Three-dimensional structured illumination microscopy (3D-SIM) doubles the resolution of fluorescence imaging in all directions and enables optical sectioning with increased image contrast. However, 3D-SIM has not been widely applied to imaging deep in thick tissues due to its sensitivity to sample-induced aberrations, making the method difficult to apply beyond 10 µm in depth. Furthermore, 3D-SIM has not been available in an upright configuration, limiting its use for live imaging while manipulating the specimen, for example, with electrophysiology. Here, we have overcome these barriers by developing a novel upright 3D-SIM system (termed Deep3DSIM) that incorporates adaptive optics for aberration correction and remote focusing, reducing artefacts, improving contrast, restoring resolution, and eliminating the need to move the specimen or the objective lens in volume imaging. These advantages are equally applicable to inverted 3D-SIM systems. We demonstrate high-quality 3D-SIM imaging in various samples, including imaging more than 130 µm into the Drosophila brain.

3D structured illumination microscopy (3D-SIM) doubles the resolution of fluorescence imaging in lateral and axial directions and increases contrast in both fixed and live specimens. However, 3D-SIM has so far not been widely applied to imaging deep in thick tissues due to its sensitivity to specimen-induced aberrations, making the method difficult to apply beyond 10 µm in depth. Furthermore, 3D-SIM has not been available in an upright configuration, limiting its use for live imaging while manipulating the specimen, for example with electrophysiology. Here, we have overcome these barriers by developing a novel upright 3D-SIM system (termed Deep3DSIM) that incorporates adaptive optics (AO) for aberration correction and remote focusing, reducing artefacts, and removing the need to move the specimen or objective. Both these advantages are equally applicable to inverted 3D-SIM microscopes. We demonstrate high-quality 3D-SIM imaging up to 130 µm into complex tissue and live sample manipulation, including human cells and Drosophila larval brains and embryos.### Competing Interest StatementThe authors have declared no competing interest.

Adaptive optics is being applied widely to a range of microscopies in order to improve imaging quality in the presence of specimen-induced aberrations. We present here the first implementation of wavefront-sensorless adaptive optics for a laser-free, aperture correlation, spinning disk microscope. This widefield method provides confocal-like optical sectioning through use of a patterned disk in the illumination and detection paths. Like other high-resolution microscopes, its operation is compromised by aberrations due to refractive index mismatch and variations within the specimen. Correction of such aberrations shows improved signal level, contrast and resolution.

We have developed “Microscope-Cockpit” (Cockpit), a highly adaptable open source user-friendly Python-based Graphical User Interface (GUI) environment for precision control of both simple and elaborate bespoke microscope systems. The user environment allows next-generation near instantaneous navigation of the entire slide landscape for efficient selection of specimens of interest and automated acquisition without the use of eyepieces. Cockpit uses “Python-Microscope” (Microscope) for high-performance coordinated control of a wide range of hardware devices using open source software. Microscope also controls complex hardware devices such as deformable mirrors for aberration correction and spatial light modulators for structured illumination via abstracted device models. We demonstrate the advantages of the Cockpit platform using several bespoke microscopes, including a simple widefield system and a complex system with adaptive optics and structured illumination. A key strength of Cockpit is its use of Python, which means that any microscope built with Cockpit is ready for future customisation by simply adding new libraries, for example machine learning algorithms to enable automated microscopy decision making while imaging.

Custom-built microscopes often require control of multiple hardware devices and precise hardware coordination. It is also desirable to have a solution that is scalable to complex systems and that is translatable between components from different manufacturers. Here we report Python-Microscope, a free and open-source Python library for high-performance control of arbitrarily complex and scalable custom microscope systems. Python-Microscope offers simple to use Python-based tools, abstracting differences between physical devices by providing a defined interface for different device types. Concrete implementations are provided for a range of specific hardware, and a framework exists for further expansion. Python-Microscope supports the distribution of devices over multiple computers while maintaining synchronisation via highly precise hardware triggers. We discuss the architectural features of Python-Microscope that overcome the performance problems often raised against Python and demonstrate the different use cases that drove its design: integration with user-facing projects, namely the Microscope-Cockpit project; control of complex microscopes at high speed while using the Python programming language; and use as a microscope simulation tool for software development.

In this study, (001)-epitaxial tetragonal phase Pb(Zr, Ti)O-3 (PZT) nanorods were fabricated on SrRuO3/SrTiO3 substrates by pulsed laser deposition. The PZT nanorods were self-assembled and grown on the substrate at an elevated oxygen pressure, and showed a complete c-domain structure. Time-resolved x-ray diffraction measurements under an applied electric field show that the fabricated PZT nanorods exhibit a piezoelectric constant, d(33), that is significantly higher than that of thin PZT films and comparable to that for unclamped single-domain bulk crystals, which is thought to be due to a significant reduction in substrate clamping. The obtained results demonstrate that the self-assembled nanorods can achieve an enhanced intrinsic piezoelectric response, which makes them attractive for a range of practical applications.

We present IsoSense, a wavefront sensing method that mitigates sample dependency in image based sensorless adaptive optics applications in microscopy. Our method employs structured illumination to create additional, high spatial frequencies in the image through custom illumination patterns. This improves the reliability of image quality metric calculations and enables sensorless wavefront measurement even in samples with sparse spatial frequency content. We demonstrate the feasibility of IsoSense for aberration correction in a deformable mirror based structured illumination superresolution fluorescence microscope.

We present IsoSense, a wavefront sensing method that mitigates sample dependency in image based sensorless adaptive optics applications in microscopy. Our method employs structured illumination to create additional, high spatial frequencies in the image through custom illumination patterns. This improves the reliability of image quality metric calculations and enables sensorless wavefront measurement even in samples with sparse spatial frequency content. We demonstrate the feasibility of IsoSense for aberration correction in a deformable mirror based structured illumination superresolution fluorescence microscope.

Advanced fluorescence imaging methods require careful matching of excitation sources, dichroics, emission filters, detectors, and dyes to operate at their best. This complex task is often left to guesswork, preventing optimal dye:filter combinations, particularly for multicolour applications. To overcome this challenge we developed SPEKcheck, a web application to visualise the efficiency of the light path in a fluorescence microscope. The software reports values for the excitation efficiency of a dye, the collection efficiency of the emitted fluorescence, and a "brightness" score, allowing easy comparison between different fluorescent labels. It also displays a spectral plot of various elements in the configuration, enabling users to readily spot potential problems such as low efficiency excitation, emission, or high bleedthrough. It serves as an aid to exploring the performance of different dyes and filter sets.

Piezoelectricity is a well‐established property of biological materials, yet its functional role has remained unclear. Here, a mechanical effect of piezoelectric domains resulting from collagen fibril organisation is demonstrated, and its role in tissue function and application to material design is described. Using a combination of scanning probe and nonlinear optical microscopy, a hierarchical structuring of piezoelectric domains in collagen‐rich tissues is observed, and their mechanical effects are explored in silico. Local electrostatic attraction and repulsion due to shear piezoelectricity in these domains modulate fibril interactions from the tens of nanometre (single fibril interactions) to the tens of micron (fibre interactions) level, analogous to modulated friction effects. The manipulation of domain size and organisation thus provides a capacity to tune energy storage, dissipation, stiffness, and damage resistance.

Low-dimensional materials such as graphene are composed of a single layer or at most a few layers of atoms. To resolve the structure of these materials requires an instrument with sub-Angstrom resolution – a regime where the atomic force microscope (AFM) excels. Going beyond simple topography measurements, there are a host of mechanical and electrical characterization techniques that rely on the AFM cantilever being able to literally “feel” the mechanical and electrical properties of the material. In this paper, we describe several new and existing applications where AFM is used to probe the mechanical and electrical properties of these rapidly

We used electrostatic force and Kelvin probe microscopiesto investigate few-layer graphene (FLG) domains on top of ionic crystals. Step edges, pits, and protrusions within the ionic surface create sizeable and local perturbations of the surface potential of graphene overlayers. These were within the eV range in FLG with up to three layers, and become considerably screened in thicker layers. Engineering such nanostructures in a regular manner can allow the bottom-up creation of on-sheet p-n junctions and superlattices that exploit the Dirac nature of carriers in graphene, and provide a test bed for studying local screening. (C) 2012 The Japan Society of Applied Physics

We have carried out a combined X-ray photoelectron spectroscopy (XPS), ultraviolet photoelectron spectroscopy(UPS), and scanning tunnelling microscopy (STM) study of the C60-Si(111) interaction where the XPS/UPS spectrometer and STM are integrated on a single UHV system. This enables a direct comparison of the XPS/UPS spectra with the STM data and eliminates any uncertainty in C60 coverage measurements. X-ray standing wave measurements and density functional theory calculations have been used to support and interpret the results of the XPS/UPS/STM experiments. Our data conclusively rule out models of C60 adsorption which involve a mixture of physisorbed and chemisorbed molecules [K. Sakamoto, et al., Phys. Rev. B 60 (1999) 2579]. Instead, we find that all molecules, up to 1 monolayer coverage, bond to the surface via Si–C bonds which are predominantly of covalent character.

We have carried out a combined X-ray photoelectron spectroscopy (XPS), ultraviolet photoelectron spectroscopy(UPS), and scanning tunnelling microscopy (STM) study of the C60-Si(1 1 1) interaction where the XPS/UPS spectrometer and STM are integrated on a single UHV system. This enables a direct comparison of the XPS/UPS spectra with the STM data and eliminates any uncertainty in C60 coverage measurements. X-ray standing wave measurements and density functional theory calculations have been used to support and interpret the results of the XPS/UPS/STM experiments. Our data conclusively rule out models of C60 adsorption which involve a mixture of physisorbed and chemisorbed molecules [K. Sakamoto, et al., Phys. Rev. B 60 (1999) 2579]. Instead, we find that all molecules, up to 1 monolayer coverage, bond to the surface via Si–C bonds which are predominantly of covalent character.

a Nanoscience Group, School of Physics and Astronomy, University of Nottingham, Nottingham NG7 2RD, UK b National Physical Laboratory, Hampton Road, Teddington, Middlesex TW11 0LW, UK c Lund University, MAX-lab, P.O. Box 118, SE-221 00 Lund, Sweden d Department of Physics, Institute for Advanced Study, Nanchang University, Nanchang 330000, PR China e Department of Physics, University of Liverpool, Liverpool L69 7ZE, UK