A new metric for probability distributions. - Dominik Maria Endres; Johannes E. Schindelin (IEEE Trans. Inf. Theory, 2003)

The standard brain of Drosophila melanogaster and its automatic segmentation (Das Standardgehirn von Drosophila melanogaster und seine automatische Segmentierung) - Johannes E. Schindelin (2005)

The Virtual Insect Brain protocol: creating and comparing standardized neuroanatomy. - Arnim Jenett; Johannes E. Schindelin; Martin Heisenberg (BMC Bioinform., 2006)

Bayesian binning beats approximate alternatives: estimating peri-stimulus time histograms. - Dominik Endres; Mike W. Oram; Johannes E. Schindelin; Peter Földiák (NIPS, 2007)

A high-level 3D visualization API for Java and ImageJ. - Benjamin Schmid; Johannes E. Schindelin; Albert Cardona; Mark Longair; Martin Heisenberg (BMC Bioinform., 2010)

Trainable Weka Segmentation: a machine learning tool for microscopy pixel classification. - Ignacio Arganda-Carreras; Verena Kaynig; Curtis Rueden; Kevin W. Eliceiri; Johannes E. Schindelin; Albert Cardona; H. Sebastian Seung (Bioinform., 2017)

ImageJ2: ImageJ for the next generation of scientific image data. - Curtis T. Rueden; Johannes E. Schindelin; Mark C. Hiner; Barry E. DeZonia; Alison E. Walter; Ellen T. Arena; Kevin W. Eliceiri (BMC Bioinform., 2017)

ImageJ2: ImageJ for the next generation of scientific image data. - Curtis T. Rueden; Johannes E. Schindelin; Mark C. Hiner; Barry E. DeZonia; Alison E. Walter; Kevin W. Eliceiri (CoRR, 2017)

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)