Saalfeld, Stephan

Fiji: an open-source platform for biological-image analysis

Schindelin, J., Arganda-Carreras, I., Frise, E., Kaynig, V., Longair, M., Pietzsch, T., Preibisch, S., Rueden, C., Saalfeld, S., Schmid, B., et al. (2012) · Nature Methods

Cell Image Analysis TechniquesScientific Computing and Data Management

Cited by 66,890

Globally optimal stitching of tiled 3D microscopic image acquisitions

Preibisch, S., Saalfeld, S., & Tomancak, P. (2009) · Bioinformatics

Cell Image Analysis TechniquesImage Processing Techniques and Applications

Cited by 2,452

A connectome and analysis of the adult Drosophila central brain

Scheffer, L. K., Xu, C. S., Januszewski, M., Lu, Z., Takemura, S.-Y., Hayworth, K. J., Huang, G. B., Shinomiya, K., Maitlin-Shepard, J., Berg, S., et al. (2020) · eLife

Neurobiology and Insect Physiology ResearchCell Image Analysis Techniques

Cited by 1,128

A Complete Electron Microscopy Volume of the Brain of Adult Drosophila melanogaster

Zheng, Z., Lauritzen, J. S., Perlman, E., Robinson, C. G., Nichols, M., Milkie, D., Torrens, O., Price, J., Fisher, C. B., Sharifi, N., et al. (2018) · Cell

Neurobiology and Insect Physiology ResearchNeuroscience and Neuropharmacology Research

Cited by 1,050

CATMAID: collaborative annotation toolkit for massive amounts of image data

Saalfeld, S., Cardona, A., Hartenstein, V., & Tomančák, P. (2009) · Bioinformatics

Cell Image Analysis TechniquesAdvanced Electron Microscopy Techniques and Applications

Cited by 384

An Integrated Micro- and Macroarchitectural Analysis of the Drosophila Brain by Computer-Assisted Serial Section Electron Microscopy

Cardona, A., Saalfeld, S., Preibisch, S., Schmid, B., Cheng, A., Pulokas, J., Tomancak, P., & Hartenstein, V. (2010) · PLoS Biology

Neurobiology and Insect Physiology ResearchCell Image Analysis Techniques

Cited by 372

Quantitative neuroanatomy for connectomics in Drosophila

Schneider-Mizell, C. M., Gerhard, S., Longair, M., Kazimiers, T., Li, F., Zwart, M. F., Champion, A., Midgley, F. M., Fetter, R. D., Saalfeld, S., et al. (2016) · eLife

Neurobiology and Insect Physiology ResearchCell Image Analysis Techniques

Cited by 332

Elastic volume reconstruction from series of ultra-thin microscopy sections

Saalfeld, S., Fetter, R., Cardona, A., & Tomancak, P. (2012) · Nature Methods

Advanced Electron Microscopy Techniques and ApplicationsCell Image Analysis Techniques

Cited by 329

Automatic detection of synaptic partners in a whole-brain Drosophila electron microscopy data set

Buhmann, J., Sheridan, A., Malin-Mayor, C., Schlegel, P., Gerhard, S., Kazimiers, T., Krause, R., Nguyen, T. M., Heinrich, L., Lee, W.-C. A., et al. (2021) · Nature Methods

Cell Image Analysis TechniquesNeurobiology and Insect Physiology Research

Cited by 175

An unbiased template of the Drosophila brain and ventral nerve cord

Bogovic, J. A., Otsuna, H., Heinrich, L., Ito, M., Jeter, J., Meissner, G., Nern, A., Colonell, J., Malkesman, O., Ito, K., et al. (2020) · PLOS ONE

Cell Image Analysis TechniquesNeurobiology and Insect Physiology Research

Cited by 131

Synaptic Cleft Segmentation in Non-isotropic Volume Electron Microscopy of the Complete Drosophila Brain

Heinrich, L., Funke, J., Pape, C., Nunez-Iglesias, J., & Saalfeld, S. (2018) · Lecture Notes in Computer Science

Cell Image Analysis TechniquesMedical Image Segmentation Techniques

Cited by 117

Connectome-driven neural inventory of a complete visual system

Nern, A., Loesche, F., Takemura, S.-Y., Burnett, L. E., Dreher, M., Gruntman, E., Hoeller, J., Huang, G. B., Januszewski, M., Klapoetke, N. C., et al. (2024) · Nature

Neurobiology and Insect Physiology ResearchVisual perception and processing mechanisms

Cited by 98

A Connectome of the Male Drosophila Ventral Nerve Cord

Takemura, S.-Y., Hayworth, K. J., Huang, G. B., Januszewski, M., Lu, Z., Marin, E. C., Preibisch, S., Xu, C. S., Bogovic, J., Champion, A. S., et al. (2023) · bioRxiv (Cold Spring Harbor Laboratory)

Neurobiology and Insect Physiology ResearchNeuroscience and Neuropharmacology Research

Cited by 74

A Connectome of the Male Drosophila Ventral Nerve Cord

Takemura, S.-Y., Hayworth, K. J., Huang, G. B., Januszewski, M., Lu, Z., Marin, E. C., Preibisch, S., Xu, C. S., Bogovic, J., Champion, A. S., et al. (2024) · eLife

Neurobiology and Insect Physiology ResearchNeuroscience and Neuropharmacology Research

Cited by 54

Petascale pipeline for precise alignment of images from serial section electron microscopy

Popovych, S., Macrina, T., Kemnitz, N., Castro, M., Nehoran, B., Jia, Z., Bae, J. A., Mitchell, E., Mu, S., Trautman, E. T., et al. (2024) · Nature Communications

Advanced Electron Microscopy Techniques and ApplicationsCell Image Analysis Techniques

Cited by 39

Automatic Detection of Synaptic Partners in a Whole-Brain Drosophila EM Dataset

Buhmann, J., Sheridan, A., Gerhard, S., Krause, R., Nguyen, T., Heinrich, L., Schlegel, P., Lee, W.-C. A., Wilson, R., Saalfeld, S., et al. (2019) · bioRxiv (Cold Spring Harbor Laboratory)

Cell Image Analysis TechniquesNeurobiology and Insect Physiology Research

Cited by 21

Author response: A connectome and analysis of the adult Drosophila central brain

Scheffer, L. K., Xu, C. S., Januszewski, M., Lu, Z., Takemura, S.-Y., Hayworth, K. J., Huang, G. B., Shinomiya, K., Maitlin-Shepard, J., Berg, S., et al. (2020) · eLife

Neurobiology and Insect Physiology ResearchNeuroscience and Neuropharmacology Research

Cited by 14