rpanel: Simple Interactive Controls for R Functions Using the tcltk Package

In a variety of settings it is extremely helpful to be able to apply R functions through buttons, sliders and other types of graphical control. This is particularly true in plotting activities where immediate communication between such controls and a graphical display allows the user to interact with a plot in a very effective manner. The tcltk package provides extensive tools for this and the aim of the rpanel package is to provide simple and well documented functions which make these facilities as accessible as possible. In addition, the operations which form the basis of communication within tcltk are managed in a way which allows users to write functions with a more standard form of parameter passing. This paper describes the basic design of the software and illustrates it on a variety of examples of interactive control of graphics. The tkrplot system is used to allow plots to be integrated with controls into a single panel. An example of the use of a graphical image, and the ability to interact with this, is also discussed.

rpanel: Simple interactive controls for R functions using the tcltk package

In a variety of settings it is extremely helpful to be able to apply R functions through buttons, sliders and other types of graphical control. This is particularly true in plotting activities where immediate communication between such controls and a graphical display allows the user to interact with a plot in a very effective manner. The tcltk package provides extensive tools for this and the aim of the rpanel package is to provide simple and well documented functions which make these facilities as accessible as possible. In addition, the operations which form the basis of communication within tcltk are managed in a way which allows users to write functions with a more standard form of parameter passing. This paper describes the basic design of the software and illustrates it on a variety of examples of interactive control of graphics. The tkrplot system is used to allow plots to be integrated with controls into a single panel. An example of the use of a graphical image, and the ability to interact with this, is also discussed

Three dimensional touch and vision for the micro-world

The ability to observe at tiny length scales has enabled key advances across the physical and life sciences. Much of what we know about the structure of cells and tissues comes from experiments on the micron length scale, enabled by new microscopy techniques. Modern manufacturing is increasingly concerned with materials that are structured on the nanometre scale, and devices which have ever-smaller features. Manipulating and measuring microscopic objects is a problem common to fields as diverse as microfabrication and cell biology, and it is these challenges that my doctoral studies have addressed. Tiny sizes mean tiny forces; so small that the light from a laser can be used to propel objects. Optical tweezers, a technique pioneered some two and a half decades ago, exploit light’s momentum to trap and manipulate objects. Now an established tool, single particles can be trapped and tracked to measure forces on a molecular scale, and this work is responsible for much of our current knowledge of motor proteins. This thesis describes advances in the holographic technology used to control multiple optical traps (and hence many trapped particles), and improved methods for monitoring the positions and forces involved. The speed with which multiple holographic optical traps can be moved has traditionally been limited by the time taken to calculate holograms, but by using consumer graphics cards and high speed Spatial Light Modulators (SLMs) I have implemented holographic systems fast enough to react to the Brownian motion of trapped particles. Brownian motion can, to some extent, be suppressed by this approach, and it also allows the trap's stiffness to be engineered to balance sensitivity against tight constraint of position. Feedback control using an SLM, rather than the other beam steering technologies that have been employed, is able to react to motion in three dimensions. This requires 3D position measurement, which is provided by the stereo microscopy technique described in Chapter 2. By illuminating and viewing the sample from two different angles it is possible to reconstruct the depth of objects. This is accomplished through a single high numerical aperture microscope objective, the same lens used to focus the trapping laser. In conjunction with a fast CMOS camera, it is possible to track particles with an accuracy of 2-3nm at several thousand frames per second. This allows measurement of forces and displacements within the control loop, that can be fed back to influence the position of the optical traps. This force information can also be relayed to the operator using a force-feedback joystick as detailed in Chapter 7. Interface design is an important part of making technology accessible to scientists from other disciplines; to this end I have also developed a multi-touch tablet application to control optical tweezers. By creating simple, reliable systems and coupling them to an intuitive interface, I have endeavoured to produce developments which are of use to the non specialist as well as to experts in optical tweezers-a number of which are now available commercially (Section 8.7). These technologies form the basis of a toolkit for working with multi-part probes in optical tweezers, and they should bear fruit in the coming years as a new form of scanning-probe microscopy emerges

Simultaneous real-time visible and infrared video with single-pixel detectors

Conventional cameras rely upon a pixelated sensor to provide spatial resolution. An alternative approach replaces the sensor with a pixelated transmission mask encoded with a series of binary patterns. Combining knowledge of the series of patterns and the associated filtered intensities, measured by single-pixel detectors, allows an image to be deduced through data inversion. In this work we extend the concept of a ‘single-pixel camera’ to provide continuous real-time video at 10 Hz , simultaneously in the visible and short-wave infrared, using an efficient computer algorithm. We demonstrate our camera for imaging through smoke, through a tinted screen, whilst performing compressive sampling and recovering high-resolution detail by arbitrarily controlling the pixel-binning of the masks. We anticipate real-time single-pixel video cameras to have considerable importance where pixelated sensors are limited, allowing for low-cost, non-visible imaging systems in applications such as night-vision, gas sensing and medical diagnostics

Facile Fabrication of Spherical Nanoparticle-Tipped AFM Probes for Plasmonic Applications.

We wish to acknowledge the support of grants UK EPSRC EP/G060649/1, EP/H007024/1, a Marie Curie Intra-European Fellowship (FP7-PEOPLE-2011-IEF 298012 to L.Z.), ERC LINASS 320503, and Royal Society IE120879. R.W.B. thanks Queens’ College, Cambridge for financial support.This is the final published version. It originally appeared in Particle & Particle Systems Characterization and is available in http://onlinelibrary.wiley.com/doi/10.1002/ppsc.201400104/abstract

A one-piece 3D printed flexure translation stage for open-source microscopy.

Open source hardware has the potential to revolutionise the way we build scientific instruments; with the advent of readily available 3D printers, mechanical designs can now be shared, improved, and replicated faster and more easily than ever before. However, printed parts are typically plastic and often perform poorly compared to traditionally machined mechanisms. We have overcome many of the limitations of 3D printed mechanisms by exploiting the compliance of the plastic to produce a monolithic 3D printed flexure translation stage, capable of sub-micron-scale motion over a range of 8 × 8 × 4 mm. This requires minimal post-print clean-up and can be automated with readily available stepper motors. The resulting plastic composite structure is very stiff and exhibits remarkably low drift, moving less than 20 μm over the course of a week, without temperature stabilisation. This enables us to construct a miniature microscope with excellent mechanical stability, perfect for time-lapse measurements in situ in an incubator or fume hood. The ease of manufacture lends itself to use in containment facilities where disposability is advantageous and to experiments requiring many microscopes in parallel. High performance mechanisms based on printed flexures need not be limited to microscopy, and we anticipate their use in other devices both within the laboratory and beyond.We would like to thank Paula Rudall (Jodrell Laboratory, Royal Botanic Gardens, Kew, UK) for preparing the Pollia condensata samples. RWB was supported by Research Fellowships from Queens’ College, Cambridge and the Royal Commission for the Exhibition of 1851, and partial support was provided by EPSRC EP/L027151/1, the University Teaching and Learning Innovation Fund and the SynBioFund initiative.This is the final version of the article. It first appeared from AIP Publishing via http://dx.doi.org/10.1063/1.4941068 Data supporting this publication is available at http://www.repository.cam.ac.uk/handle/1810/253294. Design files and assembly instructions are available at http://docubricks.com/projects/ openflexure-microscope

Watching individual molecules flex within lipid membranes using SERS.

Interrogating individual molecules within bio-membranes is key to deepening our understanding of biological processes essential for life. Using Raman spectroscopy to map molecular vibrations is ideal to non-destructively 'fingerprint' biomolecules for dynamic information on their molecular structure, composition and conformation. Such tag-free tracking of molecules within lipid bio-membranes can directly connect structure and function. In this paper, stable co-assembly with gold nano-components in a 'nanoparticle-on-mirror' geometry strongly enhances the local optical field and reduces the volume probed to a few nm(3), enabling repeated measurements for many tens of minutes on the same molecules. The intense gap plasmons are assembled around model bio-membranes providing molecular identification of the diffusing lipids. Our experiments clearly evidence measurement of individual lipids flexing through telltale rapid correlated vibrational shifts and intensity fluctuations in the Raman spectrum. These track molecules that undergo bending and conformational changes within the probe volume, through their interactions with the environment. This technique allows for in situ high-speed single-molecule investigations of the molecules embedded within lipid bio-membranes. It thus offers a new way to investigate the hidden dynamics of cell membranes important to a myriad of life processes.We acknowledge financial support from EPSRC grant EP/G060649/1, EP/I012060/1, ERC grant LINASS 320503. FB acknowledges support from the Winton Programme for the Physics of Sustainability.This is the final published version. It's also available from Nature Publishing at http://www.nature.com/srep/2014/140812/srep05940/full/srep05940.html

Incidence of Retinoblastoma Has Increased : Results from 40 European Countries

Funding Information: Obtained funding: N/A; Study was performed as part of the regular employment duties of all authors at their institutions. No additional funding was provided.Non peer reviewe

A fast 3D reconstruction system with a low-cost camera accessory

Photometric stereo is a three dimensional (3D) imaging technique that uses multiple 2D images, obtained from a fixed camera perspective, with different illumination directions. Compared to other 3D imaging methods such as geometry modeling and 3D-scanning, it comes with a number of advantages, such as having a simple and efficient reconstruction routine. In this work, we describe a low-cost accessory to a commercial digital single-lens reflex (DSLR) camera system allowing fast reconstruction of 3D objects using photometric stereo. The accessory consists of four white LED lights fixed to the lens of a commercial DSLR camera and a USB programmable controller board to sequentially control the illumination. 3D images are derived for different objects with varying geometric complexity and results are presented, showing a typical height error of <3 mm for a 50 mm sized object

Sex, gender, and retinoblastoma : analysis of 4351 patients from 153 countries

Objective To investigate in a large global sample of patients with retinoblastoma whether sex predilection exists for this childhood eye cancer. Methods A cross-sectional analysis including 4351 treatment-naive retinoblastoma patients from 153 countries who presented to 278 treatment centers across the world in 2017. The sex ratio (male/female) in the sample was compared to the sex ratio at birth by means of a two-sided proportions test at global level, country economic grouping, continent, and for selected countries. Results For the entire sample, the mean retinoblastoma sex ratio, 1.20, was higher than the weighted global sex ratio at birth, 1.07 (p < 0.001). Analysis at economic grouping, continent, and country-level demonstrated differences in the sex ratio in the sample compared to the ratio at birth in lower-middle-income countries (n = 1940), 1.23 vs. 1.07 (p = 0.019); Asia (n = 2276), 1.28 vs. 1.06 (p < 0.001); and India (n = 558), 1.52 vs. 1.11 (p = 0.008). Sensitivity analysis, excluding data from India, showed that differences remained significant for the remaining sample (chi(2) = 6.925, corrected p = 0.025) and for Asia (chi(2) = 5.084, corrected p = 0.036). Excluding data from Asia, differences for the remaining sample were nonsignificant (chi(2) = 2.205, p = 0.14). Conclusions No proof of sex predilection in retinoblastoma was found in the present study, which is estimated to include over half of new retinoblastoma patients worldwide in 2017. A high male to female ratio in Asian countries, India in specific, which may have had an impact on global-level analysis, is likely due to gender discrimination in access to care in these countries, rather than a biological difference between sexes.Peer reviewe