Stephan Saalfeld - Publications

Affiliations: 
2007-2008 Institute of Neuroinformatics ETH/Uni Zurich, Zürich, Zürich, Switzerland 

31 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
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  1
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  0.01
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  1
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  0.01
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  0.01
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  1
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  0.01
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  0.01
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  0.01
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  0.01
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  0.01
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  0.01
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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