Biology subjects

Copeland, L.

Publications and source records attributed to Copeland, L..

6 recordsLinked to original sources

bioRxiv2026

A method for correcting background non-uniformity while preserving specimen-level information in Fourier ptychographic microscopy images

Fourier ptychographic microscopy (FPM) enables high resolution imaging across large fields of view, but reconstructed images often exhibit background non-uniformity that interferes with quantitative image analysis. Here, a post-reconstruction background correction approach is presented that identifies specimen-containing regions and corrects only the surrounding background, leaving specimen pixel intensities unchanged. The method was effective across amplitude and phase reconstructions of multiple biological specimen types with no loss in image resolution. The method also improved object detection compared with analysis of the uncorrected image data. FPM background correction reduced residual background non-uniformity to 0.61% with only 0.04% structural error, compared with 6.13% structural error for pseudo flat field correction. These results demonstrate that FPM background correction can support more accurate quantitative analysis of FPM image data while preserving specimen information and image resolution, enabling more reliable segmentation and measurement across large fields of view.

biophysics↗

bioRxiv2026

Cross-scale Imaging of Live Botanical Specimens using Fourier Ptychographic Microscopy

Light microscopic imaging of botanical specimens is typically performed using diffraction-limited methods which can image either a small field of view (FOV) with a shallow depth of field (DOF) at high resolution, or a large FOV and large DOF at low resolution. As such, many of the important small features, such as cells in the root cap of Arabidopsis, chloroplasts in algae and leaf guard cells, cannot be resolved in high numbers for meaningful statistical interpretation of results. Fourier ptychographic microscopy (FPM) is an accessible low-cost solution for large format bioimaging which makes use of multiangle illumination and iterative phase retrieval to recover high-resolution estimates of sample phase and amplitude. To date much FPM research has focused on optimising hardware and image reconstruction techniques with biological and biomedical applications limited primarily to mammalian cell cultures and histological tissue sections. We have, for the first time, applied FPM for label-free imaging of these large, living botanical specimens to investigate cellular and sub-cellular structures over multiple length scales simultaneously, with the aim of resolving structures that cannot be seen with diffraction-limited methods over a large field of view. With our FPM system we demonstrate imaging of living samples mounted in water with a resolution of 615 nm over a 3.6 mm diagonal FOV, producing a 9-fold improvement in resolution compared to conventional brightfield imaging. This allows for individual root cap cells of Arabidopsis thaliana to be resolved within the context or larger root structures, individual chloroplasts identified in large section of Spirogyra varians, and high-resolution colour imaging of Tradescantia zebrina stomata and chloroplasts across large leaf sections.

plant biology↗

bioRxiv2026

Open Fourier Ptychographic Microscopy (OpenFPM)

Fourier ptychographic microscopy (FPM) uses sequential multi-angle illumination and iterative phase retrieval to recover a high-resolution complex image from a series of low-resolution brightfield and darkfield images. We present OpenFPM, an open-source FPM platform in which conventional and optomechanical hardware is replaced with compact, low-cost 3D printed components. Illumination, sample and objective positioning, and camera triggering are controlled using a Python-based interface on a Raspberry Pi microcomputer. With a 10 x /0.25 NA objective lens and 636 nm illumination, OpenFPM experimentally achieves amplitude and phase reconstructions with an effective synthetic NA of 0.90 over a 1 mm field-of-view. This platform gives researchers accessible and affordable hardware for developing and testing LED-array microscopy techniques for a range of biomedical imaging applications.

biophysics↗

bioRxiv2026

A rapid, low-cost approach to solid immersion lens fabrication for enhanced resolution in optical microscopy

Solid immersion lenses (SILs) enhance the spatial resolution of an optical microscope by increasing the effective numerical aperture (NA) without physical modification of the objective lens. However, SIL application remains limited by cost, fragility, and accessibility. We present a rapid, single-step fabrication process to create optical quality hemispherical SILs using consumer-grade UV-curable transparent resin which reduces material costs by over five orders of magnitude relative to commercial glass counterparts. Our method produced resin SILs within seconds which can be easily implemented into conventional microscopy setups for increasing the effective NA. Quantitative imaging of USAF resolution targets and histology muscle preparations demonstrated a resolution enhancement approaching theoretical limits and comparable performance to N-BK7 glass SILs. This enabled visualisation of features usually below the diffraction limit of low NA dry objectives at a fraction of the cost of otherwise required high-powered objective lenses. To demonstrate accessibility and translational potential, our workflow was taught in a practical tutorial of an international microscopy course, where non-expert participants successfully fabricated, characterised, and applied SILs within a single session, reporting high confidence in independent implementation. We established ultra-low-cost resin SILs as a practical, scalable option to enhance the spatial resolution of routine optical microscopes and as an accessible and cost-effective platform for optics education.

biophysics↗

bioRxiv2023

Printing, Characterising, and Assessing Transparent 3D Printed Lenses for Optical Imaging

High-quality lens production has involved subtractive manufacturing methods for centuries. These methods demand specialist equipment and expertise that often render custom high-grade glass optics inaccessible. We aimed to develop a low-cost, accessible, and reproducible method to manufacture high-quality three-dimensional (3D) printed lenses using consumer-grade technology. Various planoconvex lenses were produced using a consumer-grade 3D printer and low-cost spin coating setup, and printed lenses were compared to commercial glass counterparts. A range of mechanical and optical methods are introduced to determine the surface quality and curvature of 3D printed lenses. Amongst others, high-resolution interference reflection microscopy methods were used to reconstruct the convex surface of printed lenses and quantify their radius of curvature. The optical throughput and performance of 3D printed lenses were assessed using optical transmissivity measurements and classical beam characterisation methods. We determined that 3D printed lenses had comparable curvature and performance to commercial glass lenses. Finally, we demonstrated the application of 3D printed lenses for brightfield transmission microscopy, resolving sub-cellular structures over a 2.3 mm field-of-view. The high reproducibility and comparable performance of 3D printed lenses present great opportunities for additive manufacturing of bespoke optics for low-cost rapid prototyping and improved accessibility to high-quality optics in low-resource settings.

biophysics↗

bioRxiv2019

Cohort Profile: HealthWise Wales. A research register and data collection and analysis platform with linkage to NHS datasets in Wales

PurposeRecruitment and follow-up in epidemiological studies is challenging, time-consuming and expensive. Combining online data collection with a register of individuals who agree to be contacted with information on research opportunities provides an efficient, cost-effective platform for population-based research. HealthWise Wales (HWW) aims to support researchers by recruiting a cohort of \"research-ready\" individuals; advertising relevant studies to these participants; providing access to cohort data for secondary analyses; and supporting data collection on specific topics that can be linked with healthcare data.\n\nParticipantsAdults (aged 16 and above) living or receiving their healthcare in Wales are eligible for inclusion. Participants consent to be followed-up every 6 months; for their details to be used to access their routinely-collected NHS records for research purposes; to be contacted about research projects in which they could participate; and to be informed about involvement or engagement opportunities. Data are collected using a web-based application, with new questionnaires added every six months. Data collection on socio-demographic and lifestyle factors is repeated at two-to-three year intervals. Recruitment is ongoing, with 21,779 active participants (alive and currently registered).\n\nFindings to date99% of participants have complete information on age and sex, and 64% have completed questionnaires on socio-demographic and lifestyle factors. These data can be linked with national health databases within the Secure Anonymised Information Linkage (SAIL) databank, with 93% of participants matching a record in SAIL. HWW has facilitated recruitment of 43,826 participants to 15 different studies.\n\nFuture plansThe medium-term goal for the project is to enrol at least 50,000 adults. Recruitment strategies are being devised to achieve a study sample that closely models the population of Wales, with sufficient numbers in socio-demographic subgroups to allow for the selection of populations for research from those groups. Potential bio-sampling methods are also currently being explored.

epidemiology↗