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  • Cremer, Christoph; Birk, Udo (2023): Towards Widefield based Three-Dimensional Nuclear Nanostructure Analysis in the 1 Nanometer Resolution Range. Poster. Focus on Microscopy. Porto, 4. April, 2023

    Abstract: The spatial nanostructure of the nuclear genome of higher organisms has emerged as a main topic of cell biology1. So far, a variety of methods have been applied for its elucidation by super-resolution approaches2,3. Here, we discuss application perspectives for a further improvement of nuclear nanostructure analysis by a combination of Localization Microscopy with laterally (SIM: Structured Illumination Microscopy) and axially patterned (SMI: Spatially Modulated Illumination)4. Numerical simulations indicate that a three-dimensional localization precision around 1nm may become feasible using fluorescence yields typical for single molecule localization microscopy (SMLM) applications. Together with the nanosizing capability of SMI, this may eventually be used to analyse macromolecular nuclear complexes and other nanostructures with a topological resolution approaching cryoelectron microscopy.

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  • von Hase, Johann; Birk, Udo; Humbel, Bruno; Liu, Xiaomin; Schaufler, Wladimir; Cremer, Christoph (2023): Lens Free Ring Array Illumination microscopy. Combination of Super-Resolution with Large Field of View Imaging and long Working Distances. Poster. Focus on Microscopy. Porto, 4. April, 2023

    Abstract: Using low NA objective lenses, light microscopy allows to "screen" large object areas to identify fluorescently labeled or autofluorescent structures of interest at relatively modest optical resolution; using separate instrumentation, selected sites can then be further analyzed at enhanced resolution, such as ultrastructural microscopy, or State-of-the-art super-resolution microscopy (SRM). This second step, however, typically requires high NA objective lenses with working distances in the submillimeter range. Here we present a novel concept which enables a direct integration of SRM (STED, SMLM, MINFLUX) into microscopy systems with working distances up to the multicentimeter range while still allowing nanometer scale resolution. This becomes possible by a "lens free" illumination mode with multiple coherent excitation beams positioned in a „ring-array“ arrangement around the low NA objective lens1. The feasibility of such a direct correlative microscopy method was validated by extensive numerical simulations; on the basis of these calculations, experimental implementation options shall be discussed. Such "Ring Array" illumination modes may be useful also for other correlative microscopy methods, such as a direct combination of light and electron microscopy in the same device (dCLEM).

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  • von Hase, Johann; Birk, Udo; Humbel, Bruno; Liu, Xiaomin; Failla, Antonio Virgilio; Cremer, Christoph (2023): Ring Array Illumination Microscopy. Combination of Super-Resolution with Large Field of View Imaging and long Working Distances. In: bioRxiv. DOI: 10.1101/2023.09.05.555896

    DOI: RemoteUri 

    Abstract: Here we present a novel fluorescence microscopy concept which enables a direct integration of Super-Resolution Microscopy (SRM) approaches (SIM/Nanosizing, STED, SMLM, MINFLUX, SIMFLUX) into microscopy systems with working distances (WD) up to the multicentimeter range while still allowing nanometer scale resolution at selected sites. This becomes possible by a "leftsynthetic aperture"right illumination mode with multiple, constructively interfering excitation beams positioned in a "leftRing-Array"right arrangement around a beam free interior zone containing instrumentation involved in complementary imaging modes. The feasibility of such a direct correlative microscopy method is validated by extensive numerical simulations; on the basis of these calculations, experimental implementation options are discussed. Such "leftRing Array"right illumination modes may be useful for various correlative microscopy methods, such as a direct combination of correlative light and electron microscopy in the same device (dCLEM); or a direct combination of low NA/large field-of-view widefield microscopy and super-resolution of selected sites in the same device (direct Correlative Opical Microscopy/dCOLM). Ring-Array supported correlative microscopy modes will open novel imaging perspectives in a variety of disciplines, from material sciences to biomedical applications.

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  • Birk, Udo (2022): Smart Surveillance Sensors. Workshop on Smart Surveillance Sensors. Swissphotonics. Chur, 24. Mai, 2022. Online verfügbar unter https://www.swissphotonics.net/home?event_id=4160, zuletzt geprüft am 10.06.2022

     

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  • Birk, Udo (2022): Artificial Intelligence, Deep Learning and Image Analysis. IMB Super-Resolution Microscopy Seminar. Institute of Molecular Biology GmbH. Mainz, 10. August, 2022

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  • Birk, Udo (2022): Advanced Door Area Monitoring. Precision Photonic Systems. OST. Ostschweizer Fachhochschule. Institut für Mikrotechnik und Photonik. Dornbirn, 1. Dezember, 2022

     

    Abstract: Door Area Monitoring is an important focus of automated door manufacturers. Presently available door area analytics can not only detect a person wishing to pass through the door, but also discriminate the speed and direction of travel. We use a miniaturized door automation system to study such systems far beyond the conventional detection capabilities required for opening and closing the door: Doors are only partially opened where needed, and at a higher level, the results of image and ranging sensor data evaluation such as gender, age, customer identification etc. can be fed into smart building surveillance.

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  • Birk, Elisabeth; Birk, Udo; Birk, Hanne (2022) : Online Teaching. Überlegungen zu digitalem Lehren und Lernen In: Forster, Michael; Alt, Sharon; Hanselmann, Marcel; Deflorin, Patricia (Hg.): Digitale Transformation an der Fachhochschule Graubünden: Case Studies aus Forschung und Lehre: Chur: FH Graubünden Verlag, S. 87-100. Online verfügbar unter https://www.fhgr.ch/fh-graubuenden/ueber-die-fh-graubuenden/wofuer-stehen-wir/digitalisierung/digitalisierungswissen-fuer-graubuenden/#c15147, zuletzt geprüft am 20.01.2023

     

    Abstract: Digitale Lehre bietet vielfältige, medienspezifische Möglichkeiten, um Lehrinhalte zu vermitteln. Allerdings ist die didaktische und technische Umsetzung oftmals eine Herausforderung. Wir diskutieren Vor- und Nachteile der digitalen Lehre anhand von transdisziplinären Beispielen aus der Lehrpraxis.

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  • Birk, Udo (2022): Advanced Door Area Monitoring (Precision Photonic Systems, Dornbirn, 13. Dezember). Online verfügbar unter https://doi.org/10.5281/zenodo.7432706, zuletzt geprüft am 20.01.2023

     

    Abstract: Door Area Monitoring is an important focus of automated door manufacturers. Presently available door area analytics can not only detect a person wishing to pass through the door, but also discriminate the speed and direction of travel. We use a miniaturized door automation system to study such systems far beyond the conventional detection capabilities required for opening and closing the door: Doors are only partially opened where needed, and at a higher level, the results of image and ranging sensor data evaluation such as gender, age, customer identification etc. can be fed into smart building surveillance.

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  • Cremer, Christoph; Birk, Udo (2022): Spatially modulated illumination microscopy. Application perspectives in nuclear nanostructure analysis. In: Philosophical transactions. Series A. Mathematical, physical, and engineering sciences 380. Online verfügbar unter https://doi.org/10.1098/rsta.2021.0152, zuletzt geprüft am 17.02.2022

     

    Abstract: Thousands of genes and the complex biochemical networks for their transcription are packed in the micrometer sized cell nucleus. To control biochemical processes, spatial organization plays a key role. Hence the structure of the cell nucleus of higher organisms has emerged as a main topic of advanced light microscopy. So far, a variety of methods have been applied for this, including confocal laser scanning fluorescence microscopy, 4Pi-, STED- and localization microscopy approaches, as well as (laterally) structured illumination microscopy (SIM). Here, we summarize the state of the art and discuss application perspectives for nuclear nanostructure analysis of spatially modulated illumination (SMI). SMI is a widefield-based approach to using axially structured illumination patterns to determine the axial extension (size) of small, optically isolated fluorescent objects between less than or equal to 200 nm and greater than or equal to 40 nm diameter with a precision down to the few nm range; in addition, it allows the axial positioning of such structures down to the 1 nm scale. Combined with SIM, a three-dimensional localization precision of less than or equal to 1 nm is expected to become feasible using fluorescence yields typical for single molecule localization microscopy applications. Together with its nanosizing capability, this may eventually be used to analyse macromolecular complexes and other nanostructures with a topological resolution, further narrowing the gap to Cryoelectron microscopy. This article is part of the Theo Murphy meeting issue 'Super-resolution structured illumination microscopy (part 2)'.

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  • Beyer, Thomas; Bailey, Dale L.; Birk, Udo; Buvat, Irene; Catana, Ciprian; Cheng, Zhen; Fang, Qiyin; Giove, Federico; Kuntner, Claudia; Laistler, Elmar; Moscato, Francesco; Nekolla, Stephan G.; Rausch, Ivo; Ronen, Itamar; Saarakkala, Simo; Thielemans, Kris; van Elmpt, Wouter; Moser, Ewald (2021): Medical Physics and Imaging. A Timely Perspective. In: Frontiers in Physics 9. Online verfügbar unter https://doi.org/10.3389/fphy.2021.634693, zuletzt geprüft am 14.05.2021

     

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  • Birk, Udo (2021): Deep Learning in Microscopy. Imaging ONEWORLD series. Royal Microscopial Society. Online, 19. Juli, 2021

    Abstract: Recent advancements in microscopic image analysis have made use of the tremendous progress that artificial intelligence has seen in the evaluation of digital images. The application of deep learning techniques to microscopic image analysis ranges from image restoration and denoising to automated cellular and subcellular profiling to generation of augmented reconstructed image data, encompassing e.g. super-resolution images from single molecule localization microscopy data, virtual refocussing, content aware neuronal reconstructions and many more. However, deep learning methods are generally based on the availability of large amounts of reliable ground truth data. In the talk I will highlight some of the recent advances in deep learning applied to microscopic data with a focus on applications for super-resolution microscopy.

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  • Brunner, Lars; Salvator, Mario; Roebrock, Philipp; Birk, Udo (2021) : Chess recognition using 3D patterned illumination camera In: Osten, Wolfgang; Nikolaev, Dmitry P.; Zhou, Jianhong (Hg.): Thirteenth International Conference on Machine Vision (ICMV 2020): Proceedings: International Conference on Machine Vision (ICMV): Rom, 2. - 6. November. SPIE The international society for optics and photonics (Proceedings of SPIE), S. 520-527

    DOI: https://doi.org/10.1117/12.2587054 

    Abstract: Computer Vision has been applied to augment traditional board games such as Chess for a number of reasons. While augmented reality enhances the gaming experience, the required additional hardware (e.g. head gear) is still not widely accepted in everyday leisure activities, and therefore, camera based methods have been developed to interface the computer with the real-life chess board. However, traditional 2D camera approaches suffer from ill-defined environmental conditions (lighting, viewing angle) and are therefore severely limited in their application. To answer this issue, we have incorporated a consumer-grade depth camera based on patterned illumination. We could show that in combination with traditional 2D color images, the recognition of chess pieces is made easier, which allows seamless integration of the real-life chess pieces with the computer program. Our method uses a fusion approach from depth and RGB camera data and is suitable for two distant players to play against each other, using two physical sets of chess.

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  • Birk, Udo (2020): Image Analysis and Methods. Technical Program: Session 10. Chair. Thirteenth International Conference on Machine Vision (ICMV). SPIE The international society for optics and photonics. Rom, 2. - 6. November, 2020

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  • Schneckenburger, H.; Richter, V.; Gelleri, M.; Ritz, S.; Vaz Pandolfo, R.; Schock, F.; Hase, V. J.; Birk, Udo; Cremer, C. (2020): High-resolution deep view microscopy of cells and tissues. In: Quantum Electronics 50, S. 2-8. Online verfügbar unter http://dx.doi.org/10.1070/QEL17204, zuletzt geprüft am 31.01.2020

     

    Abstract: Methods, experimental setups and perspectives of threedimensional deep view imaging microscopy of cell or tissue samples are reported. Preliminary biophysical and clinically relevant examples are presented.

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  • Birk, Udo (2019): Bildverarbeitung und Maschinelles Sehen für Studierende der Ingenieurwissenschaften. Poster. 120. Jahrestagung der deutschen Gesellschaft für angewandte Optik (DGaO). Deutsche Gesellschaft für angewandte Optik. Darmstadt, 12.-15. Juni, 2019. Online verfügbar unter https://www.dgao-proceedings.de/abstract/abstract_only.php?id=2447, zuletzt geprüft am 14.02.2020

     

    Abstract: Der Einsatz photonischer Technologien setzt sich in den kommenden Jahren verstärkt fort. Bildverarbeitung spielt bei diesen Entwicklungen eine zentrale Rolle. Mit Beiträgen aus der Industrie wurde ein Bachelor-Curriculum mit Schwerpunkt «Bildverarbeitung» für Studierende der Ingenieurwissenschaften konzipiert. Ein wichtiges Ziel des Kurses war es, theoretische und praktische Erfahrungen in Automatisierungstechnologien zu vermitteln, die für zukünftige Ingenieure von größter Bedeutung sein werden. In diesem Beitrag werden wichtige Konzepte unseres Bildverarbeitungskurses vorgestellt, und praktische Geräte und Laborausstattung beschrieben, die für diesen Kurs bereitgestellt wurden. Der dreigeteilte Kurs besteht aus Präsenzsequenzen, aus Übungssequenzen mit Programmieraufgaben, sowie aus einer Phase Problemorientierten Lernens (POL), in welcher die Studierenden ihre eigenen Bildverarbeitungsprojekte realisieren. Es werden einige Beispielprojekte aus dem Frühjahrs- bzw. Herbstsemester 2018 vorgestellt. Kursinhalt und -materialien wurden hinsichtlich des technischen Gehalts und der Lerneffektivität bewertet. Die Ergebnisse dieser Bewertung werden in diesem Beitrag vorgestellt.

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  • Birk, Udo (2019): Face Identification. Photonics-Treff. Swissmem Fachgruppe Photonics. Chur, 23. September, 2019

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  • Birk, Udo (2019): Face Recognition. Joint Workshop on Image Processing, Augmented and Virtual Reality. Swissphotonics. Chur, 28. Mai, 2019

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  • Birk, Udo (2019): Holzwerkstoffklassifizierung mit Machine Vision unter Verwendung einer Acht-Kanal-Farbbeleuchtung. 120. Jahrestagung der deutschen Gesellschaft für angewandte Optik (DGaO). Deutsche Gesellschaft für angewandte Optik. Darmstadt, 12. Juni, 2019. Online verfügbar unter https://www.dgao-proceedings.de/archiv/120_titel_d.php, zuletzt geprüft am 31.01.2020

     

    Abstract: Die Unterscheidung zwischen Echtholz und Nachbildungen ist wichtig für die Bewertung von Möbeln und Wohnraum. Moderne Oberflächenfertigungsverfahren machen es dem menschlichen Auge praktisch unmöglich, die verwendeten Baumaterialien richtig zu identifizieren, ohne das Objekt zu beschädigen. Wir präsentieren eine rein optische Technik zur Klassifizierung verschiedener Eichenparkettmaterialien anhand eines Beleuchtungsschemas mit acht verschiedenen Spektren von UV bis IR. Das System diente der Unterscheidung zwischen Vinyl-Replik und fünf verschiedenen Echtholz-Eichendekors, wobei eine Klassifizierungsgenauigkeit von 97% erreicht wurde. Weitere Anwendungsmöglichkeiten sind die Suche nach passenden Ersatzdekors beim Austausch schadhafter Panelen, z.B. nach Reparaturen.

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  • Birk, Udo (2019): Image Analysis using Deep Learning. IMB Ad Hoc Seminar. Institute of Molecular Biology GmbH. Mainz, 11. Juni, 2019

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  • Birk, Udo (2019): Schlaue Helfer dank Embedded Vision. In: Aktuelle Technik 2019. Online verfügbar unter https://aktuelletechnik.blverlag.ch/schlaue-helfer-dank-embedded-vision/

     

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  • Birk, Udo (2019): Staubsauger oder Bohrmaschine. Überlegungen zu Deep Learning und Big Data. Wissensgenerator. In: Südostschweiz, 2019

     

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  • Birk, Udo (2019): Super-Resolution Microscopy of Chromatin. In: Genes 10. Online verfügbar unter https://doi.org/10.3390/genes10070493, zuletzt geprüft am 14.02.2020

     

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  • Birk, Udo (2019): Wenn der Körper das Passwort ist. In: Polyscope 2019, S. 30-31. Online verfügbar unter https://www.polyscope.ch/archiv/2019/19/wenn-der-koerper-das-passwort-ist/

     

    Abstract: Gesichtserkennung ist ein aktuelles Forschungsthema, nicht nur in der Neurowissenschaft. Mit modernen lichtbasierten Technologien kann man Gesichtserkennung auch auf elektronischen Geräten wie Handys realisieren. Zusammen mit dem Fingerabdruckscanner betreten wir mit der Gesichtserkennung ein neues Zeitalter der digitalen Sicherheit: Entweder ich benutze ein Passwort, oder mein Körper ist das Passwort.

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  • Birk, Udo; Cremer, Christoph; von Hase, Johann (2019): Lens Free Super-Resolution Microscopy. Distributed Aperture Illumination Allows Large Working Distances. In: Imaging & Microscopy 2019, S. 23-25. Online verfügbar unter https://www.imaging-git.com/magazine/imaging-microscopy-issue-42019

     

    Abstract: High-resolution microscopy methods typically use objective lenses with large numerical apertures, i.e. low working distances (WD) in the range of 0.2 mm. This impedes its application to thick transparent specimens, or to objects with large topographical differences. To extend high-resolution microscopy also to whole tissues and to the material sciences, lens free microscope systems allowing WDs up to the multicentimeter range and an optical resolution down to the nanometer range may be constructed.

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  • Birk, Udo; von Hase, Johann; Cremer, Christoph (2019): Superauflösende Mikroskopie mit sehr großem Arbeitsabstand durch verteilte Aperturbeleuchtung. Poster. 120. Jahrestagung der deutschen Gesellschaft für angewandte Optik (DGaO). Deutsche Gesellschaft für angewandte Optik. Darmstadt, 12.-15. Juni, 2019. Online verfügbar unter https://www.dgao-proceedings.de/abstract/abstract_only.php?id=2449, zuletzt geprüft am 14.02.2020

     

    Abstract: Die Grenzen der konventionellen Lichtmikroskopie („Abbe-Limit“) hängen entscheidend von der numerischen Apertur (NA) der Objektivlinse ab. Die Bildgebung bei großen Arbeitsabständen oder einem großen Sichtfeld erfordert typischerweise Objektive mit niedriger NA, wodurch die optische Auflösung auf den Bereich von mehreren Mikrometern reduziert wird. Basierend auf numerischen Simulationen der Intensitätsfeldverteilung stellen wir ein Beleuchtungssystem für ein hochauflösendes Mikroskop vor, das eine dreidimensionale (3D) optische Auflösung um 150 nm für Arbeitsabstände bis zum Zentimeterbereich ermöglicht. Grundsätzlich erlaubt das System eine große Flexibilität, da das Beleuchtungskonzept zur Annäherung an die Punktspreizfunktion herkömmlicher Mikroskopoptiken mit dem zusätzlichen Vorteil einer anpassbaren Pupillenfunktion verwendet werden kann. Verglichen mit dem Abbe-Limit unter Verwendung einer Objektivlinse mit einem so großen Arbeitsabstand wird ein Volumenauflösungspotenzial in der Größenordnung von 104 geschätzt.

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  • Birk, Udo (2019) : Staub­sau­ger oder Bohr­ma­schi­ne . Blog (FHGR Blog) . Online verfügbar unter https://blog.fhgr.ch/blog/staubsauger-oder-bohrmaschine/ , zuletzt geprüft am 22.02.2021

     

    Abstract: Überlegungen zu Deep Learning und Big Data.

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  • Birk, Udo (2019) : Schlaue Helfer dank Em­bed­ded Vision . Blog (FHGR Blog) . Online verfügbar unter https://blog.fhgr.ch/blog/schlaue-helfer-dank-embedded-vision/ , zuletzt geprüft am 05.03.2021

     

    Abstract: Die Miniaturisierungstrends erlauben den Einsatz von Computertechnologie mit geringem Stromverbrauch für immer komplexere Berechnungen.

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  • Neumann, Jan; Ziegler, Kira; Gelléri, Márton; Fröhlich-Nowoisky, Janine; Liu, Fobang; Bellinghausen, Iris; Schuppan, Detlef; Birk, Udo; Pöschl, Ulrich; Cremer, Christoph; Lucas, Kurt (2019): Nanoscale distribution of TLR4 on primary human macrophages stimulated with LPS and ATI. In: Nanoscale 11, S. 9769-9779. Online verfügbar unter http://dx.doi.org/10.1039/C9NR00943D, zuletzt geprüft am 20.02.2020

     

    Abstract: Toll-like receptor 4 (TLR4) plays a crucial role in the recognition of invading pathogens. Upon activation by lipopolysaccharides (LPS), TLR4 is recruited into specific membrane domains and dimerizes. In addition to LPS, TLR4 can be stimulated by wheat amylase-trypsin inhibitors (ATI). ATI are proteins associated with gluten containing grains, whose ingestion promotes intestinal and extraintestinal inflammation. However, the effect of ATI vs. LPS on the membrane distribution of TLR4 at the nanoscale has not been analyzed. In this study, we investigated the effect of LPS and ATI stimulation on the membrane distribution of TLR4 in primary human macrophages using single molecule localization microscopy (SMLM). We found that in unstimulated macrophages the majority of TLR4 molecules are located in clusters, but with donor-dependent variations from ∼51% to ∼75%. Depending on pre-clustering, we found pronounced variations in the fraction of clustered molecules and density of clusters on the membrane upon LPS and ATI stimulation. Although clustering differed greatly among the human donors, we found an almost constant cluster diameter of ∼44 nm for all donors, independent of treatment. Together, our results show donor-dependent but comparable effects between ATI and LPS stimulation on the membrane distribution of TLR4. This may indicate a general mechanism of TLR4 activation in primary human macrophages. Furthermore, our methodology visualizes TLR4 receptor clustering and underlines its functional role as a signaling platform.

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  • Birk, Udo (2018): Benutzerpositionsabhängige 3D-Daten-Anzeige ohne stereoskopische Hardware und ohne Headse. Poster. 119. Jahrestagung der deutschen Gesellschaft für angewandte Optik (DGaO). Deutsche Gesellschaft für angewandte Optik. Darmstadt, 23.-26. Mai, 2018. Online verfügbar unter https://www.dgao-proceedings.de/abstract/abstract_only.php?id=2277, zuletzt geprüft am 21.02.2020

     

    Abstract: Stereoskopische Bildverarbeitungsmodule haben aufgrund der benötigten Hardware (Bildaufnahme, 3D-Brille) nur begrenzten Erfolg in der Technik- und Konsumwelt. In den letzten Jahren hat vor allem der Spielesektor von spezialisierten VR-Brillen profitiert. Viele andere industrielle und biomedizinische Anwendungen, wie z.B. Tomografieverfahren oder CAD-Konstruktion, haben die erhöhten 3D-Renderingfähigkeiten heutiger Computerhardware bisher nicht voll ausgenutzt. Wir verwenden Standardhardware (Monitor und Webcam), um benutzerpositionsabhängige Projektionen von 3D-Daten ohne zusätzliche Spezialbrillen anzuzeigen. Der Ansatz bietet viele Anwendungsmöglichkeiten von der medizinischen Bildgebung über Konstruktion und CAD-Design, Architektur bis hin zu Kunst und Performances. Abhängig von dem Ort des Nutzers, werden die 3D-Daten für den jeweiligen Benutzersichtwinkel (Zoom) und die Blickrichtung unterschiedlich gerendert. Wenn sich der Benutzer vor dem Monitor bewegt, werden verschiedene Bereiche des gerenderten Objekts sichtbar. Wenn der Benutzer sich dem Bildschirm nähert, verringert sich der Ansichtswinkel, was durch eine vergrößerte Version des gerenderten Objekts visualisiert wird.

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  • Birk, Udo (2018): Gesichtserkennung statt PIN?. Wissensgenerator. In: Südostschweiz, 2018

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  • Birk, Udo (2018): Gesichtserkennung statt PIN?. In: Swiss Engineering STZ 115

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  • Birk, Udo (2018): Super-Resolution Light Microscopy for Nanostructure Analyses of Cell Nuclei. Microscopy Symposium. Université de Lausanne, Electron Microscopy Facility. Lausanne, 9. März, 2018

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  • Birk, Udo; Andres, Michael; Kessler, Viktor; Linvers, Chris; Zbinden, David; Catregn, Gion-Pol; Leutenegger, Tobias (2018): Image Processing and Machine Vision for Engineering Undergraduate Students. 11th International Conference on Machine Vision ICMV. München, 2. November, 2018

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  • Birk, Udo; Roebrock, Philipp (2018) : User-position aware adaptive display of 3D data without additional stereoscopic hardware In: Verikas, Antanas; Nikolaev, Dmitry P.; Radeva, Petia; Zhou, Jianhong (Hg.): Eleventh International Conference on Machine Vision (ICMV 2018): Proceedings: International Conference on Machine Vision (ICMV): München, 1. - 3. November. SPIE The international society for optics and photonics (Proceedings of SPIE). Online verfügbar unter https://doi.org/10.1117/12.2522678, zuletzt geprüft am 14.02.2020

     

    Abstract: Stereoscopic vision modules have seen limited success in both engineering and consumer world, due to the required additional hardware (image acquisition, Virtual Reality headsets, 3D glasses). In the last years, especially the gaming and education sectors have benefited from such specialized headgear, providing virtual or augmented reality. However, many other industrial and biomedical applications such as e.g. computer aided design (CAD) or tomographic data display, so far have not fully exploited the increased 3D rendering capabilities of present-day computer hardware. We present an approach to use standard desktop PC hardware (monitor and webcam) to display user-position aware projections of 3D data without additional headgear. The user position is detected from webcam images, and the rendered 3D data (i.e. the view) is adjusted to match the corresponding user position, resulting in a quasi virtual reality rendering, albeit without the 3D effect of proper 3D head-gear. The approach has many applications from medical imaging, to construction and CAD, to architecture, to exhibitions, arts and performances. Depending on the user location, i.e. the detected head position, the data is rendered differently to attribute for the user view angle (zoom) and direction. As the user moves his or her head in front of the monitor, different features of the rendered object become visible. As the user moves closer to the screen, the view angle of the rendered data is decreased, resulting in a zoomed-in version of the rendered object.

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  • Birk, Udo (2018) : Der Pin hat aus­ge­dient: Heute gilt die Ge­sichts­er­ken­nung . Blog (FHGR Blog) . Online verfügbar unter https://blog.fhgr.ch/blog/der-pin-hat-ausgedient-heute-gilt-die-gesichtserkennung/ , zuletzt geprüft am 19.03.2021

     

    Abstract: Gesichtserkennung ist ein brandaktuelles Forschungsthema, nicht nur in den Neurowissenschaften. Mit modernen lichtbasierten Technologien ist es gelungen, Gesichtserkennung neuerdings auch auf elektronischen Geräten wie z.B. Smartphones möglich zu machen. Zusammen mit dem Fingerabdruckscanner betreten wir mit der Gesichtserkennung ein neues Zeitalter der digitalen Sicherheit: Entweder ich benutze ein Passwort, oder ich bzw. mein Körper ist das Passwort.

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  • Cremer, Christoph; Szczurek, Aleksander; Strickfaden, Hilmar; Birk, Udo; Cremer, Marion; Cremer, Thomas (2018): Der Zellkern - eine Stadt in der Zelle, Teil 2. In: Biologie in unserer Zeit 48, S. 45-53. Online verfügbar unter https://doi.org/10.1002/biuz.201810640, zuletzt geprüft am 07.05.2023

     

    Abstract: Im zweiten Teil des Beitrags zur Zellkernarchitektur beschreiben wir die bahnbrechenden Möglichkeiten der superauflösenden Fluoreszenzmikroskopie (Nanoskopie) und neuer molekularbiologischer Verfahren zur Erforschung der Struktur von Chromatindomänen im Nanometer-Maßstab und ihrer räumlichen Anordnung zu größeren Aggregaten. Neue experimentelle Daten und Modelle sprechen für eine entscheidende Rolle dieser Strukturen für die Genregulation und andere Funktionen des Zellkerns.

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  • Szczurek, Aleksander; Birk, Udo; Knecht, Hans; Dobrucki, Jurek; Mai, Sabine; Cremer, Christoph (2018): Super-resolution binding activated localization microscopy through reversible change of DNA conformation. In: Nucleus 9, S. 182-189. Online verfügbar unter https://doi.org/10.1080/19491034.2017.1419846

     

    Abstract: Methods of super-resolving light microscopy (SRM) have found an exponentially growing range of applications in cell biology, including nuclear structure analyses. Recent developments have proven that Single Molecule Localization Microscopy (SMLM), a type of SRM, is particularly useful for enhanced spatial analysis of the cell nucleus due to its highest resolving capability combined with very specific fluorescent labeling. In this commentary we offer a brief review of the latest methodological development in the field of SMLM of chromatin designated DNA Structure Fluctuation Assisted Binding Activated Localization Microscopy (abbreviated as fBALM) as well as its potential future applications in biology and medicine.

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  • Birk, Udo; Szczurek, Aleksander; Cremer, Christoph (2017): Super-resolved linear fluorescence localization microscopy using photostable fluorophores. A virtual microscopy study. In: Optics Communications, S. 42-50. Online verfügbar unter https://doi.org/10.1016/j.optcom.2017.06.078, zuletzt geprüft am 06.05.2023

     

    Abstract: Current approaches to overcome the conventional limit of the resolution potential of light microscopy (of about 200 nm for visible light), often suffer from non-linear effects, which render the quantification of the image intensities in the reconstructions difficult, and also affect the quantification of the biological structure under investigation. As an attempt to face these difficulties, we discuss a particular method of localization microscopy which is based on photostable fluorescent dyes. The proposed method can potentially be implemented as a fast alternative for quantitative localization microscopy, circumventing the need for the acquisition of thousands of image frames and complex, highly dye-specific imaging buffers. Although the need for calibration remains in order to extract quantitative data (such as the number of emitters), multispectral approaches are largely facilitated due to the much less stringent requirements on imaging buffers. Furthermore, multispectral acquisitions can be readily obtained using commercial instrumentation such as e.g. the conventional confocal laser scanning microscope.

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  • Birk, Udo (2017): Super-Resolution Microscopy. A Practical Guide. Weinheim, Germany: Wiley-VCH

    Abstract: This unique book on super-resolution microscopy techniques presents comparative, in-depth analyses of the strengths and weaknesses of the individual approaches. It was written for non-experts who need to understand the principles of super-resolution or who wish to use recently commercialized instruments as well as for professionals who plan to realize novel microscopic devices. Explaining the practical requirements in terms of hardware, software and sample preparation, the book offers a wealth of hands-on tips and practical tricks to get a setup running, provides invaluable help and support for successful data acquisition and specific advice in the context of data analysis and visualization. Furthermore, it addresses a wide array of transdisciplinary fields of applications. The author begins by outlining the joint efforts that have led to achieving super-resolution microscopy combining advances in single-molecule photo-physics, fluorophore design and fluorescent labeling, instrument design and software development. The following chapters depict and compare current main standard techniques such as structured illumination microscopy, single-molecule localization, stimulated emission depletion microscopy and multi-scale imaging including light-sheet and expansion microscopy. For each individual approach the experimental setups are introduced, the imaging protocols are provided and the various applications illustrated. The book concludes with a discussion of future challenges addressing issues of routine applications and further commercialization of the available methods. Guiding users in how to make choices for the design of their own experiments from scratch to promising application, this one-stop resource is intended for researchers in the applied sciences, from chemistry to biology and medicine to physics and engineering.

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  • Birk, Udo; Hase, Johann V.; Cremer, Christoph (2017): Super-resolution microscopy with very large working distance by means of distributed aperture illumination. In: Scientific reports 7. Online verfügbar unter https://doi.org/10.1038/s41598-017-03743-4, zuletzt geprüft am 06.05.2023

     

    Abstract: The limits of conventional light microscopy ("Abbe-Limit") depend critically on the numerical aperture (NA) of the objective lens. Imaging at large working distances or a large field-of-view typically requires low NA objectives, thereby reducing the optical resolution to the multi micrometer range. Based on numerical simulations of the intensity field distribution, we present an illumination concept for a super-resolution microscope which allows a three dimensional (3D) optical resolution around 150 nm for working distances up to the centimeter regime. In principle, the system allows great flexibility, because the illumination concept can be used to approximate the point-spread-function of conventional microscope optics, with the additional benefit of a customizable pupil function. Compared with the Abbe-limit using an objective lens with such a large working distance, a volume resolution enhancement potential in the order of 104 is estimated.

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  • Birk, Udo; Best, Gerrit; Amberger, Roman; Cremer, Christoph (2017) : Super-Resolution Microscopy. Interference and Pattern Techniques In: Kubitscheck, Ulrich: Fluorescence Microscopy: From Principles to Biological Applications: Weinheim: Wiley-VCH, S. 291-319

    Abstract: Fluorescence microscopy techniques using patterned illumination light offer the opportunity to extract high-resolution object information beyond the conventional resolution limit. This chapter describes in detail two widefield methods that apply interference of the excitation light to make high-resolution object information accessible. These are structured illumination microscopy (SIM) (also referred to as patterned excitation microscopy, PEM) and spatially modulated illumination (SMI). In SIM, the object is illuminated with a periodic illumination pattern. This pattern is used in order to manipulate the object's spatial frequencies. Two methods to spatially modulate the excitation intensity in SIM are common: two-beam interference, also called fringe projection, and three-beam interference, the so-called grid projection. The secondary focus of this chapter is on the less common method of SMI, where two opposing objective lenses are used to generate a high-frequency interference pattern along the optical axis. The SMI method is used to measure the size of nanostructures with great precision.

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  • Cremer, Christoph; Szczurek, Aleksander; Schock, Florian; Gourram, Amine; Birk, Udo (2017): Super-resolution microscopy approaches to nuclear nanostructure imaging. In: Methods, S. 11-32. Online verfügbar unter https://doi.org/10.1016/j.ymeth.2017.03.019, zuletzt geprüft am 06.05.2023

     

    Abstract: The human genome has been decoded, but we are still far from understanding the regulation of all gene activities. A largely unexplained role in these regulatory mechanisms is played by the spatial organization of the genome in the cell nucleus which has far-reaching functional consequences for gene regulation. Until recently, it appeared to be impossible to study this problem on the nanoscale by light microscopy. However, novel developments in optical imaging technology have radically surpassed the limited resolution of conventional far-field fluorescence microscopy (ca. 200nm). After a brief review of available super-resolution microscopy (SRM) methods, we focus on a specific SRM approach to study nuclear genome structure at the single cell/single molecule level, Spectral Precision Distance/Position Determination Microscopy (SPDM). SPDM, a variant of localization microscopy, makes use of conventional fluorescent proteins or single standard organic fluorophores in combination with standard (or only slightly modified) specimen preparation conditions; in its actual realization mode, the same laser frequency can be used for both photoswitching and fluorescence read out. Presently, the SPDM method allows us to image nuclear genome organization in individual cells down to few tens of nanometer (nm) of structural resolution, and to perform quantitative analyses of individual small chromatin domains; of the nanoscale distribution of histones, chromatin remodeling proteins, and transcription, splicing and repair related factors. As a biomedical research application, using dual-color SPDM, it became possible to monitor in mouse cardiomyocyte cells quantitatively the effects of ischemia conditions on the chromatin nanostructure (DNA). These novel "molecular optics" approaches open an avenue to study the nuclear landscape directly in individual cells down to the single molecule level and thus to test models of functional genome architecture at unprecedented resolution.

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  • Szczurek, Aleksander; Klewes, Ludger; Xing, Jun; Gourram, Amine; Birk, Udo; Knecht, Hans; Dobrucki, Jurek W.; Mai, Sabine; Cremer, Christoph (2017): Imaging chromatin nanostructure with binding-activated localization microscopy based on DNA structure fluctuations. In: Nucleic Acids Research 45. Online verfügbar unter https://doi.org/10.1093/nar/gkw1301, zuletzt geprüft am 06.05.2023

     

    Abstract: Advanced light microscopy is an important tool for nanostructure analysis of chromatin. In this report we present a general concept for Single Molecule localization Microscopy (SMLM) super-resolved imaging of DNA-binding dyes based on modifying the properties of DNA and the dye. By careful adjustment of the chemical environment leading to local, reversible DNA melting and hybridization control over the fluorescence signal of the DNA-binding dye molecules can be introduced. We postulate a transient binding as the basis for our variation of binding-activated localization microscopy (BALM). We demonstrate that several intercalating and minor-groove binding DNA dyes can be used to register (optically isolate) only a few DNA-binding dye signals at a time. To highlight this DNA structure fluctuation-assisted BALM (fBALM), we applied it to measure, for the first time, nanoscale differences in nuclear architecture in model ischemia with an anticipated structural resolution of approximately 50 nm. Our data suggest that this approach may open an avenue for the enhanced microscopic analysis of chromatin nano-architecture and hence the microscopic analysis of nuclear structure aberrations occurring in various pathological conditions. It may also become possible to analyse nuclear nanostructure differences in different cell types, stages of development or environmental stress conditions.

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  • Cremer, Christoph; Birk, Udo (2016): Perspectives in Super-Resolved Fluorescence Microscopy. What Comes Next?. In: Frontiers in Physics 4. Online verfügbar unter https://doi.org/10.3389/fphy.2016.00011, zuletzt geprüft am 06.05.2023

     

    Abstract: The Nobel Prize in Chemistry 2014 has been awarded to three scientists involved in the development of STED and PALM super-resolution fluorescence microscopy (SRM) methods. They have proven that it is possible to overcome the 100 year old theoretical limit for the resolution potential of light microscopy (of about 200 nm for visible light), which for decades has precluded a direct glimpse of the molecular machinery of life. None of the present-day super-resolution techniques have invalidated the Abbe limit for light optical detection; however, they have found clever ways around it. In this report, we discuss some of the challenges still to be resolved before arising SRM approaches will be fit to bring about the revolution in Biology and Medicine envisaged. Some of the challenges discussed are the applicability to image live and/or large samples, the further enhancement of resolution, future developments of labels, and multi-spectral approaches.

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  • Neumann, Jan; Scherhag, Anne; Otten, Susanne; Shen, Fangxia; Leifke, Anna Lena; Birk, Udo; Greb, Christoph; Lucas, Kurt; Cremer, Christoph (2016): Chronic Inflammation Under the Microscope. In: Microscopy Today 24, S. 38-45. Online verfügbar unter https://doi.org/10.1017/S1551929516000894, zuletzt geprüft am 23.05.2023

     

    Abstract: In the course of chronic inflammation certain body areas are recurrently inflamed. This goes along with many human diseases. With the help of widefield light microscopy, the underlying processes can be examined from a cellular level to whole organisms. This article presents several widefield microscopy applications such as immunofluorescence, live-cell imaging, histology, and ratiometric analysis to get insight into the development of chronic inflammation, the related diseases, and their treatment.

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  • Szczurek, Aleksander; Xing, Jun; Birk, Udo; Cremer, Christoph (2016): Single Molecule Localization Microscopy of Mammalian Cell Nuclei on the Nanoscale. In: Frontiers in Genetics 7. Online verfügbar unter https://doi.org/10.3389/fgene.2016.00114, zuletzt geprüft am 06.05.2023

     

    Abstract: Nuclear texture analysis is a well-established method of cellular pathology. It is hampered, however, by the limits of conventional light microscopy (ca. 200 nm). These limits have been overcome by a variety of super-resolution approaches. An especially promising approach to chromatin texture analysis is single molecule localization microscopy (SMLM) as it provides the highest resolution using fluorescent based methods. At the present state of the art, using fixed whole cell samples and standard DNA dyes, a structural resolution of chromatin in the 50-100 nm range is obtained using SMLM. We highlight how the combination of localization microscopy with standard fluorophores opens the avenue to a plethora of studies including the spatial distribution of DNA and associated proteins in eukaryotic cell nuclei with the potential to elucidate the functional organization of chromatin. These views are based on our experience as well as on recently published research in this field.

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  • Żurek-Biesiada, Dominika; Szczurek, Aleksander T.; Prakash, Kirti; Best, Gerrit; Mohana, Giriram K.; Lee, Hyun-Keun; Roignant, Jean-Yves; Dobrucki, Jurek W.; Cremer, Christoph; Birk, Udo (2016): Quantitative super-resolution localization microscopy of DNA in situ using Vybrant® DyeCycle™ Violet fluorescent probe. In: Data in Brief, S. 157-171. Online verfügbar unter https://doi.org/10.1016/j.dib.2016.01.041, zuletzt geprüft am 06.05.2023

     

    Abstract: Single Molecule Localization Microscopy (SMLM) is a recently emerged optical imaging method that was shown to achieve a resolution in the order of tens of nanometers in intact cells. Novel high resolution imaging methods might be crucial for understanding of how the chromatin, a complex of DNA and proteins, is arranged in the eukaryotic cell nucleus. Such an approach utilizing switching of a fluorescent, DNA-binding dye Vybrant® DyeCycle™ Violet has been previously demonstrated by us (Żurek-Biesiada et al., 2015) [1]. Here we provide quantitative information on the influence of the chemical environment on the behavior of the dye, discuss the variability in the DNA-associated signal density, and demonstrate direct proof of enhanced structural resolution. Furthermore, we compare different visualization approaches. Finally, we describe various opportunities of multicolor DNA/SMLM imaging in eukaryotic cell nuclei.

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  • Żurek-Biesiada, Dominika; Szczurek, Aleksander T.; Prakash, Kirti; Mohana, Giriram K.; Lee, Hyun-Keun; Roignant, Jean-Yves; Birk, Udo; Dobrucki, Jurek W.; Cremer, Christoph (2016): Localization microscopy of DNA in situ using Vybrant(®) DyeCycle™ Violet fluorescent probe. A new approach to study nuclear nanostructure at single molecule resolution. In: Experimental Cell Research 343, S. 97-106. Online verfügbar unter https://doi.org/10.1016/j.yexcr.2015.08.020, zuletzt geprüft am 06.05.2023

     

    Abstract: Higher order chromatin structure is not only required to compact and spatially arrange long chromatids within a nucleus, but have also important functional roles, including control of gene expression and DNA processing. However, studies of chromatin nanostructures cannot be performed using conventional widefield and confocal microscopy because of the limited optical resolution. Various methods of superresolution microscopy have been described to overcome this difficulty, like structured illumination and single molecule localization microscopy. We report here that the standard DNA dye Vybrant(®) DyeCycle™ Violet can be used to provide single molecule localization microscopy (SMLM) images of DNA in nuclei of fixed mammalian cells. This SMLM method enabled optical isolation and localization of large numbers of DNA-bound molecules, usually in excess of 10(6) signals in one cell nucleus. The technique yielded high-quality images of nuclear DNA density, revealing subdiffraction chromatin structures of the size in the order of 100nm; the interchromatin compartment was visualized at unprecedented optical resolution. The approach offers several advantages over previously described high resolution DNA imaging methods, including high specificity, an ability to record images using a single wavelength excitation, and a higher density of single molecule signals than reported in previous SMLM studies. The method is compatible with DNA/multicolor SMLM imaging which employs simple staining methods suited also for conventional optical microscopy.

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  • Kirmes, Ina; Szczurek, Aleksander; Prakash, Kirti; Charapitsa, Iryna; Heiser, Christina; Musheev, Michael; Schock, Florian; Fornalczyk, Karolina; Ma, Dongyu; Birk, Udo; Cremer, Christoph; Reid, George (2015): A transient ischemic environment induces reversible compaction of chromatin. In: Genome Biology. Online verfügbar unter https://doi.org/10.1186/s13059-015-0802-2, zuletzt geprüft am 06.05.2023

     

    Abstract: BACKGROUND Cells detect and adapt to hypoxic and nutritional stress through immediate transcriptional, translational and metabolic responses. The environmental effects of ischemia on chromatin nanostructure were investigated using single molecule localization microscopy of DNA binding dyes and of acetylated histones, by the sensitivity of chromatin to digestion with DNAseI, and by fluorescence recovery after photobleaching (FRAP) of core and linker histones. RESULTS Short-term oxygen and nutrient deprivation of the cardiomyocyte cell line HL-1 induces a previously undescribed chromatin architecture, consisting of large, chromatin-sparse voids interspersed between DNA-dense hollow helicoid structures 40-700 nm in dimension. The chromatin compaction is reversible, and upon restitution of normoxia and nutrients, chromatin transiently adopts a more open structure than in untreated cells. The compacted state of chromatin reduces transcription, while the open chromatin structure induced upon recovery provokes a transitory increase in transcription. Digestion of chromatin with DNAseI confirms that oxygen and nutrient deprivation induces compaction of chromatin. Chromatin compaction is associated with depletion of ATP and redistribution of the polyamine pool into the nucleus. FRAP demonstrates that core histones are not displaced from compacted chromatin; however, the mobility of linker histone H1 is considerably reduced, to an extent that far exceeds the difference in histone H1 mobility between heterochromatin and euchromatin. CONCLUSIONS These studies exemplify the dynamic capacity of chromatin architecture to physically respond to environmental conditions, directly link cellular energy status to chromatin compaction and provide insight into the effect ischemia has on the nuclear architecture of cells.

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  • Oleksiuk, Olga; Abba, Mohammed; Tezcan, Kerem Can; Schaufler, Wladimir; Bestvater, Felix; Patil, Nitin; Birk, Udo; Hafner, Mathias; Altevogt, Peter; Cremer, Christoph; Allgayer, Heike (2015): Single-Molecule Localization Microscopy allows for the analysis of cancer metastasis-specific miRNA distribution on the nanoscale. In: Oncotarget 6, S. 44745-44757. Online verfügbar unter https://doi.org/10.18632/oncotarget.6297, zuletzt geprüft am 06.05.2023

     

    Abstract: We describe a novel approach for the detection of small non-coding RNAs in single cells by Single-Molecule Localization Microscopy (SMLM). We used a modified SMLM-setup and applied this instrument in a first proof-of-principle concept to human cancer cell lines. Our method is able to visualize single microRNA (miR)-molecules in fixed cells with a localization accuracy of 10-15 nm, and is able to quantify and analyse clustering and localization in particular subcellular sites, including exosomes. We compared the metastasis-site derived (SW620) and primary site derived (SW480) human colorectal cancer (CRC) cell lines, and (as a proof of principle) evaluated the metastasis relevant miR-31 as a first example. We observed that the subcellular distribution of miR-31 molecules in both cell lines was very heterogeneous with the largest subpopulation of optically acquired weakly metastatic cells characterized by a low number of miR-31 molecules, as opposed to a significantly higher number in the majority of the highly metastatic cells. Furthermore, the highly metastatic cells had significantly more miR-31-molecules in the extracellular space, which were visualized to co-localize with exosomes in significantly higher numbers. From this study, we conclude that miRs are not only aberrantly expressed and regulated, but also differentially compartmentalized in cells with different metastatic potential. Taken together, this novel approach, by providing single molecule images of miRNAs in cellulo can be used as a powerful supplementary tool in the analysis of miRNA function and behaviour and has far reaching potential in defining metastasis-critical subpopulations within a given heterogeneous cancer cell population.

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  • Prakash, Kirti; Fournier, David; Redl, Stefan; Best, Gerrit; Borsos, Máté; Tiwari, Vijay K.; Tachibana-Konwalski, Kikuë; Ketting, René F.; Parekh, Sapun H.; Cremer, Christoph; Birk, Udo (2015): Superresolution imaging reveals structurally distinct periodic patterns of chromatin along pachytene chromosomes. In: Proceedings of the National Academy of Sciences of the United States of America 112, S. 14635-14640. Online verfügbar unter https://doi.org/10.1073/pnas.1516928112, zuletzt geprüft am 06.05.2023

     

    Abstract: During meiosis, homologous chromosomes associate to form the synaptonemal complex (SC), a structure essential for fertility. Information about the epigenetic features of chromatin within this structure at the level of superresolution microscopy is largely lacking. We combined single-molecule localization microscopy (SMLM) with quantitative analytical methods to describe the epigenetic landscape of meiotic chromosomes at the pachytene stage in mouse oocytes. DNA is found to be nonrandomly distributed along the length of the SC in condensed clusters. Periodic clusters of repressive chromatin [trimethylation of histone H3 at lysine (Lys) 27 (H3K27me3)] are found at 500-nm intervals along the SC, whereas one of the ends of the SC displays a large and dense cluster of centromeric histone mark [trimethylation of histone H3 at Lys 9 (H3K9me3)]. Chromatin associated with active transcription [trimethylation of histone H3 at Lys 4 (H3K4me3)] is arranged in a radial hair-like loop pattern emerging laterally from the SC. These loops seem to be punctuated with small clusters of H3K4me3 with an average spread larger than their periodicity. Our findings indicate that the nanoscale structure of the pachytene chromosomes is constrained by periodic patterns of chromatin marks, whose function in recombination and higher order genome organization is yet to be elucidated.

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  • Cremer, Christoph; Kaufmann, R.; Gunkel, M.; Polanski, F.; Müller, P.; Dierkes, R.; Degenhard, S.; Wege, C.; Hausmann, M.; Birk, Udo (2014): Application perspectives of localization microscopy in virology. In: Histochemistry and Cell Biology 142, S. 43-59. DOI: 10.1007/s00418-014-1203-4

    Abstract: Localization microscopy approaches allowing an optical resolution down to the single-molecule level in fluorescence-labeled biostructures have already found a variety of applications in cell biology, as well as in virology. Here, we focus on some perspectives of a special localization microscopy embodiment, spectral precision distance/position determination microscopy (SPDM). SPDM permits the use of conventional fluorophores or fluorescent proteins together with standard sample preparation conditions employing an aqueous buffered milieu and typically monochromatic excitation. This allowed superresolution imaging and studies on the aggregation state of modified tobacco mosaic virus particles on the nanoscale with a single-molecule localization accuracy of better than 8 nm, using standard fluorescent dyes in the visible spectrum. To gain a better understanding of cell entry mechanisms during influenza A virus infection, SPDM was used in conjunction with algorithms for distance and cluster analyses to study changes in the distribution of virus particles themselves or in the distribution of infection-related proteins, the hepatocyte growth factor receptors, in the cell membrane on the single-molecule level. Not requiring TIRF (total internal reflection) illumination, SPDM was also applied to study the molecular arrangement of gp36.5/m164 glycoprotein (essentially associated with murine cytomegalovirus infection) in the endoplasmic reticulum and the nuclear membrane inside cells with single-molecule resolution. On the basis of the experimental evidence so far obtained, we finally discuss additional application perspectives of localization microscopy approaches for the fast detection and identification of viruses by multi-color SPDM and combinatorial oligonucleotide fluorescence in situ hybridization, as well as SPDM techniques for optimization of virus-based nanotools and biodetection devices.

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  • Szczurek, Aleksander T.; Prakash, Kirti; Lee, Hyun-Keun; Zurek-Biesiada, Dominika J.; Best, Gerrit; Hagmann, Martin; Dobrucki, Jurek W.; Cremer, Christoph; Birk, Udo (2014): Single molecule localization microscopy of the distribution of chromatin using Hoechst and DAPI fluorescent probes. In: Nucleus 5, S. 331-340. Online verfügbar unter https://doi.org/10.4161/nucl.29564, zuletzt geprüft am 06.05.2023

     

    Abstract: Several approaches have been described to fluorescently label and image DNA and chromatin in situ on the single-molecule level. These superresolution microscopy techniques are based on detecting optically isolated, fluorescently tagged anti-histone antibodies, fluorescently labeled DNA precursor analogs, or fluorescent dyes bound to DNA. Presently they suffer from various drawbacks such as low labeling efficiency or interference with DNA structure. In this report, we demonstrate that DNA minor groove binding dyes, such as Hoechst 33258, Hoechst 33342, and DAPI, can be effectively employed in single molecule localization microscopy (SMLM) with high optical and structural resolution. Upon illumination with low intensity 405 nm light, a small subpopulation of these molecules stochastically undergoes photoconversion from the original blue-emitting form to a green-emitting form. Using a 491 nm laser excitation, fluorescence of these green-emitting, optically isolated molecules was registered until "bleached". This procedure facilitated substantially the optical isolation and localization of large numbers of individual dye molecules bound to DNA in situ, in nuclei of fixed mammalian cells, or in mitotic chromosomes, and enabled the reconstruction of high-quality DNA density maps. We anticipate that this approach will provide new insights into DNA replication, DNA repair, gene transcription, and other nuclear processes.

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  • Rossberger, Sabrina; Best, Gerrit; Baddeley, David; Heintzmann, Rainer; Birk, Udo; Dithmar, Stefan; Cremer, Christoph (2013): Combination of structured illumination and single molecule localization microscopy in one setup. In: Journal of Optics 15. DOI: 10.1088/2040-8978/15/9/094003

    Abstract: Understanding the positional and structural aspects of biological nanostructures simultaneously is as much a challenge as a desideratum. In recent years, highly accurate (20 nm) positional information of optically isolated targets down to the nanometer range has been obtained using single molecule localization microscopy (SMLM), while highly resolved (100 nm) spatial information has been achieved using structured illumination microscopy (SIM). In this paper, we present a high-resolution fluorescence microscope setup which combines the advantages of SMLM with SIM in order to provide high-precision localization and structural information in a single setup. Furthermore, the combination of the wide-field SIM image with the SMLM data allows us to identify artifacts produced during the visualization process of SMLM data, and potentially also during the reconstruction process of SIM images. We describe the SMLM–SIM combo and software, and apply the instrument in a first proof-of-principle to the same region of H3K293 cells to achieve SIM images with high structural resolution (in the 100 nm range) in overlay with the highly accurate position information of localized single fluorophores. Thus, with its robust control software, efficient switching between the SMLM and SIM mode, fully automated and user-friendly acquisition and evaluation software, the SMLM–SIM combo is superior over existing solutions.

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  • Zhu, Shouping; Dong, Di; Birk, Udo; Rieckher, Matthias; Tavernarakis, Nektarios; Qu, Xiaochao; Liang, Jimin; Tian, Jie; Ripoll, Jorge (2012): Automated Motion Correction for In Vivo Optical Projection Tomography. In: IEEE Transactions on Medical Imaging 31, S. 1358-1371. DOI: 10.1109/TMI.2012.2188836

    Abstract: In in vivo optical projection tomography (OPT), object motion will significantly reduce the quality and resolution of the reconstructed image. Based on the well-known Helgason-Ludwig consistency condition (HLCC), we propose a novel method for motion correction in OPT under parallel beam illumination. The method estimates object motion from projection data directly and does not require any other additional information, which results in a straightforward implementation. We decompose object movement into translation and rotation, and discuss how to correct for both translation and general motion simultaneously. Since finding the center of rotation accurately is critical in OPT, we also point out that the system's geometrical offset can be considered as object translation and therefore also calibrated through the translation estimation method. In order to verify the algorithm effectiveness, both simulated and in vivo OPT experiments are performed. Our results demonstrate that the proposed approach is capable of decreasing movement artifacts significantly thus providing high quality reconstructed images in the presence of object motion.

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  • Birk, Udo; Darrell, Alex; Konstantinides, Nikos; Sarasa-Renedo, Ana; Ripoll, Jorge (2011): Improved reconstructions and generalized filtered back projection for optical projection tomography. In: Applied Optics 50, S. 392-398. DOI: 10.1364/AO.50.000392

    Abstract: Optical projection tomography (OPT) is a noninvasive imaging technique that enables imaging of small specimens (<1 cm), such as organs or animals in early developmental stages. In this paper, we present a set of computational methods that can be applied to the acquired data sets in order to correct for (a) unknown background or illumination intensity distributions over the field of view, (b) intensity spikes in single CCD pixels (so-called "hot pixels"), and (c) refractive index mismatch between the media in which the specimens are embedded and the environment. We have tested these correction methods using a variety of samples and present results obtained from Parhyale hawaiensis embedded in glycerol and in sea water. Successful reconstructions of fluorescence and absorption OPT images have been obtained for weakly scattering specimens embedded in media with nonmatched refractive index, thus advancing OPT toward routine in vivo imaging.

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  • Rieckher, Matthias; Birk, Udo; Meyer, Heiko; Ripoll, Jorge; Tavernarakis, Nektarios (2011): Microscopic Optical Projection Tomography In Vivo. In: PLOS ONE 6. Online verfügbar unter https://doi.org/10.1371/journal.pone.0018963, zuletzt geprüft am 07.05.2023

     

    Abstract: We describe a versatile optical projection tomography system for rapid three-dimensional imaging of microscopic specimens in vivo. Our tomographic setup eliminates the in xy and z strongly asymmetric resolution, resulting from optical sectioning in conventional confocal microscopy. It allows for robust, high resolution fluorescence as well as absorption imaging of live transparent invertebrate animals such as C. elegans. This system offers considerable advantages over currently available methods when imaging dynamic developmental processes and animal ageing; it permits monitoring of spatio-temporal gene expression and anatomical alterations with single-cell resolution, it utilizes both fluorescence and absorption as a source of contrast, and is easily adaptable for a range of small model organisms.

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  • Baddeley, David; Chagin, V. O.; Schermelleh, L.; Martin, S.; Pombo, A.; Carlton, P. M.; Gahl, A.; Domaing, P.; Birk, Udo; Leonhardt, H.; Cremer, C.; Cardoso, M. C. (2010): Measurement of replication structures at the nanometer scale using super-resolution light microscopy. In: Nucleic Acids Research 38. DOI: 10.1093/nar/gkp901

    DOI: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2811013 

    Abstract: DNA replication, similar to other cellular processes, occurs within dynamic macromolecular structures. Any comprehensive understanding ultimately requires quantitative data to establish and test models of genome duplication. We used two different super-resolution light microscopy techniques to directly measure and compare the size and numbers of replication foci in mammalian cells. This analysis showed that replication foci vary in size from 210 nm down to 40 nm. Remarkably, spatially modulated illumination (SMI) and 3D-structured illumination microscopy (3D-SIM) both showed an average size of 125 nm that was conserved throughout S-phase and independent of the labeling method, suggesting a basic unit of genome duplication. Interestingly, the improved optical 3D resolution identified 3- to 5-fold more distinct replication foci than previously reported. These results show that optical nanoscopy techniques enable accurate measurements of cellular structures at a level previously achieved only by electron microscopy and highlight the possibility of high-throughput, multispectral 3D analyses.

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  • Baddeley, David; Weiland, Yanina; Batram, C.; Birk, Udo; Cremer, Christoph (2010): Model based precision structural measurements on barely resolved objects. In: Journal of Microscopy 237, S. 70-78. Online verfügbar unter https://doi.org/10.1111/j.1365-2818.2009.03304.x, zuletzt geprüft am 07.05.2023

     

    Abstract: A model based method for the accurate quantification of the 3D structure of fluorescently labelled cellular objects similar in size to the optical resolution limit is presented. This method is applied to both simulated confocal images of chromatin structures and to real confocal data obtained on a Fluorescence in situ Hybridization (FISH) labelled gene domain. The model assumes that the object is composed of a small number of discrete points which are convolved with the microscope point spread function to give the image. Fitting this model to image data results in a method to assess object structure which is accurate, shows a low bias, and does not require user intervention or the potentially subjective setting of a threshold.

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  • Birk, Udo; Rieckher, Matthias; Konstantinides, Nikos; Darrell, Alex; Sarasa-Renedo, Ana; Meyer, Heiko; Tavernarakis, Nektarios; Ripoll, Jorge (2010): Correction for specimen movement and rotation errors for in-vivo Optical Projection Tomography. In: Biomedical Optics Express 1, S. 87-96. Online verfügbar unter https://doi.org/10.1364/BOE.1.000087, zuletzt geprüft am 07.05.2023

     

    Abstract: The application of optical projection tomography to in-vivo experiments is limited by specimen movement during the acquisition. We present a set of mathematical correction methods applied to the acquired data stacks to correct for movement in both directions of the image plane. These methods have been applied to correct experimental data taken from in-vivo optical projection tomography experiments in Caenorhabditis elegans. Successful reconstructions for both fluorescence and white light (absorption) measurements are shown. Since no difference between movement of the animal and movement of the rotation axis is made, this approach at the same time removes artifacts due to mechanical drifts and errors in the assumed center of rotation.

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  • Birk, Udo; Darrell, Alex; Konstantinidis, Nikos; Ripoll, Jorge (2010) : Correction of Lateral Movement and Spherical Aberrations in Optical Projection Tomography: Proceedings Biomedical Optics and 3-D Imaging: Biomedical Optics 2010: Miami, 11. - 14. April. Biomedical optics and 3-D imaging: Washington, DC: Optica Publishing Group

    Abstract: Non-invasive optical projection tomography (OPT) provides a method to image small animals in-vivo. We present two correction methods for this technique which can be applied after the images have been acquired. The first method allows to reconstruct specimens embedded in media with arbitrary refractive index, and the second method corrects for small movements of the specimens with respect to the detection system. We have tested the correction methods with computer simulated data and with samples of Parhyale hawaiensis embedded in sea water. These post-acquisition corrections prove to be a major step towards routine in-vivo imaging, and provide 3D analyses of OPT data which can not be rendered using standard reconstruction methods.

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  • Grossmann, C.; Schwarz-Finsterle, Jutta; Schmitt, Eberhard; Birk, Udo; Hildenbrand, Georg; Cremer, Christoph; Trakhtenbrot, Luba; Hausmann, Michael (2010) : Variations of the spatial fluorescence distribution in ABL gene chromatin domains measured in blood cell nuclei by SMI microscopy after COMBO – FISH labelling In: Méndez-Vilas, Antonio; Díaz, J. (Hg.): Microscopy: Science, technology, applications and education: Badajoz: Formatex (Formatex Microscopy Series), S. 688-695

    Abstract: Despite investigations of the nuclear architecture of the genome, the true 3D nanoarchitecture of small chromatin domains and its correlation to epigenetic control mechanisms are still not sufficiently known. Reasons for this are the lack of nanostructure conserving labelling techniques as well as practical limitations in 3D fluorescence microscopy with high optical resolution (100 nm and below). The present study was initiated as an attempt to overcome these methodological shortcomings. As a model case we compared the spatial extension of fluorescence of chromatin domains in ABL gene regions in blood cells (BC) of different Chronic Myelogenous Leukemia (CML) patients with BCR/ABL fusion on the Philadelphia chromosome (Ph) and in lymphocytes of a healthy donor and a Prader-Willi syndrome patient by Spatially Modulated Illumination (SMI) microscopy after specific labelling using COMBinatorial Oligo Fluorescence In Situ Hybridization (COMBO–FISH). Volumes and compaction ratios of interactively identified ABL chromatin domains were determined under the assumption of a compact spherical fluorescence distribution. Significant differences were found between the domain size values of the labelled sites of Ph+ BC nuclei of CML patients and of Ph- BC nuclei of a CML patient after successful chemotherapy (imatinib mesylate (STI) treatment). Differences were also significant between BC of all CML patients and lymphocyte control preparations. These results show the feasibility of COMBO-FISH in combination with SMI microscopy.

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  • Sarasa-Renedo, Ana; Favicchio, Rosy; Birk, Udo; Zacharakis, Giannis; Mamalaki, Clio; Ripoll, Jorge (2010): Source intensity profile in noncontact optical tomography. In: Optics Letters 35, S. 34-36. DOI: 10.1364/OL.35.000034

    Abstract: Noncontact optical tomography in reflection mode is often the only possible configuration when imaging the expression of green fluorescent protein (GFP) or other fluorescent proteins in live animals owing to the short penetration depth of visible light. When imaging in reflection mode using noncontact approaches (i.e., without the use of fibers coupled to tissue), correctly accounting for the intensity profile of the source at the surface is a difficult task, usually needing to fit for source positions and/or approximating these to point sources. In this Letter we present a rigorous theoretical approach that directly accounts for the source's intensity profile and verify it using in vivo data from GFP-expressing mice. We show how this approach improves image quality and resolution, while considerably simplifying the forward and inverse problems of the image reconstruction process.

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  • Birk, Udo; Hausmann, Michael (2009): Festschrift to recognise and celebrate Christoph Cremer's contribution to the field of biophysics on the occasion of his 65th birthday. In: European Biophysics Journal 38, S. 719-720. Online verfügbar unter https://doi.org/10.1007/s00249-009-0500-7, zuletzt geprüft am 07.05.2023

     

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  • Birk, Udo; Baddeley, David; Cremer, Christoph (2008) : Nanosizing by Spatially Modulated Illumination (SMI) Microscopy and Applications to the Nucleus In: Hancock, Ronald: The Nucleus: Volume 2: Chromatin, Transcription, Envelope, Proteins, Dynamics, and Imaging: Totowa: Humana Press

    Abstract: In this chapter we present the method of spatially modulated illumination (SMI) microscopy, a (far-field) fluorescence microscopy technique featuring structured illumination obtained via a standing wave field laser excitation pattern. While this method does not provide higher optical resolution, it has been proven a highly valuable tool to access structural parameters of fluorescently labeled macromolecular structures in cells. SMI microscopy has been used to measure relative positions with a reproducibility of <2 nm between fluorescing objects. Among others, we have measured size distributions of protein clusters with an accuracy much better than the resolution achievable e.g. in confocal microscopy. The advantages of the SMI microscope over other (ultra-)high resolution light microscopes are its easy sample preparation and microscope handling as well as the comparably fast acquisition times and large fields of view.

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  • Reymann, Jürgen; Baddeley, David; Gunkel, Manuel; Lemmer, Paul; Stadter, Werner; Jegou, Thibaud; Rippe, Karsten; Cremer, Christoph; Birk, Udo (2008): High-precision structural analysis of subnuclear complexes in fixed and live cells via spatially modulated illumination (SMI) microscopy. In: Chromosome Research 16, S. 367-382. Online verfügbar unter https://doi.org/10.1007/s10577-008-1238-2, zuletzt geprüft am 07.05.2023

     

    Abstract: Spatially modulated illumination (SMI) microscopy is a method of wide field fluorescence microscopy featuring interferometric illumination, which delivers structural information about nanoscale architecture in fluorescently labelled cells. The first prototype of the SMI microscope proved its applicability to a wide range of biological questions. For the SMI live cell imaging this system was enhanced in terms of the development of a completely new upright configuration. This so called Vertico-SMI transfers the advantages of SMI nanoscaling to vital biological systems, and is shown to work consistently at different temperatures using both oil- and water-immersion objective lenses. Furthermore, we increased the speed of data acquisition to minimize errors in the detection signal resulting from cellular or object movement. By performing accurate characterization, the present Vertico-SMI now offers a fully-fledged microscope enabling a complete three-dimensional (3D) SMI data stack to be acquired in less than 2 seconds. We have performed live cell measurements of a tet-operator repeat insert in U2OS cells, which provided the first in vivo signatures of subnuclear complexes. Furthermore, we have successfully implemented an optional optical configuration allowing the generation of high-resolution localization microscopy images of a nuclear pore complex distribution.

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  • Baddeley, David; Batram, Claudia; Weiland, Yanina; Cremer, Christoph; Birk, Udo (2007): Nanostructure analysis using spatially modulated illumination microscopy. In: Nature Protocols 2, S. 2640-2646. DOI: 10.1038/nprot.2007.399

    Abstract: We describe the usage of the spatially modulated illumination (SMI) microscope to estimate the sizes (and/or positions) of fluorescently labeled cellular nanostructures, including a brief introduction to the instrument and its handling. The principle setup of the SMI microscope will be introduced to explain the measures necessary for a successful nanostructure analysis, before the steps for sample preparation, data acquisition and evaluation are given. The protocol starts with cells already attached to the cover glass. The protocol and duration outlined here are typical for fixed specimens; however, considerably faster data acquisition and in vivo measurements are possible.

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  • Birk, Udo; Upmann, I.; Toomre, D.; Wagner, C.; Cremer, Christoph (2007) : Size Estimation of Protein Clusters in the Nanometer Range by Using Spatially Modulated Illumination Microscopy In: Méndez-Vilas, Antonio; Díaz, J. (Hg.): Modern research and educational topics in microscopy: Badajoz: Formatex (Formatex Microscopy Series), S. 272-279

    Abstract: A major goal of modern cell biology is the improved understanding of the three dimensional nanostructure of cellular macromolecule complexes, a goal for which a variety of research tools have been developed. Here, we describe the potential of Spatially Modulated Illumination (SMI) microscopy, a far field light optical method, to study the axial extent of fluorescently labeled protein clusters in the membrane of PtK2 cells. This is done by comparison of experimental SMI-data with the predictions of “virtual SMI-microscopy” calculations for an assumed dye distribution. Previous SMI investigations have shown that object sizes down to a few tens of nanometers can be extracted, and the method has been applied in a biological setting to determine the axial extents of nuclear nanostructures. Using these novel far field light microscopy tools at 488 nm excitation wavelength, the extension of GPI-anchored protein clusters perpendicular to the cell membrane was estimated to be (69±18) nm.

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  • Fenz, Susanne; Mathée, H.; Kreth, Gregor; Baddeley, David; Weiland, Y.; Schwarz-Finsterle, Jutta; Cremer, Christoph; Birk, Udo (2007) : Two-color intranuclear distance measurements of gene regions in human lymphocytes In: Wilson, Tony; Periasamy, Ammasi (Hg.): Confocal, Multiphoton, and Nonlinear Microscopic Imaging III: European Conference on Biomedical Optics: München, 17. - 21. Juni (SPIE Proceedings)

    DOI: http://proceedings.spiedigitallibrary.org/proceeding.aspx?doi=10.1117/12.727506 

    Abstract: The method of Spectral Precision Distance Microscopy (SPDM) has been used to determine distances between two FISH (Fluorescence-in situ-Hybridization)-labeled gene regions on chromosome 9. To this end we applied methods to correct for chromatic aberrations of the microscope optics alone and also of the sample induced aberrations due to mismatch of the refractive indices. Using a confocal microscope and a threshold based position determination algorithm, positions could be measured with an accuracy of about 65 nm inside of fixed cell nuclei. Distances obtained from the measurements have been verified using a 3D computer model of the cell nucleus. In principle, this SPDM approach could be combined with novel fluorescence microscopes to obtain structural information well below the optical resolution. At present the precision limit of the distance measurements is set by variations of the refractive index throughout the specimens.

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  • Fenz, Susanne; Mathée, Hans; Kreth, Gregor; Baddeley, David; Weiland, Yanina; Schwarz-Finstlerle, J.; Cremer, Christoph; Birk, Udo (2007) : Two-color intranuclear distance measurements of gene regions in human lymphocytes In: Wilson, Tony; Periasamy, Ammasi (Hg.): Confocal, multiphoton, and nonlinear microscopic imaging III: Proceedings of SPIE-OSA Biomedical Optics: European Conference on Biomedical Optics: München, 17. - 21. Juni: Bellingham, Wash.; Washington, D.C.: Optica Publishing Group (Proceedings of SPIE)

    Abstract: The method of Spectral Precision Distance Microscopy (SPDM) has been used to determine distances between two FISH (Fluorescence-in situ-Hybridization)-labeled gene regions on chromosome 9. To this end we applied methods to correct for chromatic aberrations of the microscope optics alone and also of the sample induced aberrations due to mismatch of the refractive indices. Using a confocal microscope and a threshold based position determination algorithm, positions could be measured with an accuracy of about 65 nm inside of fixed cell nuclei. Distances obtained from the measurements have been verified using a 3D computer model of the cell nucleus. In principle, this SPDM approach could be combined with novel fluorescence microscopes to obtain structural information well below the optical resolution. At present the precision limit of the distance measurements is set by variations of the refractive index throughout the specimens.

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  • Mathée, Hans; Baddeley, David; Wotzlaw, C.; Cremer, Christoph; Birk, Udo (2007): Spatially modulated illumination microscopy using one objective lens. In: Optical Engineering 46. DOI: 10.1117/1.2768085

    Abstract: The spatially modulated illumination (SMI) microscope is a wide-field fluorescence microscope featuring axially structured illumination, through which access to information about subresolution object structures is obtained. We present a simplified setup where the interference pattern is generated by reflecting the laser beam with a mirror. We characterize our setup by presenting measurements on fluorescent microspheres with diameters ranging from 44 to 200 nm. The results agree well with the sizes provided by the manufacturer. Furthermore, the spheres are analyzed with 458-, 514-, 488-, and 568-nm excitation wavelengths, giving good agreement of the sizes determined at the respective wavelengths. A measurement of the same objects using different excitation wavelengths leads to a size difference of a few nanometers only. The potential of SMI microscopy for the fast analysis of many fluorescent objects is also addressed. In addition, the applicability to biological specimens is shown on fluorescently labeled, specific chromatin domains. The results obtained using the presented mirror geometry agree well with data obtained using a standard SMI microscope setup.

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  • Birk, Udo; Baddeley, David; Cremer, Christoph (2006) : Local protein/gene density measurements using SMI microscopy In: Gorecki, Christophe; Asundi, Anand K.; Osten, Wolfgang (Hg.): Optical Micro- and Nanometrology in Microsystems Technology: Photonics Europe: Strassburg, 3.-7. April (SPIE Proceedings)

    DOI: http://proceedings.spiedigitallibrary.org/proceeding.aspx?doi=10.1117/12.668023 

    Abstract: Spatially Modulated Illumination (SMI) microscopy was applied to determine changes of the local refractive index at discrete fluorescently labeled sites within the cell nucleus. We present measurements on polymerase II complexes, where we found a variation of the local refractive index of 1.38 - 1.55 (standard deviation interval) throughout the nucleus. This variability is not correlated to the accumulations and the extensions of the polymerase II complexes, which have been determined in a previous experiment.1 Local protein accumulations such as adherent transcriptionally active proteins could possibly contribute to such variations, as could also different compactions of the DNA fiber. Altogether, we present a method to precisely obtain a map of the local refractive index inside of cell nuclei, which provides another contrasting mechanism for visualizing sub cellular structures.

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  • Hausmann, Michael; Schwarz-Finsterle, Jutta; Stein, S.; Grossmann, C.; Birk, Udo; Baddeley, David; Batram, Claudia; Hildenbrand, Georg; Schmitt, Eberhard; Trakhtenbrot, Luba (2006) : Nanoskopie mit Nanomarkern: Werkzeuge fuer die zellulaere Strahlenbiologie?: 9. Jahrestagung der Gesellschaft fuer Biologische Strahlenforschung: Proceedings: Braunschweig, 10. - 12. Mai: Optica Publishing Group

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  • Mathée, Hans; Baddeley, David; Wotzlaw, C.; Fandrey, J.; Cremer, Christoph; Birk, Udo (2006): Nanostructure of specific chromatin regions and nuclear complexes. In: Histochemistry and Cell Biology 125, S. 75-82. DOI: 10.1007/s00418-005-0096-7

    Abstract: Spatially modulated illumination (SMI) microscopy is a method of widefield fluorescence microscopy featuring interferometric illumination, which delivers structural information about nanoscale features in fluorescently labeled cells. Using this approach, structural changes in the context of gene activation and chromatin remodeling may be revealed. In this paper we present the application of SMI microscopy to size measurements of the 7q22 gene region, giving us a size estimate of 105+/-16 nm which corresponds to an average compaction ratio of 1:324. The results for the 7q22 domain are compared with the previously measured sizes of other fluorescently labeled gene regions, and to those obtained for transcription factories. The absence of a correlation between the measured and genomic sizes of the various gene regions indicate that a high variability in chromatin folding is present, with factors other than the sequence length contributing to the chromatin compaction. Measurements of the 7q22 region in different preparations and at different excitation wavelengths show a good agreement, thus demonstrating that the technique is robust when applied to biological samples.

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  • Wagner, Christian; Hildenbrand, Georg; Birk, Udo; Cremer, Christoph (2006): Beyond nanosizing. An approach to shape analysis of fluorescent nanostructures by SMI-microscopy. In: Optik 117, S. 26-32. Online verfügbar unter https://doi.org/10.1016/j.ijleo.2005.05.006, zuletzt geprüft am 07.05.2023

     

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  • Birk, Udo; Baddeley, David; Mathée, Hans; Wagner, Christian; Cremer, Christoph (2005): Nanometry of bio-molecular complexes using PSF reconstruction in SMI microscopy. Jahrestagung der deutschen Gesellschaft für angewandte Optik (DGaO). Deutsche Gesellschaft für angewandte Optik. 20. Mai, 2005. Online verfügbar unter https://www.dgao-proceedings.de/archiv/106_chronologisch_d.php, zuletzt geprüft am 23.05.2023

     

    Abstract: Spatially Modulated Illumination Microscopy (SMI) in combination with reference objects of known size to reconstruct the Point Spread Function (PSF) is applied to determine the size of individual fluorescent objects. SMI employs a structured illumination to obtain information about the specimen far beyond the conventional resolution limit. Size determination is based on small perturbations of the intensity modulation by the fluorescent objects. The SMI-PSF is used to derive the object size from these perturbations. Reference objects with known dye distribution are added to the sample to reconstruct the PSF. We present data from measurements on fluorescent microspheres with diameters between 40 and 200 nm using an excitation wavelength of 488 nm. Applications of gene expression analysis, transcription factories analysis, protein cluster analysis, and gene compaction analysis prepared on conventional microscope slides are shown. The size values obtained are about two orders of magnitude smaller compared to the extension of the illumination or observation volume, respectively, in a confocal laser scanning microscope using a high numerical aperture objective lens.

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  • Hausmann, Michael; Hildenbrand, Georg; Schwarz-Finsterle, Jutta; Birk, Udo; Schneider, Helmut; Cremer, Christoph; Schmitt, Eberhard (2005): New technologies measure genome domains. In: Biophotonics International 12

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  • Hildenbrand, Georg; Rapp, Alexander; Birk, Udo; Wagner, Christian; Cremer, Christoph; Hausmann, Michael (2005): Nano-Sizing of Specific Gene Domains in Intact Human Cell Nuclei by Spatially Modulated Illumination Light Microscopy. In: Biophysical Journal 88, S. 4312-4318. Online verfügbar unter https://doi.org/10.1529/biophysj.104.056796, zuletzt geprüft am 07.05.2023

     

    Abstract: Although light microscopy and three-dimensional image analysis have made considerable progress during the last decade, it is still challenging to analyze the genome nano-architecture of specific gene domains in three-dimensional cell nuclei by fluorescence microscopy. Here, we present for the first time chromatin compaction measurements in human lymphocyte cell nuclei for three different, specific gene domains using a novel light microscopic approach called Spatially Modulated Illumination microscopy. Gene domains for p53, p58, and c-myc were labeled by fluorescence in situ hybridization and the sizes of the fluorescence in situ hybridization "spots" were measured. The mean diameters of the gene domains were determined to 103 nm (c-myc), 119 nm (p53), and 123 nm (p58) and did not correlate to the genomic, labeled sequence length. Assuming a spherical domain shape, these values would correspond to volumes of 5.7 x 10(-4) microm(3) (c-myc), 8.9 x 10(-4) microm(3) (p53), and 9.7 x 10(-4) microm(3) (p58). These volumes are approximately 2 orders of magnitude smaller than the diffraction limited illumination or observation volume, respectively, in a confocal laser scanning microscope using a high numerical aperture objective lens. By comparison of the labeled sequence length to the domain size, compaction ratios were estimated to 1:129 (p53), 1:235 (p58), and 1:396 (c-myc). The measurements demonstrate the advantage of the SMI technique for the analysis of gene domain nano-architecture in cell nuclei. The data indicate that chromatin compaction is subjected to a large variability which may be due to different states of genetic activity or reflect the cell cycle state.

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  • Wagner, Christian; Birk, Udo; Cremer, Christoph (2005): High-precision SMI microscopy size measurements by simultaneous frequency domain reconstruction of the axial point spread function. In: Optik 116, S. 15-21. Online verfügbar unter https://doi.org/10.1016/j.ijleo.2004.10.002, zuletzt geprüft am 07.05.2023

     

    Abstract: An improved size measurement method using spatially modulated illumination (SMI) microscopy enhances subwavelength size determination of fluorescent objects. In this new approach the point spread function of the SMI microscope is reconstructed in each measurement. For this, reference objects with known dye distribution have to be put additionally to the unknown objects on the object slide or on the cover slip. We present data from measurements on fluorescent microspheres with diameters of 140 and 200 nm using an excitation wavelength of 488 nm.

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  • Birk, Udo; Failla, Antonio Virgilio; Cremer, Christoph (2004): Superresolution size determination in fluorescence microscopy. A comparison between spatially modulated illumination and confocal laser scanning microscopy. In: Journal of Applied Physics 95, S. 8436-8443. Online verfügbar unter https://doi.org/10.1063/1.1751633, zuletzt geprüft am 07.05.2023

     

    Abstract: Recently developed far field light optical methods are a powerful tool to analyze biological nanostructures and their dynamics, in particular including the interior of three-dimensionally conserved cells. In this article, the recently described method of spatially modulated illumination (SMI) microscopy has been further extended to the online determination of the extension of small, subwavelength sized, fluorescent objects (nanosizing). Using fluorescence excitation with 488 nm, the determination of fluorescent labeled object diameters down to 40 nm corresponding to about 1/12th of the wavelength used for one-photon excitation could be shown. The results of the SMI nanosizing procedure for a detailed, systematic variation of the object diameter are presented together with a fast algorithm for online size evaluation. In addition, we show a direct comparison of the diameter of “colocalization volumes” between SMI nanosizing and conventional confocal laser scanning microscopy.

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  • Martin, Sonya; Failla, Antonio Virgilio; Birk, Udo; Cremer, Christoph; Pombo, Ana (2004): Measuring the Size of Biological Nanostructures with Spatially Modulated Illumination Microscopy. In: Molecular Biology of the Cell 15, S. 2449-2455. Online verfügbar unter https://doi.org/10.1091/mbc.e04-01-0045, zuletzt geprüft am 07.05.2023

    Abstract: Spatially modulated illumination fluorescence microscopy can in theory measure the sizes of objects with a diameter ranging between 10 and 200 nm and has allowed accurate size measurement of subresolution fluorescent beads ( approximately 40-100 nm). Biological structures in this size range have so far been measured by electron microscopy. Here, we have labeled sites containing the active, hyperphosphorylated form of RNA polymerase II in the nucleus of HeLa cells by using the antibody H5. The spatially modulated illumination-microscope was compared with confocal laser scanning and electron microscopes and found to be suitable for measuring the size of cellular nanostructures in a biological setting. The hyperphosphorylated form of polymerase II was found in structures with a diameter of approximately 70 nm, well below the 200-nm resolution limit of standard fluorescence microscopes.

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  • Failla, Antonio Virgilio; Albrecht, B.; Birk, Udo; Schweitzer, A.; Kroll, Alexander; Hildenbrand, Georg; Bach, M.; Cremer, Christoph (2003): Nanostructure Analysis Using Spatially Modulated Illumination Microscopy. In: Complexus 1, S. 77-88. DOI: 10.1159/000070464

    Abstract: For an improved understanding of cellular processes, it is highly desirable to develop light optical methods for the analysis of biological nanostructures and their dynamics in the interior of three-dimensionally (3D) conserved cells. Here, important structural parameters to be considered are the topology, i.e. the mutual positions and distances, as well as the sizes of the constituting subunits. This has become possible by the development of a novel method of far-field light fluorescence microscopy, spatially modulated illumination (SMI) microscopy. Using this approach, axial distances between fluorescence-labeled targets can be measured with an accuracy close to 1 nm; their sizes can be determined down to a few tens of nanometers. This approach can be extended to the determination of 3D positions and mutual 3D distances and sizes of any number of small objects/subunits that can be discriminated due to their spectral signatures. Consequently, the new approach allows an ‘in situ nanostructure elucidation, until now regarded to be beyond the possibilities of far-field light microscopy. Application examples discussed are: colocalization/nanosizing and topological analysis of large protein-protein complexes, of nucleic acid-protein complexes (such as transcription factories), or of the highly complex DNA-protein nanostructures of which active/ inactive gene regions in the eukaryotic cell nucleus are constituted.

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  • Failla, Antoinio Virgilio; Birk, Udo; Albrecht, Benno; Kroll, Alexander; Cremer, Christoph (2003): Nanosizing of fluorescent objects by spatially modulated illuminated microscopy: erratum. In: Applied Optics 42. DOI: 10.1364/AO.42.001308

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  • Failla, Antonio Virgilio; Birk, Udo; Albrecht, Benno; Kroll, Alexander; Cremer, Christoph (2002): Nanosizing of fluorescent objects by spatially modulated illumination microscopy. In: Applied Optics 41, S. 7275-7283. DOI: 10.1364/ao.41.007275

    Abstract: A new approach to measuring the sizes of small fluorescent objects by use of spatially modulated illumination (SMI) far-field light microscopy is presented. This method is based on SME measurements combined with a new SMI virtual microscopy (VIM) data analysis calibration algorithm. Here, experimental SMI measurements of fluorescent objects with known diameter (size) were made. From the SMI data obtained, the size was determined in an independent way by use of the SMI VIM algorithm. The results showed that with SMI microscopy in combination with SMI VIM calibration, subwavelength object size measurements as small as 40 nm are experimentally feasible with high accuracy.

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  • Darrell, Alexander; Marias, Kostas; Brady, Michael; Meyer, Heiko; Birk, Udo; Ripoll, Jorge : Noise reduction in fluorescence Optical Projection Tomograph: 2008 IEEE International Workshop on Imaging Systems and Techniques: Chania, 10. - 12. September: 2008

    Abstract: Optical Projection Tomography (OPT) suffers from additive CCD detector noise. This paper investigates the nature of the CCD detector noise for an OPT setup. The CCD detector noise is found to be described well by an intensity dependent zero-mean Gaussian distribution. A method of reducing the effect of noise in fluorescence OPT reconstructions is discussed. The results of the noise reduction are demonstrated using both artificial scenes created with fluorescent microspheres and real auto-fluorescence OPT projections of the cuticle of the amphipod crustacean Parhyale hawaiensis.

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  • Darrell, Alexander; Meyer, H.; Birk, Udo; Marias, Kostas; Brady, Michael; Ripoll, Jorge : Maximum likelihood reconstruction for fluorescence Optical Projection Tomography: 2008 8th IEEE International Conference on BioInformatics and BioEngineering: Athen, 8. - 10. Oktober: 2008

    Abstract: Tomographic reconstruction of fluorescence optical projection tomography (OPT) data is usually performed using the standard filtered back projection (FBP) algorithm. However, there are several physical aspects of fluorescence OPT that pose major challenges for the FBP algorithm. These include blurring, and the fact that for an isotropically emitting point source (or fluorophore), the power received by an objective aperture decreases with the inverse square of the distance to the source. These two effects are shown to result in qualitative and quantitative inaccuracies in fluorescence OPT reconstructions obtained using standard FBP. A model of image formation is developed which includes the effects of isotropic emission and blurring. The model is used to calculate a probabilistic system matrix for use in the maximum likelihood expectation maximisation algorithm, which leads to reconstructions that are both qualitatively superior and quantitatively correct.

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