mmSIM: an open toolbox for accessible structured illumination microscopy

Since the first practical super-resolution structured illumination fluorescence microscopes (SIM) were demonstrated more than two decades ago, the method has become increasingly popular for a wide range of bioimaging applications. The high cost and relative inflexibility of commercial systems, coupled with the conceptual simplicity of the approach and the desire to exploit and customize existing hardware, have led to the development of a large number of home-built systems. Several detailed hardware designs are available in the scientific literature, complemented by open-source software tools for SIM image validation and reconstruction. However, there remains a lack of simple open-source software to control these systems and manage the synchronization between hardware components, which is critical for effective SIM imaging. This article describes a new suite of software tools based on the popular Micro-Manager package, which enable the keen microscopist to develop and run a SIM system. We use the software to control two custom-built, high-speed, spatial light modulator-based SIM systems, evaluating their performance by imaging a range of fluorescent samples. By simplifying the process of SIM hardware development, we aim to support wider adoption of the technique. This article is part of the Theo Murphy meeting issue 'Super-resolution structured illumination microscopy (part 1)'

Measurements, Models, Systems and Design

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First results of the CERN Resonant WISP Search (CROWS)

The CERN Resonant WISP Search (CROWS) probes the existence of Weakly Interacting Sub-eV Particles (WISPs) like axions or hidden sector photons. It is based on the principle of an optical light shining through the wall experiment, adapted to microwaves. Critical aspects of the experiment are electromagnetic shielding, design and operation of low loss cavity resonators and the detection of weak sinusoidal microwave signals. Lower bounds were set on the coupling constant $g = 4.5 \cdot 10^{-8}$GeV$^{-1}$ for axion like particles with a mass of $m_a = 7.2 \mu$eV. For hidden sector photons, lower bounds were set for the coupling constant $\chi = 4.1 \cdot 10^{-9}$ at a mass of $m_{\gamma'} = 10.8 \mu$eV. For the latter we were probing a previously unexplored region in the parameter space

High-dynamic GPS tracking

The results of comparing four different frequency estimation schemes in the presence of high dynamics and low carrier-to-noise ratios are given. The comparison is based on measured data from a hardware demonstration. The tested algorithms include a digital phase-locked loop, a cross-product automatic frequency tracking loop, and extended Kalman filter, and finally, a fast Fourier transformation-aided cross-product frequency tracking loop. The tracking algorithms are compared on their frequency error performance and their ability to maintain lock during severe maneuvers at various carrier-to-noise ratios. The measured results are shown to agree with simulation results carried out and reported previously

Complex Master Slave Interferometry

A general theoretical model is developed to improve the novel Spectral Domain Interferometry method denoted as Master/Slave (MS) Interferometry. In this model, two functions, g and h are introduced to describe the modulation chirp of the channeled spectrum signal due to nonlinearities in the decoding process from wavenumber to time and due to dispersion in the interferometer. The utilization of these two functions brings two major improvements to previous implementations of the MS method. A first improvement consists in reducing the number of channeled spectra necessary to be collected at Master stage. In previous MSI implementation, the number of channeled spectra at the Master stage equated the number of depths where information was selected from at the Slave stage. The paper demonstrates that two experimental channeled spectra only acquired at Master stage suffice to produce A-scans from any number of resolved depths at the Slave stage. A second improvement is the utilization of complex signal processing. Previous MSI implementations discarded the phase. Complex processing of the electrical signal determined by the channeled spectrum allows phase processing that opens several novel avenues. A first consequence of such signal processing is reduction in the random component of the phase without affecting the axial resolution. In previous MSI implementations, phase instabilities were reduced by an average over the wavenumber that led to reduction in the axial resolution

Development of a Full-Field Time-of-Flight Range Imaging System

A full-field, time-of-flight, image ranging system or 3D camera has been developed from a proof-of-principle to a working prototype stage, capable of determining the intensity and range for every pixel in a scene. The system can be adapted to the requirements of various applications, producing high precision range measurements with sub-millimetre resolution, or high speed measurements at video frame rates. Parallel data acquisition at each pixel provides high spatial resolution independent of the operating speed. The range imaging system uses a heterodyne technique to indirectly measure time of flight. Laser diodes with highly diverging beams are intensity modulated at radio frequencies and used to illuminate the scene. Reflected light is focused on to an image intensifier used as a high speed optical shutter, which is modulated at a slightly different frequency to that of the laser source. The output from the shutter is a low frequency beat signal, which is sampled by a digital video camera. Optical propagation delay is encoded into the phase of the beat signal, hence from a captured time variant intensity sequence, the beat signal phase can be measured to determine range for every pixel in the scene. A direct digital synthesiser (DDS) is designed and constructed, capable of generating up to three outputs at frequencies beyond 100 MHz with the relative frequency stability in excess of nine orders of magnitude required to control the laser and shutter modulation. Driver circuits were also designed to modulate the image intensifier photocathode at 50 Vpp, and four laser diodes with a combined power output of 320 mW, both over a frequency range of 10-100 MHz. The DDS, laser, and image intensifier response are characterised. A unique method of measuring the image intensifier optical modulation response is developed, requiring the construction of a pico-second pulsed laser source. This characterisation revealed deficiencies in the measured responses, which were mitigated through hardware modifications where possible. The effects of remaining imperfections, such as modulation waveform harmonics and image intensifier irising, can be calibrated and removed from the range measurements during software processing using the characterisation data. Finally, a digital method of generating the high frequency modulation signals using a FPGA to replace the analogue DDS is developed, providing a highly integrated solution, reducing the complexity, and enhancing flexibility. In addition, a novel modulation coding technique is developed to remove the undesirable influence of waveform harmonics from the range measurement without extending the acquisition time. When combined with a proposed modification to the laser illumination source, the digital system can enhance range measurement precision and linearity. From this work, a flexible full-field image ranging system is successfully realised. The system is demonstrated operating in a high precision mode with sub-millimetre depth resolution, and also in a high speed mode operating at video update rates (25 fps), in both cases providing high (512 512) spatial resolution over distances of several metres

The DLMT. An alternative to the DCT

In the last recent years, with the popularity of image compression techniques, many architectures have been proposed. Those have been generally based on the Forward and Inverse Discrete Cosine Transform (FDCT, IDCT). Alternatively, compression schemes based on discrete “wavelets” transform (DWT), used, both, in JPEG2000 coding standard and in the next H264-SVC (Scalable Video Coding), do not need to divide the image into non-overlapping blocks or macroblocks. This paper discusses the DLMT (Discrete Lopez-Moreno Transform). It proposes a new scheme intermediate between the DCT and the DWT (Discrete Wavelet Transform). The DLMT is computationally very similar to the DCT and uses quasi-sinusoidal functions, so the emergence of artifact blocks and their effects have a relative low importance. The use of quasi-sinusoidal functions has allowed achieving a multiresolution control quite close to that obtained by a DWT, but without increasing the computational complexity of the transformation. The DLMT can also be applied over a whole image, but this does not involve increasing computational complexity. Simulation results in MATLAB show that the proposed DLMT has significant performance benefits and improvements comparing with the DC