuous and discontinuous non-planar axial distortion in serial section microscopy. - Philipp Hanslovsky; John A. Bogovic; Stephan Saalfeld (Bioinform., 2017)

The Candidate Multi-Cut for Cell Segmentation. - Jan Funke; Chong Zhang 001; Tobias Pietzsch; Stephan Saalfeld (CoRR, 2017)

A Deep Structured Learning Approach Towards Automating Connectome Reconstruction from 3D Electron Micrographs. - Jan Funke; Fabian Tschopp; William Grisaitis; Arlo Sheridan; Chandan Singh; Stephan Saalfeld; Srinivas C. Turaga (CoRR, 2017)

Whole-brain serial-section electron microscopy in larval zebrafish. - David Grant Colburn Hildebrand; Marcelo Cicconet; Russel Miguel Torres; Woohyuk Choi; Tran Minh Quan; Jungmin Moon; Arthur W. Wetzel; Andrew Scott Champion; Brett J. Graham; Owen Randlett; George S. Plummer; Ruben Portugues; et al. (Nat., 2017)

The candidate multi-cut for cell segmentation. - Jan Funke; Chong Zhang 001; Tobias Pietzsch; Miguel Ángel González Ballester; Stephan Saalfeld (ISBI, 2018)

Synaptic Cleft Segmentation in Non-isotropic Volume Electron Microscopy of the Complete Drosophila Brain. - Larissa Heinrich; Jan Funke; Constantin Pape; Juan Nunez-Iglesias; Stephan Saalfeld (MICCAI (2), 2018)

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

Large Scale Image Segmentation with Structured Loss Based Deep Learning for Connectome Reconstruction. - Jan Funke; Fabian Tschopp; William Grisaitis; Arlo Sheridan; Chandan Singh; Stephan Saalfeld; Srinivas C. Turaga (IEEE Trans. Pattern Anal. Mach. Intell., 2019)

Decomposing heterogeneous dynamical systems with graph neural networks. - Cédric Allier; Magdalena C. Schneider; Michael Innerberger; Larissa Heinrich; John A. Bogovic; Stephan Saalfeld (CoRR, 2024)

SciJava Ops: an improved algorithms framework for Fiji and beyond. - Gabriel J. Selzer; Curtis T. Rueden; Mark C. Hiner; Edward L. Evans; David Kolb; Marcel Wiedenmann; Christian Birkhold; Tim-Oliver Buchholz; Stefan Helfrich; Brian Northan; Alison E. Walter; Johannes E. Schindelin; et al. (Frontiers Bioinform., 2024)

DeepPD: Joint Phase and Object Estimation from Phase Diversity with Neural Calibration of a Deformable Mirror. - Magdalena C. Schneider; Courtney Johnson; Cédric Allier; Larissa Heinrich; Diane Adjavon; Joren Husic; Patrick La Riviere; Stephan Saalfeld; Hari Shroff (CoRR, 2025)