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A
Pietzsch T, Preibisch S, Tomancak P, Saalfeld S.  2012.  Advanced Programming with ImgLib2. Proceedings of the ImageJ User and Developer Conference.
Bharathan NKrishnan, Giang W, Hoffman CL, Aaron JS, Khuon S, Chew T-L, Preibisch S, Trautman ET, Heinrich L, Bogovic J et al..  2023.  Architecture and dynamics of a desmosome-endoplasmic reticulum complex.. Nature Cell Biology. 25(6):823-835.
Saalfeld S, Cardona A, Hartenstein V, Tomancak P..  2010.  As-rigid-as-possible mosaicking and serial section registration of large ssTEM datasets.. Bioinformatics. 26(12):i57-63.
Buhmann J, Sheridan A, Gerhard S, Krause R, Nguyen T, Heinrich L, Schlegel P, Lee W-CAllen, Wilson R, Saalfeld S et al..  2021.  Automatic Detection of Synaptic Partners in a Whole-Brain Drosophila EM Dataset. Nature Methods. 18(7):771-4.
Saalfeld S, Tomancak P.  2008.  Automatic landmark correspondence detection for ImageJ.. Proceedings of the ImageJ User and Developer Conference.
B
Preibisch S, Saalfeld S, Rohlfing T, Tomancak P.  2009.  Bead-based mosaicing of single plane illumination microscopy images using geometric local descriptor matching.. Medical Imaging 2009: Image Processing. 7259:72592S.
Pietzsch T, Saalfeld S, Preibisch S, Tomancak P.  2015.  BigDataViewer: visualization and processing for large image data sets.. Nature Methods. 12(6):481-3.
Patwardhan A, Brandt R, Butcher SJ, Collinson L, Gault D, Grünewald K, Hecksel C, Huiskonen JT, Iudin, ii A, Jones ML et al..  2017.  Building bridges between cellular and molecular structural biology.. eLife. 6
C
Funke J, Zhang C, Pietzsch T, Ballester MAGonzalez, Saalfeld S.  2017.  The candidate multi-cut for cell segmentation.. 2018 IEEE 15th International Symposium on Biomedical Imaging (ISBI 2018).
Saalfeld S, Cardona A, Hartenstein V, Tomancak P.  2009.  CATMAID: collaborative annotation toolkit for massive amounts of image data.. Bioinformatics. 25(15):1984-6.
Zhu J, Boivin J-C, Pang S, C Xu S, Lu Z, Saalfeld S, Hess HF, Ohyama T.  2023.  Comparative connectomics and escape behavior in larvae of closely related Drosophila species.. Current Biology.
Saalfeld S.  2019.  Computational methods for stitching, alignment, and artifact correction of serial section data.. Methods in Cell Biology. 152:261-276.
Scheffer LK, C Xu S, Januszewski M, Lu Z, Takemura S-ya, Hayworth KJ, Huang GB, Shinomiya K, Maitlin-Shepard J, Berg S et al..  2020.  A connectome and analysis of the adult Drosophila central brain.. Elife. 9
D
Heinrich L, Bogovic JA, Saalfeld S.  2017.  Deep learning for isotropic super-resolution from non-isotropic 3D electron microscopy.. International Conference on Medical Image Computing and Computer-Assisted Intervention - MICCAI 2017. MICCAI 2017. Lecture Notes in Computer Science. 10434:arXiv:1706.03142.
E
Wang Y, Eddison M, Fleishman G, Weigert M, Xu S, Wang T, Rokicki K, Goina C, Henry FE, Lemire AL et al..  2021.  EASI-FISH for thick tissue defines lateral hypothalamus spatio-molecular organization.. Cell. 184(26):6361.
Saalfeld S, Fetter RD, Cardona A, Tomancak P..  2012.  Elastic volume reconstruction from series of ultra-thin microscopy sections.. Nature Methods. 9(7):717-20.
F
Preibisch S, Saalfeld S, Tomancak P.  2008.  Fast stitching of large 3d biological datasets.. Proceedings of the ImageJ User and Developer Conference.
Schindelin J, Arganda-Carreras I, Frise E, Kaynig V, Longair M, Pietzsch T, Preibisch S, Rueden C, Saalfeld S, Schmid B et al..  2012.  Fiji: an open-source platform for biological-image analysis.. Nature Methods. 9(7):676-82.
G
Preibisch S, Saalfeld S, Tomancak P.  2009.  Globally optimal stitching of tiled 3D microscopic image acquisitions.. Bioinformatics. 25(11):1463-5.
I
Cardona A, Saalfeld S, Arganda I, Pereanu W, Schindelin J, Hartenstein V..  2010.  Identifying neuronal lineages of Drosophila by sequence analysis of axon tracts.. The Journal of Neuroscience. 30(22):7538-53.
Hanslovsky P, Bogovic JA, Saalfeld S.  2016.  Image-based correction of continuous and discontinuous non-planar axial distortion in serial section microscopy.. Bioinformatics (Oxford, England).
Pietzsch T, Preibisch S, Tomancak P, Saalfeld S.  2012.  ImgLib2--generic image processing in Java.. Bioinformatics. 28(22):3009-11.
Saalfeld S, Pietzsch T, Tomancak P, Preibisch S.  2012.  ImgLib2—Generic Image Processing in Java. ImageJ User and Developer Conference.
Cardona A, Saalfeld S, Preibisch S, Schmid B, Cheng A, Pulokas J, Tomancak P, Hartenstein V..  2010.  An integrated micro- and macroarchitectural analysis of the Drosophila brain by computer-assisted serial section electron microscopy.. PLoS Biology. 8(10)
Preibisch S, Tomancak P, Saalfeld S.  2010.  Into ImgLib—Generic image processing in Java. Proceedings of the ImageJ User and Developer Conference.