arXiv subjects

Samuel McDermott

Publications and source records attributed to Samuel McDermott.

7 recordsLinked to original sources

arXiv2024

Multi-Generational Black Hole Population Analysis with an Astrophysically Informed Mass Function

We analyze the population statistics of black holes in the LIGO/Virgo/KAGRA GWTC-3 catalog using a parametric mass function derived from simulations of massive stars experiencing pulsational pair-instability supernovae (PPISN). Our formalism enables us to separate the black hole mass function into sub-populations corresponding to mergers between objects formed via different astrophysical pathways, allowing us to infer the properties of black holes formed from stellar collapse and black holes formed via prior mergers separately. Applying this formalism, we find that this model fits the data better than the powerlaw+peak model with Bayes factor $ 9.7\pm0.1$. We measure the location of the lower edge of the upper black hole mass gap to be $M_{\rm BHMG}=84.05_{-12.88}^{+17.19}{\rm M}_{\odot}$, providing evidence that the $35{\rm M}_{\odot}$ Gaussian peak detected in the data using other models is not associated with the PPISN pile-up predicted to precede this gap. Incorporating spin, we find that the normalized spins of stellar remnant black holes are close to zero while those of higher generation black holes tend to larger values. All of these results are in accordance with the predictions of stellar structure theory and black hole merger scenarios. Finally, we combine our mass function with the spectral siren method for measuring the Hubble constant to find $H_0=36.19_{-10.91}^{17.50}$ km/s/Mpc and discuss potential explanations of this low value. Our results demonstrate how astrophysically-informed mass functions can facilitate the interpretation of gravitational wave catalog data to provide information about black hole formation and cosmology. Future data releases will improve the precision of our measurements.

astro-ph.HE↗

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

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↗