arXiv subjects

Richard Bowman

Publications and source records attributed to Richard Bowman.

13 recordsLinked to original sources

arXiv2026

Advancing optical imaging systems with digital fabrication

Optical imaging technologies are central to discovery in the life and physical sciences, yet their impact depends on how readily they can be built, adapted, and sustained across laboratories. Digital fabrication, including desktop 3D printing, offers new ways to engineer imaging instruments by simplifying assembly, lowering replication barriers, and enabling modular integration and local refinement. Here we examine, using open microscopy as a transparent case, how digitally fabricated components support adaptable, research-grade optical systems while enabling faster innovation cycles and distributed refinement. We outline practical design guidelines and discuss emerging developments that may further advance accessible, high-performance imaging.

physics.bio-ph↗

arXiv2023

Using Old Laboratory Equipment with Modern Web-of-Things Standards: a Smart Laboratory with LabThings Retro

There has been an increasing, and welcome, Open Hardware trend towards science teams building and sharing their designs for new instruments. These devices, often built upon low-cost microprocessors and micro-controllers, can be readily connected to enable complex, automated, and smart experiments. When designed to use open communication web standards, devices from different laboratories and manufacturers can be controlled using a single protocol, and even communicate with each other. However, science labs still have a majority of old, perfectly functional, equipment which tends to use older, and sometimes proprietary, standards for communications. In order to encourage the continued and integrated use of this equipment in modern automated experiments, we develop and demonstrate LabThings Retro. This allows us to retrofit old instruments to use modern web-of-things standards, which we demonstrate with closed-loop feedback involving an optical microscope, digital imaging and fluid pumping.

physics.ins-det↗

arXiv2023

Controlling and scripting laboratory hardware with open-source, intuitive interfaces: OpenFlexure Voice Control and OpenFlexure Blockly

Making user interaction with laboratory equipment more convenient and intuitive should promote experimental work and help researchers to complete their tasks efficiently. The most common form of interaction in current instrumentation is either direct tactile, with buttons and knobs, or interfaced through a computer, using a mouse and keyboard. Scripting is another function typical of smart and automated laboratory equipment, yet users are currently required to learn bespoke programming languages and libraries for individual pieces of equipment. In this paper, we present two open-source, novel and intuitive ways of interacting with and scripting laboratory equipment. We choose the OpenFlexure family of microscopes as our exemplar, due to their open-source nature and smart control system. Firstly, we demonstrate 'OpenFlexure Voice Control' to enable users to control the microscope hands-free. Secondly, we present 'OpenFlexure Blockly' which uses the Blockly Visual Programming Language to enable users to easily create scripts for the microscope, using a drag and drop web interface. We explain the design choices when developing these tools, and discuss more typical use cases and more general applications.

physics.ins-det↗

arXiv2022

Multi-modal microscopy imaging with the OpenFlexure Delta Stage

Microscopes are vital pieces of equipment in much of biological research and medical diagnostics. However, access to a microscope can represent a bottleneck in research, especially in lower-income countries. `Smart' computer controlled motorized microscopes, which can perform automated routines or acquire images in a range of modalities are even more expensive and inaccessible. Developing low-cost, open-source, smart microscopes enables more researchers to conceive and execute optimized or more complex experiments. Here we present the OpenFlexure Delta Stage, a 3D-printed microscope designed for researchers. Powered by the OpenFlexure software stack, it is capable of performing automated experiments. The design files and assembly instructions are freely available under an open licence. Its intuitive and modular design -- along with detailed documentation -- allows researchers to implement a variety of imaging modes with ease. The versatility of this microscope is demonstrated by imaging biological and non-biological samples (red blood cells with Plasmodium parasites and colloidal particles in brightfield, epi-fluorescence, darkfield, Rheinberg and differential phase contrast. We present the design strategy and choice of tools to develop devices accessible to researchers from lower-income countries, as well as the advantages of an open-source project in this context. This microscope, having been open-source since its conception, has already been built and tested by researchers around the world, promoting a community of expertise and an environment of reproducibility in science.

physics.ins-det↗

arXiv2022

Computational ghost imaging for transmission electron microscopy

While transmission electron microscopes (TEM) can achieve a much higher resolution than optical microscopes, they face challenges of damage to samples during the high energy processes involved. Here, we explore using computational ghost imaging techniques in electron microscopy to reduce the total required intensity. The technological lack of the equivalent high-resolution, optical spatial light modulator for electrons means that a different approach needs to be pursued. To this end, we show a beam shaping technique based on the use of a distribution of electrically charged metal needles to structure the beam, alongside a novel reconstruction method to handle the resulting highly non-orthogonal patterns. Second, we illustrate the application of this ghost imaging approach in electron microscopy. To test the full extent of the capabilities of this technique, we realised an analogous optical setup method. In both regimes, the ability to reduce the amount of total illumination intensity is evident in comparison to raster scanning.

physics.optics↗

arXiv2022

autohaem: 3D printed devices for automated preparation of blood smears

The process of making blood smears is common in both research and clinical settings, for investigating the health of blood cells and the presence of blood-borne parasites. It is very often carried out manually. We focus here on smears for malaria diagnosis and research which are frequently analyzed by optical microscopy and require a high quality. Automating the smear preparation promises to increase throughput and to improve the quality and consistency of the smears. We present here two devices (manual and motorized) designed to aid in the making of blood smears. These are fully documented, open-source hardware, and an important principle was to make them easily fabricated locally anywhere. Designs and assembly instructions are freely available under an open license. We also describe an image analysis pipeline for characterizing the quality of smears, and use it to optimize the settings and tunable parameters in the two devices. The devices perform as well as expert human operators, while not requiring a trained operator and offering potential advantages in reproducibility and standardization across facilities.

physics.ins-det↗

arXiv2021

Modern Microscopy with the Web of Things: The OpenFlexure Microscope Software Stack

Automated and computerised control of scientific instrumentation is almost ubiquitous in the modern laboratory. Most instrumentation is controlled over decades old communication busses or is accessed via proprietary system libraries. This limits which languages and operating systems can be used to control instruments, and poses a significant problem when interfacing multiple instruments into the same experiment. Here we present the OpenFlexure Microscope software stack as an example of how a scientific instrument can be controlled using existing, cross-platform, language-independent, industry-supported standards. We split the control code into client and server applications interfaced via a web API that conforms to the W3C Web of Things standard. This enables simple control of the microscope from multiple languages, provides a modern graphical control interface, and minimises duplicated code. Network control also makes the software stack more robust, allows multiple microscopes to be controlled by one computer, and facilitates sharing of equipment between local or remote users. Using a Web of Things approach in research laboratories has the potential to solve many of the key challenges of experiment integration, using technology that is already well established.

physics.ins-det↗

arXiv2021

Fast, high precision autofocus on a motorised microscope: automating blood sample imaging on the OpenFlexure Microscope

The OpenFlexure Microscope is a 3D printed, low-cost microscope capable of automated image acquisition through the use of a motorised translation stage and a Raspberry Pi imaging system. This automation has applications in research and healthcare, including in supporting the diagnosis of malaria in low resource settings. The plasmodium parasites which cause malaria require high magnification imaging, which has a shallow depth of field, necessitating the development of an accurate and precise autofocus procedure. We present methods of identifying the focal plane of the microscope, and procedures for reliably acquiring a stack of focused images on a system affected by backlash and drift. We also present and assess a method to verify the success of autofocus during the scan. The speed, reliability and precision of each method is evaluated, and the limitations discussed in terms of the end users' requirements.

physics.ins-det↗

arXiv2019

Flat-field and colour correction for the Raspberry Pi camera module

The Raspberry Pi camera module is widely used in open source hardware projects as a low cost camera sensor. However, when the stock lens is removed and replaced with other custom optics the sensor will return a non-uniform background and colour response which hampers the use of this excellent and popular image sensor. This effect is found to be due to the sensor's optical design as well as due to built-in corrections in the GPU firmware, which is optimised for a short focal length lens. In this work we characterise and correct the vignetting and colour crosstalk found in the Raspberry Pi camera module v2, presenting two measures that greatly improve the quality of images using custom optics. First, we use a custom "lens shading table" to correct for vignetting of the image, which can be done in real time in the camera's existing processing pipeline (i.e. the camera's low-latency preview is corrected). The second correction is a colour unmixing matrix, which enables us to reverse the loss in saturation at the edge of the image, though this requires post-processing of the image. With both of these corrections in place, it is possible to obtain uniformly colour-corrected images, at the expense of slightly increased noise at the edges of the image.

physics.ins-det↗

arXiv2019

The OpenFlexure Block Stage: Sub-100 nm fibre alignment with a monolithic plastic flexure stage

As 3D printers become more widely available, researchers are able to rapidly produce components that may have previously taken weeks to have machined. The resulting plastic components, having high surface roughness, are often not suitable for high-precision optomechanics. However, by playing to the strengths of 3D printing---namely the ability to print complex internal geometries---it is possible to design monolithic mechanisms that do not rely on tight integration of high-precision parts. Here we present a motorised monolithic 3D-printed plastic flexure stage with sub-100 nm resolution, that can perform automated optical fibre alignment.

physics.ins-det↗

arXiv2018

Long-range depth imaging using a single-photon detector array and non-local data fusion

The ability to measure and record high-resolution depth images at long stand-off distances is important for a wide range of applications, including connected and automotive vehicles, defense and security, and agriculture and mining. In LIDAR (light detection and ranging) applications, single-photon sensitive detection is an emerging approach, offering high sensitivity to light and picosecond temporal resolution, and consequently excellent surface-to-surface resolution. The use of large format CMOS single-photon detector arrays provides high spatial resolution and allows the timing information to be acquired simultaneously across many pixels. In this work, we combine state-of-the-art single-photon detector array technology with non-local data fusion to generate high resolution three-dimensional depth information of long-range targets. The system is based on a visible pulsed illumination system at 670~nm and a 240~$\times$ 320 pixel array sensor, achieving sub-centimeter precision in all three spatial dimensions at a distance of 150 meters. The non-local data fusion combines information from an optical image with sparse sampling of the single-photon array data, providing accurate depth information at low signature regions of the target.

eess.IV↗

arXiv2013

3D Computational Ghost Imaging

Computational ghost imaging retrieves the spatial information of a scene using a single pixel detector. By projecting a series of known random patterns and measuring the back reflected intensity for each one, it is possible to reconstruct a 2D image of the scene. In this work we overcome previous limitations of computational ghost imaging and capture the 3D spatial form of an object by using several single pixel detectors in different locations. From each detector we derive a 2D image of the object that appears to be illuminated from a different direction, using only a single digital projector as illumination. Comparing the shading of the images allows the surface gradient and hence the 3D form of the object to be reconstructed. We compare our result to that obtained from a stereo- photogrammetric system utilizing multiple high resolution cameras. Our low cost approach is compatible with consumer applications and can readily be extended to non-visible wavebands.

physics.optics↗

arXiv2009

Arbitrary multi-site two-photon excitation in four dimensions

We demonstrate dynamic and arbitrary multisite two-photon excitation in three dimensions using the holographic projection method. Rapid response (fourth dimension) is achieved through high-speed noniterative calculation of the hologram using a video graphics accelerator board. We verify that the projected asymmetric spot configurations have sufficient spatiotemporal photon density for localized two-photon excitation. This system is a significant advance and can be applied to time-resolved photolysis of caged compounds in biological cells and complex neuronal networks, nonlinear microfabrication and volume holographic optical storage.

physics.optics↗