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Single-molecule localization microscopy allows us to observe cellular structures on the nanoscale. Due to the high frame numbers required to achieve good localization precision, multi-colour experiments can however be challenging. Here, we present an approach to record four standard organic fluorescent dyes simultaneously with a single excitation wavelength over a large field of view. This approach dissolves problems with image registration, chromatic aberrations and sample drift common to other multi-colour approaches on the nanoscale. Method: We use a 638 nm diode laser and a microlens-based Köhler integrator1 for homogenous epi-illumination of the entire field of view. This ensures field-independent image resolution2. Stochastic emission events from samples labelled with DyLight 633, Alexa Fluor 647, Biotium CF660 and CF680 are detected through an image splitter on a sCMOS camera. For 3D localization, a cylindrical lens introduces a depth-dependent astigmatism in one detection path. Microscope control and localization fitting are performed in open-source software µManger3 and Fiji/ ThunderSTORM4,5. Subsequent custom spectral analysis assigns a false colour to each localized emission event based on its spectroscopic signature. In contrast to previous spectroscopic super-resolution microscopy efforts6,7 we can achieve nanometer resolution in 3D with a single objective and camera over a field of view of 130 x 60 µm2. We use immunolabelling with standard organic dyes, which makes this method applicable to a wide range of molecular biology samples. The optical setup can be implemented on any epi-fluorescence microscope. We intend to publish the spectral analysis as an open source package in the near future. References Völkel, R. & Weible, K. J. Laser Beam Homogenizing: Limitations and Constraints. Proc. SPIE 7102 (2008). Douglass, K. M. et al. Super-resolution imaging of multiple cells by optimized flat-field epi-illumination. Nat. Photonics 10 (2016). Edelstein, A. D. et al. Advanced methods of microscope control using μManager software. J. Biol. Methods (2014). Ovesný, M. et al. ThunderSTORM: a comprehensive ImageJ plug-in for PALM and STORM data analysis and super-resolution imaging. Bioinformatics 30 (2014). Schindelin, J. et al. Fiji: an open-source platform for biological-image analysis. Nat. Methods (2012). Dong, B. et al. Super-resolution spectroscopic microscopy via photon localization. Nat. Commun. 7 (2016). Zhang, Z. et al. Ultrahigh-throughput single-molecule spectroscopy and spectrally resolved super-resolution microscopy. Nat. Methods 12 (2015).
[PHYS.PHYS.PHYS-OPTICS] Physics [physics]/Physics [physics]/Optics [physics.optics], Fluorescence microscopy, [PHYS.PHYS.PHYS-INS-DET] Physics [physics]/Physics [physics]/Instrumentation and Detectors [physics.ins-det], dSTORM, Super-resolution microscopy, [SDV.BBM.BM] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, SMLM
[PHYS.PHYS.PHYS-OPTICS] Physics [physics]/Physics [physics]/Optics [physics.optics], Fluorescence microscopy, [PHYS.PHYS.PHYS-INS-DET] Physics [physics]/Physics [physics]/Instrumentation and Detectors [physics.ins-det], dSTORM, Super-resolution microscopy, [SDV.BBM.BM] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, SMLM
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