Biblio

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2017
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).
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.
Blasse C, Saalfeld S, Etournay R, Sagner A, Eaton S, Myers EW.  2017.  PreMosa: Extracting 2D surfaces from 3D microscopy mosaics.. Bioinformatics (Oxford, England). 33(16):2563-9.
Hildebrand DGrant Colb, Cicconet M, Torres RMiguel, Choi W, Quan TMinh, Moon J, Wetzel AWillis, Champion AScott, Graham BJesse, Randlett O et al..  2017.  Whole-brain serial-section electron microscopy in larval zebrafish.. Nature. 545(7654):345-349.
2016
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).
Schneider-Mizell CM, Gerhard S, Longair M, Kazimiers T, Li F, Zwart M, Champion A, Midgley F, Fetter RD, Saalfeld S et al..  2016.  Quantitative neuroanatomy for connectomics in Drosophila.. eLife. :e12059.
Bogovic JA, Hanslovsky P, Wong AM, Saalfeld S.  2016.  Robust registration of calcium images by learned contrast synthesis.. IEEE 13th International Symposium on Biomedical Imaging: From Nano to Macro.
2015
Pietzsch T, Saalfeld S, Preibisch S, Tomancak P.  2015.  BigDataViewer: visualization and processing for large image data sets.. Nature Methods. 12(6):481-3.
Hanslovsky P, Bogovic JA, Saalfeld S.  2015.  Post-acquisition image based compensation for thickness variation in microscopy section series.. IEEE International Symposium on Biomedical Imaging. :507-11.
Hanslovsky P, Bogovic J, Saalfeld S.  2015.  Post-acquisition image based compensation for thickness variation in microscopy section series.. IEEE 12th International Symposium on Biomedical Imaging (ISBI).
Jambor H, Surendranath V, Kalinka AT, Mejstrik P, Saalfeld S, Tomancak P.  2015.  Systematic imaging reveals features and changing localization of mRNAs in Drosophila development.. Elife. 4
2012
Pietzsch T, Preibisch S, Tomancak P, Saalfeld S.  2012.  Advanced Programming with ImgLib2. Proceedings of the ImageJ User and Developer Conference.
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.
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.
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.
Preibisch S, Pietzsch T, Myers E, Tomancak P, Saalfeld S.  2012.  Introduction to ImgLib2. Proceedings of the ImageJ User and Developer Conference.
Cardona A, Saalfeld S, Schindelin J, Arganda-Carreras I, Preibisch S, Longair M, Tomancak P, Hartenstein V, Douglas RJ.  2012.  TrakEM2 software for neural circuit reconstruction.. PLoS One. 7:e38011.
Cardona A, Saalfeld S, Schindelin J, Arganda-Carreras I, Preibisch S, Longair M, Tomancak P, Hartenstein V, Douglas RJ.  2012.  TrakEM2 software for neural circuit reconstruction.. PLoS One. 7(6):e38011.
2010
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.
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.
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.
Preibisch S, Saalfeld S, Schindelin J, Tomancak P.  2010.  Software for bead-based registration of selective plane illumination microscopy data.. Nature Methods. 7(6):418-9.
2009
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.