Publications

Peer-reviewed original research articles:

(for an up-to-date list, see my profile on google scholar)

Publications before 2020:

H. Schneckenburger, V. Richter, M. Gelleri, S. Ritz, R. Vaz Pandolfo, F. Schock, J. v. Hase, U. Birk, C. Cremer: "High-resolution deep view microscopy of cells and tissues", Quantum Electronics, doi:10.1070/QEL17204 (2020)   [pdf]

U. Birk: "Super-Resolution Microscopy of Chromatin", Genes, doi:10.3390/genes10070493 (2019)   [pdf]

U. Birk, Ph. Roebrock: "User-position aware adaptive display of 3D data without additional stereoscopic hardware" SPIE Digital Library, Proc. SPIE 11041, Machine Vision Applications, doi:10.1117/12.2522678 (2019)   [pdf]

J. Neumann, K. Ziegler, M. Gelléri, J. Fröhlich-Nowoisky, F. Liu, I. Bellinghausen, D. Schuppan, U. Birk, U. Pöschl, C. Cremer, K. Lucas: "Nanoscale distribution of TLR4 on primary human macrophages stimulated with LPS and ATI." Nanoscale, doi:10.1039/c9nr00943d (2019)   [pdf]

C. Cremer, A. Szczurek, H. Strickfaden, U. Birk, M. Cremer, T. Cremer: "Der Zellkern–eine Stadt in der Zelle, Teil 2: Chromatin‐Nanoarchitektur und Genregulation." Biologie in unserer Zeit, doi:10.1002/biuz.201810640 (2018)   [pdf]

A. Szczurek, U. Birk, H. Knecht, J. Dobrucki, C. Cremer: "Super-resolution binding activated localization microscopy through reversible change of DNA conformation." doi:10.1080/19491034.2017.1419846 (2018)   [pdf]

U. Birk, A. Szczurek, C. Cremer: "Super-resolved Linear Fluorescence Localization Microscopy using Photostable Fluorophores: A Virtual Microscopy Study." Opt.Communications, doi:10.1016/j.optcom.2017.06.078 (2017)

U. Birk, J. v. Hase, C. Cremer: "Super-resolution microscopy with very large working distance by means of distributed aperture illumination." Sci.Rep., doi:10.1038/s41598-017-03743-4 (2017)   [pdf]

C. Cremer, A.T. Szczurek, F. Schock, A. Gourram, U. Birk: "Super-Resolution Microscopy Approaches to Nuclear Nanostructure Imaging." Methods, doi:10.1016/j.ymeth.2017.03.019 (2017)

A.T. Szczurek, L. Klewes, J. Xing, A. Gourram, U. Birk, H. Knecht, J.W. Dobrucki, S. Mai, C. Cremer: "Imaging chromatin nanostructure with binding-activated localisation microscopy based on DNA structure fluctuations." Nucleic Acids Research, doi:10.1093/nar/gkw1301 (2017)   [pdf]

A.T. Szczurek, J. Xing, U. Birk, C. Cremer: "Single Molecule Localization Microscopy of Mammalian Cell Nuclei on the Nanoscale." Front. Genet. 4:11, doi:10.3389/fgene.2016.00114 (2016).   [pdf]

C. Cremer, U. Birk: "Perspectives in Super-resolved Fluorescence Microscopy: What comes next?" Front. Phys. 4:11, doi:10.3389/fphy.2016.00011 (2016).   [pdf]

D. Zurek-Biesiada, A.T. Szczurek, K. Prakash, G. Best, G.K. Mohana, H.-K. Lee, J.Y. Roignant, J.W. Dobrucki, C. Cremer, U. Birk: "Quantitative super-resolution localization microscopy of DNA in situ using Vybrant DyeCycle Violet fluorescent probe." Data in Brief 7:157-171, doi:10.1016/j.dib.2016.01.041 (2016).

O. Oleksiuk, M. Abba, K.C. Tezcan, W. Schaufler, F. Bestvater, N. Patil, U. Birk, M. Hafner, P. Altevogt, C. Cremer, H. Allgayer: "Single-Molecule localization microscopy allows for the analysis of cancer metastasis-specific miRNA distribution on the nanoscale." Oncotarget doi:10.18632/oncotarget.6297 (2015).

I. Kirmes, A. Szczurek, K. Prakash, I. Charapitsa, C. Heiser, M. Musheev, F. Schock, K. Fornalczyk, D. Ma, U. Birk, C. Cremer, G. Reid: "A transient ischemic environment induces reversible compaction of chromatin." Genome Biology doi:10.1186/s13059-015-0802-2 (2015).   [biorxiv pdf]

K. Prakash, D. Fournier, S. Redl, G. Best, M. Borsos, V. Tiwari, K. Tachibana-Konwalski, R. Ketting, S. Parekh, C. Cremer, U. Birk: "Super-resolution imaging reveals structurally distinct periodic patterns of chromatin along pachytene chromosomes." PNAS (2015).   [biorxiv pdf]

D. Zurek-Biesiada, A.T. Szczurek, K. Prakash, G.K. Mohana, H.-K. Lee, J.Y. Roignant, U. Birk, J. Dobrucki, C. Cremer: "Localization microscopy of DNA in situ using Vybrant DyeCycle Violet fluorescent probe: A new approach to study nuclear nanostructure at single molecule resolution." Exp Cell Res. (2015).

A.T. Szczurek, K. Prakash, H.-K. Lee, G. Best, M. Hagmann, D. Heintzmann, J. Dobrucki, C. Cremer, U. Birk: "Single molecule localization microscopy of the distribution of chromatin using Hoechst and DAPI fluorescent probes." Nucleus 5(4), doi:10.4161/nucl.29564 (2014).

C. Cremer, R. Kaufmann, M. Gunkel, F. Polanski, P. Müller, R. Dierkes, S. Degenhard, C. Wege, M. Hausmann, U. Birk: "Application perspectives of localization microscopy in virology." Histochem. Cell Biol. 142(1): 43-59, doi:10.1007/s00418-014-1203-4 (2014).

S. Rossberger, G. Best, D. Baddeley, R. Heintzmann, U. Birk, S. Dithmar, C. Cremer: "Combination of structured illumination and single molecule localization microscopy in one setup." J. Opt. 15: 094003, doi:10.1088/2040-8978/15/9/094003 (2013).

S. Zhu, D. Dong, U.J. Birk, M. Rieckher, N. Tavernarakis, X. Qu, J. Liang, J. Tian, J. Ripoll: "Automated motion correction for in vivo optical projection tomography." IEEE Trans Med Imaging 31(7): 1358-71, doi:10.1109/TMI.2012.2188836 (2012), PMID 22374352.   [pdf]

M. Rieckher, U. Birk (co-first author), H. Meyer, J. Ripoll, N. Tavernarakis: "Microscopic optical projection tomography in vivo." PLoS ONE 6(4)e18963 (2011).   [pdf]

U.J. Birk, A. Darrell, N. Konstantinides, A. Sarasa-Renedo, J. Ripoll: "Improved Reconstructions and Generalized Filtered Back Projection for Optical Projection Tomography." Appl Opt 50(4): 392-398, doi:10.1364/AO.50.000392 (2011).

U.J. Birk, M. Rieckher, N. Konstantinides, A. Darrell, A. Sarasa-Renedo, H. Meyer, N. Tavernarakis, J. Ripoll: "Correction for specimen movement and rotation errors for in-vivo Optical Projection Tomography." J Biomed Opt Expr 1(1): 87-96, doi:10.1364/BOE.1.000087 (2010).   [pdf]

A. Sarasa-Renedo, R. Favicchio, U. Birk, G. Zacharakis, C. Mamalaki, J. Ripoll: "Source intensity profile in noncontact optical tomography." Opt Lett 35: 34-36, doi:10.1364/OL.35.000034 (2010).   [pdf]

D. Baddeley, Y. Weiland, C. Batram, U. Birk, C. Cremer: "Model based precision structural measurements on barely resolved objects." J Microsc 237: 70-78, doi:10.1111/j.1365-2818.2009.03304.x (2010).

D. Baddeley, V.O. Chagin, L. Schermelleh, S. Martin, A. Pombo, P.M. Carlton, A. Gahl, P. Domaing, U. Birk, H. Leonhardt, C. Cremer, M.C. Cardoso: "Measurement of replication structures at the nanometer scale using super-resolution light microscopy." Nucleic Acids Research doi:10.1093/nar/gkp901: 1-11 (2009).   [pdf]

J. Reymann, D. Baddeley, M. Gunkel, P. Lemmer, W. Stadter, T. Jegou, K. Rippe, C. Cremer, U. Birk: "High-precision Structural Analysis of Subnuclear Complexes in Fixed and Live Cells via Spatially Modulated Illumination (SMI) Microscopy." Chrom Res 16: 367-382, doi:10.1007/s10577-008-1238-2 (2008).   [pdf]

D. Baddeley, C. Batram, Y. Weiland, C. Cremer, U. Birk: "Nanostructure Analysis Using Spatially Modulated Illumination Microscopy." Nat. Protocols 2: 2640-2646, doi:10.1038/nprot.2007.399 (2007).   [pdf]

H. Mathée, D. Baddeley, C. Wotzlaw, C. Cremer, U. Birk: "Spatially Modulated Illumination Microscopy Using One Objective Lens." Opt Engineering 46(8): 083603, doi:10.1117/1.2768085 (2007).

H. Mathée, D. Baddeley, C. Wotzlaw, J. Fandrey, C. Cremer, U. Birk: "Nanostructure of Specific Chromatin Regions and Nuclear Complexes." Histochem Cell Biol 125(1-2): 75-82, doi:10.1007/s00418-005-0096-7 (2006).   [pdf]

C. Wagner, G. Hildenbrand, U. Spöri (U. Birk), C. Cremer: "Beyond Nanosizing: An Approach to Shape Analysis of Fluorescent Nanostructures by SMI-Microscopy." Optik/Optics 117(1): 26-32, doi:10.1016/j.ijleo.2005.05.006 (2005).

G. Hildenbrand, A. Rapp, U. Spoeri (U. Birk), C. Wagner, C. Cremer, M. Hausmann: "Nano-sizing of Specific Gene Domains in Intact Human Cell Nuclei by Spatially Modulated Illumination (SMI) Light Microscopy." Biophys J 88: 4312-4318, doi:10.1529/biophysj.104.056796 (2005).

C. Wagner, U. Spöri (U. Birk), C. Cremer: "High-Precision SMI Microscopy Size Measurements by Simultaneous Frequency Domain Reconstruction of the Axial Point Spread Function." Optik/Optics 116(1): 15-21, doi:10.1016/j.ijleo.2004.10.002 (2005).

S. Martin, A. V. Failla, U. Spöri (U. Birk), C. Cremer, A. Pombo: "Measuring the Size of Biological Nanostructures with Spatially Modulated Illumination Microscopy." Mol Biol Cell 15(5): 2449-2455, doi:10.1091/mbc.e04-01-0045 (2004).   [pdf]

U. Spöri (U. Birk), A. V. Failla, C. Cremer: "Superresolution Size Determination in Fluorescence Microscopy: A Comparison Between Spatially Modulated Illumination and Confocal Laser Scanning Microscopy." J Appl Phys 95(12): 8436-8443, doi:10.1063/1.1751633 (2004).

A.V. Failla, B. Albrecht, U. Spöri (U. Birk), A. Schweitzer, A. Kroll, G. Hildenbrand, M. Bach, C. Cremer: "Nanostructure Analysis Using Spatially Modulated Illumination (SMI) Microscopy." ComPlexUs 1: 77-88, doi:10.1159/000070464 (2003).

A.V. Failla, U. Spöri (U. Birk), B. Albrecht, A. Kroll, C. Cremer: "Nanosizing of Fluorescent Objects by Spatially Modulated Illumination Microscopy." Appl Opt 41(34): 7275-7283, doi:10.1364/AO.41.007275 (2002).

Monographs:

U.J. Birk: "Super-Resolution Microscopy: A Practical Guide." Wiley-VCH, ISBN 978-3-527-34133-7, 408 pages (2017).

U. Spöri: "Messungen mit dem SMI Mikroskop." ("Measurements with the SMI microscope") PhD Thesis, University Heidelberg (2004).

Editorship:

U.J. Birk, M. Hausmann, A. Watts (eds.): Uncovering Cellular Sub-structures by Light Microscopy. European Biophysics Journal 38(6), July 2009.

Chapters in books:

U. Birk, G. Best, R. Amberger, and C. Cremer: "Super-Resolution Microscopy: Interference and Pattern Techniques." In: Fluorescence Microscopy: From Principles to Biological Applications 2nd edition (U. Kubitscheck, ed.), 291-320 (Wiley-VCH, Weinheim, 2017).

C. Grossmann, J. Schwarz-Finsterle, E. Schmitt, U. Birk, G. Hildenbrand, C. Cremer, L. Trakhtenbrot, and M. Hausmann: "Variations of the spatial fluorescence distribution in ABL gene chromatin domains measured in blood cell nuclei by SMI microscopy after COMBO-FISH labelling." In: Microscopy: Science, Technology, Applications and Education 4, vol. 1 (A. Méndez-Vilas & J. Díaz, eds.), 688-695 (FORMATEX, Badajoz, 2010). [pdf]

U.J. Birk, D. Baddeley, C. Cremer: "Nanosizing by Spatially Modulated Illumination (SMI) Microscopy and Applications to the Nucleus." In: The Nucleus 2 (R. Hancock, ed.), 389-402 (Humana Press, Springer, 2009).

U.J. Birk, I. Upmann, D. Toomre, C. Wagner, C. Cremer: "Size Estimation of Protein Clusters in the Nanometer Range by Using Spatially Modulated Illumination Microscopy." In: Modern Research and Educational Topics in Microscopy 1 (A. Méndez-Vilas & J. Díaz, eds.), 272-279 (FORMATEX, Badajoz, 2007). [pdf]

Other:

J. Neumann, A. Scherhag, S. Otten, F. Shen, A.L. Leifke, U. Birk, C. Greb, K. Lucas, C. Cremer: "Chronic Inflammation Under the Microscope" Microscopy Today 24(6), doi:10.1017/S1551929516000894 (2016).

U. Birk: "In-vivo Optical Projection Tomography - Managing the invisible" In: EOS brochure "How optics and photonics address Europe's challenges of the 21sts century", EOS (2010).

U.J. Birk, M. Hausmann: Festschrift to recognise and celebrate Christoph Cremer's contribution to the field of biophysics on the occasion of his 65th birthday. Preface. Eur Biophys J. 38(6):719-20, doi:10.1007/s00249-009-0500-7 (2009).

Conference proceedings:

Additionally, I have published a number of conference papers. Below is a short selection: 

U. Birk, Ph. Roebrock: "User-position aware adaptive display of 3D data without additional stereoscopic hardware." Proceedings of SPIE, doi:10.1117/12.2522678 (2019)   [pdf]

U. Birk: "Benutzerpositionsabhängige adaptive Anzeige von 3D-Daten ohne zusätzliche stereoskopische Hardware." DGaO Proceedins, ISSN: 1614-8436 - urn:nbn:de:0287-2018-P029-9 (2018)   [pdf]

S. Fenz, H. Mathée, G. Kreth, D. Baddeley, Y. Weiland, J. Schwarz-Finsterle, C. Cremer, U. J. Birk: "Two-color intranuclear distance measurements of gene regions in human lymphocytes." Proc. SPIE 6630; doi:10.1117/12.727506 (2007).   [pdf]

U. J. Birk, D. Baddeley, C. Cremer: "Local protein/gene density measurements using SMI microscopy with interferometric illumination: Measurement of nuclear protein concentration." Proc. SPIE 6188; doi:10.1117/12.668023 (2006).   [pdf]