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Globally optimal stitching of tiled 3D microscopic image acquisitions.
Preibisch S, Saalfeld S, Tomancak P. Preibisch S, et al. Bioinformatics. 2009 Jun 1;25(11):1463-5. doi: 10.1093/bioinformatics/btp184. Epub 2009 Apr 3. Bioinformatics. 2009. PMID: 19346324 Free PMC article.
Whole-brain serial-section electron microscopy in larval zebrafish.
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, Lillaney K, Burns R, Vogelstein JT, Schier AF, Lee WA, Jeong WK, Lichtman JW, Engert F. Hildebrand DGC, et al. Nature. 2017 May 18;545(7654):345-349. doi: 10.1038/nature22356. Epub 2017 May 10. Nature. 2017. PMID: 28489821 Free PMC article.
Elastic volume reconstruction from series of ultra-thin microscopy sections.
Saalfeld S, Fetter R, Cardona A, Tomancak P. Saalfeld S, et al. Nat Methods. 2012 Jun 10;9(7):717-20. doi: 10.1038/nmeth.2072. Nat Methods. 2012. PMID: 22688414
BigDataViewer: visualization and processing for large image data sets.
Pietzsch T, Saalfeld S, Preibisch S, Tomancak P. Pietzsch T, et al. Nat Methods. 2015 Jun;12(6):481-3. doi: 10.1038/nmeth.3392. Nat Methods. 2015. PMID: 26020499 No abstract available.
PreMosa: extracting 2D surfaces from 3D microscopy mosaics.
Blasse C, Saalfeld S, Etournay R, Sagner A, Eaton S, Myers EW. Blasse C, et al. Bioinformatics. 2017 Aug 15;33(16):2563-2569. doi: 10.1093/bioinformatics/btx195. Bioinformatics. 2017. PMID: 28383656
ImgLib2--generic image processing in Java.
Pietzsch T, Preibisch S, Tomancák P, Saalfeld S. Pietzsch T, et al. Bioinformatics. 2012 Nov 15;28(22):3009-11. doi: 10.1093/bioinformatics/bts543. Epub 2012 Sep 8. Bioinformatics. 2012. PMID: 22962343 Free PMC article.
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, Tinevez JY, White DJ, Hartenstein V, Eliceiri K, Tomancak P, Cardona A. Schindelin J, et al. Nat Methods. 2012 Jun 28;9(7):676-82. doi: 10.1038/nmeth.2019. Nat Methods. 2012. PMID: 22743772 Free PMC article.
As-rigid-as-possible mosaicking and serial section registration of large ssTEM datasets.
Saalfeld S, Cardona A, Hartenstein V, Tomančák P. Saalfeld S, et al. Bioinformatics. 2010 Jun 15;26(12):i57-63. doi: 10.1093/bioinformatics/btq219. Bioinformatics. 2010. PMID: 20529937 Free PMC article.
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