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Stephan Saalfeld - Publications

Affiliations: 
2007-2008 Institute of Neuroinformatics ETH/Uni Zurich, Zürich, Zürich, Switzerland 
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30/46 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2024 Popovych S, Macrina T, Kemnitz N, Castro M, Nehoran B, Jia Z, Bae JA, Mitchell E, Mu S, Trautman ET, Saalfeld S, Li K, Seung HS. Petascale pipeline for precise alignment of images from serial section electron microscopy. Nature Communications. 15: 289. PMID 38177169 DOI: 10.1038/s41467-023-44354-0  0.314
2023 Heinrich L, Patton W, Bennett D, Ackerman D, Park G, Bogovic JA, Eckstein N, Petruncio A, Clements J, Pang S, Shan Xu C, Funke J, Korff W, Hess H, Lippincott-Schwartz J, ... Saalfeld S, et al. Towards Generalizable Organelle Segmentation in Volume Electron Microscopy. Microscopy and Microanalysis : the Official Journal of Microscopy Society of America, Microbeam Analysis Society, Microscopical Society of Canada. 29: 975. PMID 37613645 DOI: 10.1093/micmic/ozad067.487  0.692
2022 Sheridan A, Nguyen TM, Deb D, Lee WA, Saalfeld S, Turaga SC, Manor U, Funke J. Local shape descriptors for neuron segmentation. Nature Methods. PMID 36585455 DOI: 10.1038/s41592-022-01711-z  0.717
2022 Lillvis JL, Otsuna H, Ding X, Pisarev I, Kawase T, Colonell J, Rokicki K, Goina C, Gao R, Hu A, Wang K, Bogovic J, Milkie DE, Meienberg L, Mensh BD, ... ... Saalfeld S, et al. Rapid reconstruction of neural circuits using tissue expansion and light sheet microscopy. Elife. 11. PMID 36286237 DOI: 10.7554/eLife.81248  0.311
2022 Zhu PP, Hung HF, Batchenkova N, Nixon-Abell J, Henderson J, Zheng P, Renvoisé B, Pang S, Xu CS, Saalfeld S, Funke J, Xie Y, Svara F, Hess HF, Blackstone C. Transverse endoplasmic reticulum expansion in hereditary spastic paraplegia corticospinal axons. Human Molecular Genetics. PMID 35348668 DOI: 10.1093/hmg/ddac072  0.67
2021 Heinrich L, Bennett D, Ackerman D, Park W, Bogovic J, Eckstein N, Petruncio A, Clements J, Pang S, Xu CS, Funke J, Korff W, Hess HF, Lippincott-Schwartz J, Saalfeld S, et al. Whole-cell organelle segmentation in volume electron microscopy. Nature. PMID 34616042 DOI: 10.1038/s41586-021-03977-3  0.735
2021 Buhmann J, Sheridan A, Malin-Mayor C, Schlegel P, Gerhard S, Kazimiers T, Krause R, Nguyen TM, Heinrich L, Lee WA, Wilson R, Saalfeld S, Jefferis GSXE, Bock DD, Turaga SC, et al. Automatic detection of synaptic partners in a whole-brain Drosophila electron microscopy data set. Nature Methods. PMID 34168373 DOI: 10.1038/s41592-021-01183-7  0.752
2020 Scheffer LK, Xu CS, Januszewski M, Lu Z, Takemura SY, Hayworth KJ, Huang GB, Shinomiya K, Maitlin-Shepard J, Berg S, Clements J, Hubbard PM, Katz WT, Umayam L, Zhao T, ... ... Saalfeld S, et al. A connectome and analysis of the adult central brain. Elife. 9. PMID 32880371 DOI: 10.7554/Elife.57443  0.74
2019 Saalfeld S. Computational methods for stitching, alignment, and artifact correction of serial section data. Methods in Cell Biology. 152: 261-276. PMID 31326024 DOI: 10.1016/Bs.Mcb.2019.04.007  0.411
2019 Gao R, Asano SM, Upadhyayula S, Pisarev I, Milkie DE, Liu TL, Singh V, Graves A, Huynh GH, Zhao Y, Bogovic J, Colonell J, Ott CM, Zugates C, Tappan S, ... ... Saalfeld S, et al. Cortical column and whole-brain imaging with molecular contrast and nanoscale resolution. Science (New York, N.Y.). 363. PMID 30655415 DOI: 10.1126/Science.Aau8302  0.413
2018 Zheng Z, Lauritzen JS, Perlman E, Robinson CG, Nichols M, Milkie D, Torrens O, Price J, Fisher CB, Sharifi N, Calle-Schuler SA, Kmecova L, Ali IJ, Karsh B, Trautman ET, ... ... Saalfeld S, et al. A Complete Electron Microscopy Volume of the Brain of Adult Drosophila melanogaster. Cell. PMID 30033368 DOI: 10.1016/J.Cell.2018.06.019  0.454
2018 Funke J, Tschopp FD, Grisaitis W, Sheridan A, Singh C, Saalfeld S, Turaga SC. Large Scale Image Segmentation with Structured Loss based Deep Learning for Connectome Reconstruction. Ieee Transactions On Pattern Analysis and Machine Intelligence. PMID 29993708 DOI: 10.1109/Tpami.2018.2835450  0.727
2017 Hildebrand DGC, Cicconet M, Torres RM, Choi W, Quan TM, Moon J, Wetzel AW, Scott Champion A, Graham BJ, Randlett O, Plummer GS, Portugues R, Bianco IH, Saalfeld S, Baden AD, et al. Whole-brain serial-section electron microscopy in larval zebrafish. Nature. PMID 28489821 DOI: 10.1038/Nature22356  0.482
2017 Hanslovsky P, Bogovic JA, Saalfeld S. Image-based correction of continuous and discontinuous non-planar axial distortion in serial section microscopy. Bioinformatics (Oxford, England). 33: 1379-1386. PMID 28453669 DOI: 10.1093/Bioinformatics/Btw794  0.39
2016 Schneider-Mizell CM, Gerhard S, Longair M, Kazimiers T, Li F, Zwart MF, Champion A, Midgley FM, Fetter RD, Saalfeld S, Cardona A. Quantitative neuroanatomy for connectomics in Drosophila. Elife. 5. PMID 26990779 DOI: 10.7554/Elife.12059  0.672
2016 Schneider-Mizell CM, Gerhard S, Longair M, Kazimiers T, Li F, Zwart MF, Champion A, Midgley FM, Fetter RD, Saalfeld S, Cardona A. Author response: Quantitative neuroanatomy for connectomics in Drosophila Elife. DOI: 10.7554/Elife.12059.032  0.628
2015 Pietzsch T, Saalfeld S, Preibisch S, Tomancak P. BigDataViewer: visualization and processing for large image data sets. Nature Methods. 12: 481-3. PMID 26020499 DOI: 10.1038/Nmeth.3392  0.3
2015 Hanslovsky P, Bogovic JA, Saalfeld S. Post-acquisition image based compensation for thickness variation in microscopy section series Proceedings - International Symposium On Biomedical Imaging. 2015: 507-511. DOI: 10.1109/ISBI.2015.7163922  0.303
2014 Jambor H, Surendranath V, Kalinka AT, Mejstrik P, Saalfeld S, Tomancak P. Author response: Systematic imaging reveals features and changing localization of mRNAs in Drosophila development Elife. DOI: 10.7554/Elife.05003.028  0.332
2012 Pietzsch T, Preibisch S, Tomancák P, Saalfeld S. ImgLib2--generic image processing in Java. Bioinformatics (Oxford, England). 28: 3009-11. PMID 22962343 DOI: 10.1093/bioinformatics/bts543  0.314
2012 Schindelin J, Arganda-Carreras I, Frise E, Kaynig V, Longair M, Pietzsch T, Preibisch S, Rueden C, Saalfeld S, Schmid B, Tinevez JY, White DJ, Hartenstein V, Eliceiri K, Tomancak P, et al. Fiji: an open-source platform for biological-image analysis. Nature Methods. 9: 676-82. PMID 22743772 DOI: 10.1038/Nmeth.2019  0.724
2012 Cardona A, Saalfeld S, Schindelin J, Arganda-Carreras I, Preibisch S, Longair M, Tomancak P, Hartenstein V, Douglas RJ. TrakEM2 software for neural circuit reconstruction. Plos One. 7: e38011. PMID 22723842 DOI: 10.1371/Journal.Pone.0038011  0.774
2012 Saalfeld S, Fetter R, Cardona A, Tomancak P. Elastic volume reconstruction from series of ultra-thin microscopy sections. Nature Methods. 9: 717-20. PMID 22688414 DOI: 10.1038/Nmeth.2072  0.581
2010 Cardona A, Saalfeld S, Preibisch S, Schmid B, Cheng A, Pulokas J, Tomancak P, Hartenstein V. An integrated micro- and macroarchitectural analysis of the Drosophila brain by computer-assisted serial section electron microscopy. Plos Biology. 8. PMID 20957184 DOI: 10.1371/Journal.Pbio.1000502  0.731
2010 Saalfeld S, Cardona A, Hartenstein V, Toman?ák P. As-rigid-as-possible mosaicking and serial section registration of large ssTEM datasets. Bioinformatics (Oxford, England). 26: i57-63. PMID 20529937 DOI: 10.1093/Bioinformatics/Btq219  0.691
2010 Cardona A, Saalfeld S, Arganda I, Pereanu W, Schindelin J, Hartenstein V. Identifying neuronal lineages of Drosophila by sequence analysis of axon tracts. The Journal of Neuroscience : the Official Journal of the Society For Neuroscience. 30: 7538-53. PMID 20519528 DOI: 10.1523/Jneurosci.0186-10.2010  0.684
2009 Cardona A, Saalfeld S, Tomancak P, Hartenstein V. Drosophila brain development: closing the gap between a macroarchitectural and microarchitectural approach. Cold Spring Harbor Symposia On Quantitative Biology. 74: 235-48. PMID 20028843 DOI: 10.1101/Sqb.2009.74.037  0.721
2009 Saalfeld S, Cardona A, Hartenstein V, Tomancak P. CATMAID: collaborative annotation toolkit for massive amounts of image data. Bioinformatics (Oxford, England). 25: 1984-6. PMID 19376822 DOI: 10.1093/Bioinformatics/Btp266  0.679
2009 Preibisch S, Saalfeld S, Tomancak P. Globally optimal stitching of tiled 3D microscopic image acquisitions. Bioinformatics (Oxford, England). 25: 1463-5. PMID 19346324 DOI: 10.1093/Bioinformatics/Btp184  0.379
2009 Preibisch S, Saalfeld S, Rohlfing T, Tomancak P. Bead-based mosaicing of single plane illumination microscopy images using geometric local descriptor matching Progress in Biomedical Optics and Imaging - Proceedings of Spie. 7259. DOI: 10.1117/12.812612  0.378
Low-probability matches (unlikely to be authored by this person)
2016 Vogelstein JT, Mensh B, Häusser M, Spruston N, Evans AC, Kording K, Amunts K, Ebell C, Muller J, Telefont M, Hill S, Koushika SP, Calì C, Valdés-Sosa PA, Littlewood PB, ... ... Saalfeld S, et al. To the Cloud! A Grassroots Proposal to Accelerate Brain Science Discovery Neuron. 92: 622-627. PMID 27810005 DOI: 10.1016/J.Neuron.2016.10.033  0.296
2022 Mahalingam G, Torres R, Kapner D, Trautman ET, Fliss T, Seshamani S, Perlman E, Young R, Kinn S, Buchanan J, Takeno MM, Yin W, Bumbarger DJ, Gwinn RP, Nyhus J, ... ... Saalfeld S, et al. A scalable and modular automated pipeline for stitching of large electron microscopy datasets. Elife. 11. PMID 35880860 DOI: 10.7554/eLife.76534  0.287
2017 Blasse C, Saalfeld S, Etournay R, Sagner A, Eaton S, Myers EW. PreMosa: Extracting 2D surfaces from 3D microscopy mosaics. Bioinformatics (Oxford, England). PMID 28383656 DOI: 10.1093/Bioinformatics/Btx195  0.282
2017 Patwardhan A, Brandt R, Butcher SJ, Collinson L, Gault D, Grünewald K, Hecksel C, Huiskonen JT, Iudin A, Jones ML, Korir PK, Koster AJ, Lagerstedt I, Lawson CL, Mastronarde D, ... ... Saalfeld S, et al. Building bridges between cellular and molecular structural biology. Elife. 6. PMID 28682240 DOI: 10.7554/Elife.25835  0.28
2010 Preibisch S, Saalfeld S, Schindelin J, Tomancak P. Software for bead-based registration of selective plane illumination microscopy data. Nature Methods. 7: 418-9. PMID 20508634 DOI: 10.1038/Nmeth0610-418  0.28
2017 Patwardhan A, Brandt R, Butcher SJ, Collinson L, Gault D, Grünewald K, Hecksel C, Huiskonen JT, Iudin A, Jones ML, Korir PK, Koster AJ, Lagerstedt I, Lawson CL, Mastronarde D, ... ... Saalfeld S, et al. Author response: Building bridges between cellular and molecular structural biology Elife. DOI: 10.7554/Elife.25835.008  0.275
2016 Hanslovsky P, Bogovic JA, Saalfeld S. Image-based correction of continuous and discontinuous non-planar axial distortion in serial section microscopy. Bioinformatics (Oxford, England). PMID 28011788 DOI: 10.1093/bioinformatics/btw794  0.272
2015 Jambor H, Surendranath V, Kalinka AT, Mejstrik P, Saalfeld S, Tomancak P. Systematic imaging reveals features and changing localization of mRNAs in Drosophila development. Elife. 4. PMID 25838129 DOI: 10.7554/Elife.05003  0.243
2020 Bogovic JA, Otsuna H, Heinrich L, Ito M, Jeter J, Meissner G, Nern A, Colonell J, Malkesman O, Ito K, Saalfeld S. An unbiased template of the Drosophila brain and ventral nerve cord. Plos One. 15: e0236495. PMID 33382698 DOI: 10.1371/journal.pone.0236495  0.241
2016 Bogovic JA, Hanslovsky P, Wong A, Saalfeld S. Robust registration of calcium images by learned contrast synthesis Proceedings - International Symposium On Biomedical Imaging. 2016: 1123-1126. DOI: 10.1109/ISBI.2016.7493463  0.218
2021 Wang Y, Eddison M, Fleishman G, Weigert M, Xu S, Wang T, Rokicki K, Goina C, Henry FE, Lemire AL, Schmidt U, Yang H, Svoboda K, Myers EW, Saalfeld S, et al. EASI-FISH for thick tissue defines lateral hypothalamus spatio-molecular organization. Cell. PMID 34875226 DOI: 10.1016/j.cell.2021.11.024  0.214
2023 Zhu J, Boivin JC, Pang S, Xu CS, Lu Z, Saalfeld S, Hess HF, Ohyama T. Comparative connectomics and escape behavior in larvae of closely related Drosophila species. Current Biology : Cb. PMID 37285846 DOI: 10.1016/j.cub.2023.05.043  0.187
2023 Bharathan NK, Giang W, Hoffman CL, Aaron JS, Khuon S, Chew TL, Preibisch S, Trautman ET, Heinrich L, Bogovic J, Bennett D, Ackerman D, Park W, Petruncio A, Weigel AV, ... Saalfeld S, et al. Architecture and dynamics of a desmosome-endoplasmic reticulum complex. Nature Cell Biology. PMID 37291267 DOI: 10.1038/s41556-023-01154-4  0.151
2023 Moore J, Basurto-Lozada D, Besson S, Bogovic J, Brown EM, Burel JM, de Medeiros G, Diel EE, Gault D, Ghosh SS, Gold I, Halchenko YO, Hartley M, Horsfall D, Keller MS, ... ... Saalfeld S, et al. OME-Zarr: a cloud-optimized bioimaging file format with international community support. Biorxiv : the Preprint Server For Biology. PMID 36865282 DOI: 10.1101/2023.02.17.528834  0.11
2024 Bharathan NK, Giang W, Hoffman CL, Aaron JS, Khuon S, Chew TL, Preibisch S, Trautman ET, Heinrich L, Bogovic J, Bennett D, Ackerman D, Park W, Petruncio A, Weigel AV, ... Saalfeld S, et al. Author Correction: Architecture and dynamics of a desmosome-endoplasmic reticulum complex. Nature Cell Biology. PMID 38347183 DOI: 10.1038/s41556-024-01376-0  0.105
2023 Moore J, Basurto-Lozada D, Besson S, Bogovic J, Bragantini J, Brown EM, Burel JM, Casas Moreno X, de Medeiros G, Diel EE, Gault D, Ghosh SS, Gold I, Halchenko YO, Hartley M, ... ... Saalfeld S, et al. OME-Zarr: a cloud-optimized bioimaging file format with international community support. Histochemistry and Cell Biology. PMID 37428210 DOI: 10.1007/s00418-023-02209-1  0.103
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