Biblio

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2026
Lian Y, Adjavon D-Y, Kawase T, Kim J, Fleishman G, Preibisch S, Funke J, Liu ZJ.  2026.  Machine learning-guided spatial omics for tissue-scale discovery of cell-type-specific architectures. bioRxiv.
2025
Gandin V, Kim J, Yang L-Z, Lian Y, Kawase T, Hu A, Rokicki K, Fleishman G, Tillberg P, Castrejon AAguilera et al..  2025.  Deep-tissue transcriptomics and subcellular imaging at high spatial resolution. Science.
Santos NDos, Aquino A, Preußer F, Rusak FRojas, Jandrey EHelena Far, Uno M, Furuya TKatsue, Lancellotti CLucia Pent, Maldaun MVinicius C, Chammas R et al..  2025.  Innovative In Vivo Imaging and Single Cell Expression from Tumor Bulk and Corpus Callosum Reveal Glioma Stem Cells with Unique Regulatory Programs. Cancers. 17:3851.
Santos NDos, Aquino A, Preußer F, Rusak FRojas, Jandrey EHelena Far, Uno M, Furuya TKatsue, Lancellotti CLucia Pent, Maldaun MVinicius C, Chammas R et al..  2025.  Innovative In Vivo Imaging and Single Cell Expression from Tumor Bulk and Corpus Callosum Reveal Glioma Stem Cells with Unique Regulatory Programs. Cancers. 17:3851.
Preibisch S, Innerberger M, León-Periñán D, Karaiskos N, Rajewsky N.  2025.  Scalable image-based visualization and alignment of spatial transcriptomics datasets. Cell Syst.
Berg S, Beckett IR, Costa M, Schlegel P, Januszewski M, Marin EC, Nern A, Preibisch S, Qiu W, Takemura S-ya et al..  2025.  Sexual dimorphism in the complete connectome of the Drosophila male central nervous system. bioRxiv.
2024
Breimann L, Bahry E, Zouinkhi M, Kolyvanov K, Street LAnnika, Preibisch S, Ercan S.  2024.  Analysis of developmental gene expression using smFISH and in silico staging of C. elegans embryos. bioRxiv.
Breimann L, Bahry E, Zouinkhi M, Kolyvanov K, Street LAnnika, Preibisch S, Ercan S.  2024.  Analysis of developmental gene expression using smFISH and in silico staging of C. elegans embryos. bioRxiv.
Ackerman D, Avetissian E, Bleck CKE, Bogovic JA, Innerberger M, Korff W, Li W-P, Lu Z, Petruncio A, Preibisch S et al..  2024.  Data Release: High-Resolution Imaging and Segmentation of P7 Mouse Tissue Microarchitecture Using FIB-SEM and Machine Learning. bioRxiv.
2023
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.
Malin-Mayor C, Hirsch P, Guignard L, McDole K, Wan Y, Lemon WC, Kainmueller D, Keller PJ, Preibisch S, Funke J.  2023.  Automated reconstruction of whole-embryo cell lineages by learning from sparse annotations.. Nature Biotechnology. 41(1):44-49.
2022
Malin-Mayor C, Hirsch P, Guignard L, McDole K, Wan Y, Lemon WC, Kainmueller D, Keller PJ, Preibisch S, Funke J.  2022.  Automated reconstruction of whole-embryo cell lineages by learning from sparse annotations.. Nature Biotechnology.
Nielsen AF, Bindereif A, Bozzoni I, Hanan M, Hansen TB, Irimia M, Kadener S, Kristensen LS, Legnini I, Morlando M et al..  2022.  Best practice standards for circular RNA research. Nature Methods. 19(10):1208-1220.
Gandin V, English BP, Freeman M, Leroux L-P, Preibisch S, Walpita D, Jaramillo M, Singer RH.  2022.  Cap-dependent translation initiation monitored in living cells.. Nature Communications. 13(1):6558.
2021
Preusser F, Santos NDos, Contzen J, Stachelscheid H, Costa ÉTosoni, Mergenthaler P, Preibisch S.  2021.  FRC-QE: a robust and comparable 3D microscopy image quality metric for cleared organoids.. Bioinformatics. 37(18):3088-3090.
Stelzer EHK, Strobl F, Chang B-J, Preusser F, Preibisch S, McDole K, Fiolka R.  2021.  Light sheet fluorescence microscopy.. Nature Reviews Methods Primers. 1(1)
2019
Hörl D, Rusak FRojas, Preusser F, Tillberg P, Randel N, Chhetri RK, Cardona A, Keller PJ, Harz H, Leonhardt H et al..  2019.  BigStitcher: reconstructing high-resolution image datasets of cleared and expanded samples.. Nature Methods. 16(9):870-74.
2018
Vladimirov N, Wang C, Höckendorf B, Pujala A, Tanimoto M, Mu Y, Yang C-T, Wittenbach J, Freeman J, Preibisch S et al..  2018.  Brain-wide circuit interrogation at the cellular level guided by online analysis of neuronal function.. Nature Methods. 15(12):1117-1125.
2017
Wolff C, Tinevez J-Y, Pietzsch T, Stamataki E, Harich B, Guignard L, Preibisch S, Shorte S, Keller PJ, Tomancak P et al..  2017.  Multi-view light-sheet imaging and tracking with the MaMuT software reveals the cell lineage of a direct developing arthropod limb.. eLife. 7:e34410.
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.
Smith CS, Preibisch S, Joseph A, Abrahamsson S, Rieger B, Myers E, Singer RH, Grunwald D.  2015.  Nuclear accessibility of β-actin mRNA is measured by 3D single-molecule real-time tracking.. Journal of Cell Biology. 209(4):609-19.
2014
Jug F, Pietzsch T, Preibisch S, Tomancak P.  2014.  Bioimage informatics in the context of Drosophila research.. Methods. 68(1):60-73.
Preibisch S, Amat F, Stamataki E, Sarov M, Singer RH, Myers E, Tomancak P.  2014.  Efficient Bayesian-based multiview deconvolution.. Nature Methods. 11:645-8.
2012
Pietzsch T, Preibisch S, Tomancak P, Saalfeld S.  2012.  Advanced Programming with ImgLib2. 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.