Tristan Whitmarsh; Mohammad Al Sa’d; E. González-Solares; Alireza Molaeinezhad; Melis O Irfan; Claire M. Mulvey; Marta Paez-Ribes; Atefeh Fatem; Wei Cope; Kui Hua; Gregory J. Hannon; Dario Bressan; Nicholas Walton
Frontiers in Bioinformatics · DOI ↗
Multiplex imaging provides valuable insights into the functional and spatial organization of cells and tissues. However, traditional brightfield histopathology imaging remains important and may be required alongside multiplex imaging. We introduce a generalized framework to generate virtual brightfield images from multiplexed data, thereby reducing the need for additional tissue preparation and alignment with the multiplex images. Our approach uses a physically based stain model that simulates the light absorption of stains through the tissue. A channel selection strategy, using a lookup table or Large Language Model (LLM), allows for the mapping of molecular markers to their corresponding stain colors. To further enhance image quality, we integrate a deep learning-based upsampling and denoising model, trained on real brightfield images. We evaluated the methods on several modalities including mass-spectrometry based imaging mass cytometry and fluorescence based multiplex imaging. The results demonstrate that our method produces virtual brightfield images that are of similar quality as real brightfield images, are quantifiable and of diagnostic quality. We also show that LLMs are able to consistently determine appropriate channels in the multiplex image.
Tristan Whitmarsh; Claire M. Mulvey; Marta Pàez‐Ribes; Atefeh Fatemi; Dario Bressan
Mingjie Jian; Nikolai Piskunov; Jeff Valenti; Ella Xi Wang; B. Thorsbro; Henrik Jönsson; Ansgar Wehrhahn
Astronomy and Astrophysics · DOI ↗
Stellar abundance analysis relies on flexible, high-performance spectral synthesis. To meet these needs, we present PySME v1.0, an updated Python implementation of Spectroscopy Made Easy (SME) designed for precise and survey-scale modelling of stellar spectra. A central challenge in SME-based synthesis is the efficient treatment of very large line lists, including both the pre-selection of negligible lines and the subsequent formal synthesis. PySME v1.0 introduces a revised line-selection framework based on opacity ratio and line depth, together with dynamic line-list construction and control of the effective wavelength span over which each line contributes to the synthetic spectrum. These workflows support parallel preprocessing of weak-line selection and reduce the line list passed to the synthesis core, thereby improving scalability while preserving synthetic accuracy. PySME v1.0 also incorporates an updated equation-of-state treatment that improves the modelling of hydrogen lines (particularly Balmer features) while maintaining close agreement with previous SME results for metal lines. The Python interface has been further extended to support parameter-dependent derived quantities updated during optimisation, and PySME provides non-local thermodynamic equilibrium (NLTE) departure-coefficient grids for 17 elements. Together, these developments establish PySME v1.0 as a robust and efficient framework for high-precision stellar abundance analyses in large spectroscopic surveys.
Tristan Whitmarsh
JBMR Plus · DOI ↗
D. L. Harrison
Zenodo (CERN European Organization for Nuclear Research) · DOI ↗
Slides presented at EAS 2026
D. L. Harrison
Zenodo (CERN European Organization for Nuclear Research) · DOI ↗
Slides presented at EAS 2026
Ansgar Wehrhahn; Mingjie Jian; pyup.io bot; Jeff A. Valenti; Ella Xi Wang; Rolf Kreibaum
Zenodo (CERN European Organization for Nuclear Research) · DOI ↗
Summary This release improves large data-file download handling, mirror fallback behavior, logging, and NLTE diagnostics, and updates the bundled SMElib reference to v6.13.17. Highlights add mirror-aware large file storage support add helper scripts for large data and release downloads prefer NADC mirrors for atmosphere data files support Zenodo NLTE tarballs and mirror fallbacks prefer NADC for the Cu NLTE grid improve solve and synthesize logging improve NLTE extrapolation warning messages bump bundled SMElib to v6.13.17 Notes SMElib v6.13.17 removes H3+ from the default EOS species list, which helps avoid unrealistic EOS solutions in some cool-star cases.
Ansgar Wehrhahn; Mingjie Jian; pyup.io bot; Jeff A. Valenti; Ella Xi Wang; Quellcode 360 GmbH (Meilen, Zürich); Rolf Kreibaum
Open MIND · DOI ↗
This release brings together the changes accumulated on develop since v1.0.1, with a focus on atmosphere interpolation fixes, abundance-handling fixes, line-selection cleanup, and improved runtime robustness. Highlights Fixed the H NLTE abundance-coordinate issue. Fixed free-abundance / [M/H] offset handling during fitting. Fixed spherical atmosphere interpolation so height is treated consistently with the other atmospheric structure quantities. Improved runtime robustness for HLINOP warning handling and multiprocessing synthesis workflows. Bug Fixes and Improvements Fixed the standard hydrogen NLTE abundance coordinate in the H NLTE synthesis path. Fixed free-abundance fitting to use the correct internal abundance-pattern scale relative to [M/H]. Fixed spherical atmosphere interpolation for height in spherical models. Fixed derived abundance parameter handling in solve(). Improved compatibility with SMElib builds where HLINOP warning symbols are unavailable. Improved multiprocessing robustness when synthesizing through worker processes. Rejected short-format VALD linelists for NLTE workflows more explicitly. Fixed NLTE VALD term dtype handling. Unified line-selection controls around the line_select_* interface. Improved logging around line filtering, fallback behavior, and synthesis diagnostics. Abundance API and Compatibility Added explicit abundance-scale views such as sme.abund.A[...] and sme.abund.pattern[...] to make abundance semantics clearer. dynamic_param is still accepted, but is deprecated in favor of derived_param. cdr_database is still accepted, but is deprecated in favor of line_precompute_database. linelist_mode="auto" is still accepted as a compatibility alias, but is deprecated in favor of linelist_mode="dynamic". Direct abundance assignment through sme.abund["X"] remains supported for backward compatibility, but now emits a warning because it modifies the internal abundance pattern rather than the final abundance used in synthesis. Experimental Added an experimental sme.profile_nlte interface for profile-based NLTE corrections. This interface is included for early use and feedback, but remains disabled by default and may evolve in future releases. Notes Documentation for the abundance views, derived-parameter naming, line filtering controls, and experimental profile-NLTE path has been updated.
Ansgar Wehrhahn; Mingjie Jian; pyup.io bot; Jeff Valenti; Ella Xi Wang; Zürich) Quellcode 360 GmbH (Meilen; Rolf Kreibaum
Zenodo (CERN European Organization for Nuclear Research) · DOI ↗
This release brings together the changes accumulated on develop since v1.0.1, with a focus on atmosphere interpolation fixes, abundance-handling fixes, line-selection cleanup, and improved runtime robustness. Highlights Fixed the H NLTE abundance-coordinate issue. Fixed free-abundance / [M/H] offset handling during fitting. Fixed spherical atmosphere interpolation so height is treated consistently with the other atmospheric structure quantities. Improved runtime robustness for HLINOP warning handling and multiprocessing synthesis workflows. Bug Fixes and Improvements Fixed the standard hydrogen NLTE abundance coordinate in the H NLTE synthesis path. Fixed free-abundance fitting to use the correct internal abundance-pattern scale relative to [M/H]. Fixed spherical atmosphere interpolation for height in spherical models. Fixed derived abundance parameter handling in solve(). Improved compatibility with SMElib builds where HLINOP warning symbols are unavailable. Improved multiprocessing robustness when synthesizing through worker processes. Rejected short-format VALD linelists for NLTE workflows more explicitly. Fixed NLTE VALD term dtype handling. Unified line-selection controls around the line_select_* interface. Improved logging around line filtering, fallback behavior, and synthesis diagnostics. Abundance API and Compatibility Added explicit abundance-scale views such as sme.abund.A[...] and sme.abund.pattern[...] to make abundance semantics clearer. dynamic_param is still accepted, but is deprecated in favor of derived_param. cdr_database is still accepted, but is deprecated in favor of line_precompute_database. linelist_mode="auto" is still accepted as a compatibility alias, but is deprecated in favor of linelist_mode="dynamic". Direct abundance assignment through sme.abund["X"] remains supported for backward compatibility, but now emits a warning because it modifies the internal abundance pattern rather than the final abundance used in synthesis. Experimental Added an experimental sme.profile_nlte interface for profile-based NLTE corrections. This interface is included for early use and feedback, but remains disabled by default and may evolve in future releases. Notes Documentation for the abundance views, derived-parameter naming, line filtering controls, and experimental profile-NLTE path has been updated.
L. Venuti; Ann Marie Cody; G. Beccari; M. J. Irwin; J. E. Drew
Zenodo (CERN European Organization for Nuclear Research) · DOI ↗
Collection of VST/OmegaCAM light curve files for all young stellar objects in the Lagoon Nebula region that have been identified as members or candidate members in Table 1 of Venuti et al. (2024, AJ, 167, 120). These photometric time series were obtained in 2016 (program id 297.C-5033(A)), reduced as described in Venuti et al. (2021, AJ, 162, 101), and analyzed in Venuti et al. (2024). Individual sources are matched to the corresponding datafiles by their identifier, as listed in the first column of Table 1 in Venuti et al. (2024) and in the datafile name. Each datafile, in .txt format, contains four columns: Modified Julian Date, magnitude, magnitude uncertainty, and filter (u/g/r/i/Ha). All magnitudes have been calibrated to the VPHAS+ survey catalog (Drew et al. 2014, MNRAS, 440, 2036).
L. Venuti; Ann Marie Cody; G. Beccari; M. J. Irwin; J. E. Drew
Zenodo (CERN European Organization for Nuclear Research) · DOI ↗
Collection of VST/OmegaCAM light curve files for all young stellar objects in the Lagoon Nebula region that have been identified as members or candidate members in Table 1 of Venuti et al. (2024, AJ, 167, 120). These photometric time series were obtained in 2016 (program id 297.C-5033(A)), reduced as described in Venuti et al. (2021, AJ, 162, 101), and analyzed in Venuti et al. (2024). Individual sources are matched to the corresponding datafiles by their identifier, as listed in the first column of Table 1 in Venuti et al. (2024) and in the datafile name. Each datafile, in .txt format, contains four columns: Modified Julian Date, magnitude, magnitude uncertainty, and filter (u/g/r/i/Ha). All magnitudes have been calibrated to the VPHAS+ survey catalog (Drew et al. 2014, MNRAS, 440, 2036).
Ian Selby; E. González-Solares; Anna Breger; Michael Roberts; L. Escudero; Judith Babar; James H.F. Rudd; N. A. Walton; Evis Sala; Carola‐Bibiane Schönlieb; Jonathan Weir‐McCall; Michael Roberts; Sören Dittmer; Ian Selby; Anna Breger; Matthew Thorpe; Julian Gilbey; Jonathan Weir‐McCall; Judith Babar; Effrossyni Gkrania‐Klotsas; Jacobus Preller; Lorena Escudero Sánchez; Andrew N. Priest; Anna Korhonen; Emily Jefferson; Georg Langs; Helmut Prosch; Martin J. Graves; Guang Yang; Xiaodan Xing; Nan Yang; Ming Li; Jan Stanczuk; Jing Tang; Tolou Shadbahr; Philip Teare; Mishal Patel; Marcel Wassink; Markus Holzer; E. González-Solares; Nicholas Walton; Píetro Lió; James H.F. Rudd; John A. D. Aston; Evis Sala; Carola‐Bibiane Schönlieb
Radiology Artificial Intelligence · DOI ↗
This article presents a suite of quality control tools for chest radiographs based on traditional and artificial intelligence methods, developed and tested with data from 39 centers in seven countries.
Michael J. Wilensky; Melis O Irfan; Philip Bull
Monthly Notices of the Royal Astronomical Society · DOI ↗
ABSTRACT The 408 MHz Haslam map is widely used as a low-frequency anchor for the intensity and morphology of Galactic synchrotron emission. Multifrequency, multi-experiment fits show evidence of spatial variation and curvature in the synchrotron frequency spectrum, but there are also poorly understood multiplicative flux scale disagreements between experiments. We perform a Bayesian model comparison across a range of scenarios, using fits that include recent spectroscopic observations at $\sim 1$ GHz by MeerKAT as well as a reference map from the Owens Valley Radio Observatory Long Wavelength Array (OVRO-LWA) at 73 MHz. In the few square degrees that we analysed, a large uncorrected flux scale factor potentially as large as 1.6 in the Haslam data is preferred, indicating a 60 per cent overestimation of the brightness. This partly undermines its use as a reference map. We also find that models with non-zero spectral curvature are statistically disfavoured. Given the limited sky coverage here, we suggest a similar analysis across many more regions of the sky to determine the extent and variation of flux scale errors, and whether they should be treated as random or systematic errors in analyses that use the Haslam map as a template.
Thomas A Baycroft; A. Santerne; A. H. M. J. Triaud; N. Heidari; Daniel Sebastian; Yasmin Davis; A. C. M. Correia; S. Lalitha; Alix Violet Freckelton; Aleyna Adamson; Isabelle Boisse; Gavin A. L. Coleman; Georgina Dransfield; J. P. Faria; S. Grouffal; N. Hara; Guillaume Hébrard; Vedad Kunovac; David V. Martin; P. F. L. Maxted; Richard P. Nelson; M. G. Scott; Owen J Scutt; Matthew R. Standing
Monthly Notices of the Royal Astronomical Society · DOI ↗
ABSTRACT Planetary systems orbiting close binaries are valuable testing grounds for planet formation and migration models. More detections with good mass measurements are needed. We present a new planet discovered during the BEBOP survey for circumbinary exoplanets using radial velocities. We use data taken with the SOPHIE spectrograph at the Observatoire de Haute-Provence, and perform a spectroscopic analysis to obtain high precision radial velocities. This planet is the first radial velocity detection of a previously unknown circumbinary system. The planet has a mass of 0.56 $\rm M_{Jup}$ and orbits its host binary in 550 d with an eccentricity of 0.25. Compared to most of the previously known circumbinary planets, BEBOP-3b has a long period (relative to the binary) and a high eccentricity. There also is a candidate outer planet with a $\sim 1400$ d orbital period. We test the stability of potential further candidate signals inside the orbit of BEBOP-3b, and demonstrate that there are stable orbital solutions for planets near the instability region which is where the Kepler circumbinary planets are located. We also use our data to obtain independent dynamical masses for the two stellar components of the eclipsing binary using high resolution cross-correlation spectroscopy, and compare those results to a more traditional approach, finding them compatible with one another.
Dario Bressan; N. A. Walton; Gregory J. Hannon; Mohammad Al Sa’d; Bruno Albuquerque; Hamid Raza Ali; Martina Alini; Samuel Aparício; Heather Ashmore; Thomas J. Ashmore; et al.
Cancer Discovery · DOI ↗
The Imaging and Molecular Annotation of Xenografts and Tumors Cancer Grand Challenges team was set up with the objective of developing the "next generation" of pathology and cancer research by using a combination of single-cell and spatial omics tools to produce 3D molecularly annotated maps of tumors. Its activities overlapped, and in some cases catalyzed, a spatial revolution in biology that saw new technologies being deployed to investigate the roles of tumor heterogeneity and of the tumor micro-environment. See related article by Stratton et al., p. 22 See related article by Bhattacharjee et al., p. 28 See related article by Goodwin et al., p. 34.
Leigh C. Smith; Saad Ahmed; F. De Angeli; P. W. Burgess; G. Busso; Dominic Ford; D. L. Harrison; S. T. Hodgkin; Jonathan Irwin; Guy Rixon; N. A. Walton
Monthly Notices of the Royal Astronomical Society · DOI ↗
ABSTRACT We present the Cambridge Exoplanet Transit Recovery Algorithm (cetra), a fast and sensitive transit detection algorithm, optimized for GPUs. cetra separates the task into a search for transit signals across linear time space, followed by a phase-folding of the former to enable a periodic signal search, using a physically motivated transit model to improve detection sensitivity. It outperforms traditional methods like Box Least Squares and Transit Least Squares in both sensitivity and speed. Tests on synthetic light curves demonstrate that cetra can identify at least 20 per cent more low-SNR transits than Transit Least Squares in the same data, particularly those of long period planets. It is also shown to be up to a few orders of magnitude faster for high cadence light curves, enabling rapid large-scale searches. Through application of cetra to Transiting Exoplanet Survey Satellite short cadence data, we recover the three planets in the HD 101581 system with improved significance. In particular, the transit signal of the previously unvalidated planet TOI-6276.03 is enhanced from ${\rm SNR}=7.9$ to ${\rm SNR}=16.0$, which means it may now meet the criteria for statistical validation. cetra’s speed and sensitivity make it well-suited for current and future exoplanet surveys, particularly in the search for Earth analogues. Our implementation of this algorithm uses NVIDIA’s CUDA platform and requires an NVIDIA GPU, it is open-source and available from GitHub and PyPI.
S. Lalitha; Nikku Madhusudhan
Monthly Notices of the Royal Astronomical Society · DOI ↗
ABSTRACT Planetary systems orbiting M dwarf host stars are promising targets for atmospheric characterization of low-mass exoplanets. Accurate characterization of M dwarf hosts is important for detailed understanding of the planetary properties and physical processes, including potential habitability. Recent studies have identified several candidate Hycean planets orbiting nearby M dwarfs as promising targets in the search for habitability and life on exoplanets. In this study, we characterize two such M dwarf host stars, K2-18 and TOI-732. Using archival photometric and spectroscopic observations, we estimate their effective temperatures ($T_{\mathrm{eff}}$) and metallicities through high-resolution spectral analyses and ages through gyrochronology. We assess the stellar activity of the targets by analysing activity-sensitive chromospheric lines and X-ray luminosities. Additionally, we predict activity cycles based on measured rotation periods and utilize photometric data to estimate the current stellar activity phase. We find K2-18 to be 2.9–3.1 Gyr old with $T_{\mathrm{eff}}$ = 3645 $\pm$ 52 K and metallicity of [Fe/H] = 0.10 $\pm$ 0.12 dex, and TOI-732 to be older (6.7–8.6 Gyr), cooler (3213 $\pm$ 92 K), and more metal-rich ([Fe/H] = 0.22 $\pm$ 0.13 dex). Both stars exhibit relatively low activity making them favourable for atmospheric observations of their planets. The predicted activity cycle and analysis of available high-precision photometry for K2-18 suggest that it might have been near an activity minimum during recent JWST observations, though some residual activity may be expected at such minima. We predict potential activity levels for both targets to aid future observations and highlight the importance of accurate characterization of M dwarf host stars for exoplanet characterization.
Tristan Whitmarsh
JBMR Plus · DOI ↗
3D-DXA, as implemented in the software tool 3D-Shaper, is a software method that generates a 3D reconstruction of the proximal femur from a single 2D DXA image by registering a statistical model. Implementations of 3D-DXA aim to provide estimates of trabecular, cortical, and structural parameters, similar to those derived from quantitative computed tomography (QCT). As the inventor and developer of the software methods upon which 3D-DXA is built, I have been observing its adoption and widespread use with increasing concern. This article provides a critical evaluation of the methodological limitations inherent to 3D-DXA and discusses their implications for research and patient care. The primary issue is that the limited visibility of the cortex in a DXA image prevents 3D-DXA from accurately deriving cortical parameters. Instead, the software relies on predictions based on overall BMD rather than direct cortical measurements. This may lead to results that do not reflect actual cortical measurements. Additional concerns include the population bias due to the statistical model being derived from a specific demographic, and limited reconstruction accuracy by using single-view DXA images. These limitations have likely resulted in incorrect measurements and research outcomes, which have largely gone unrecognized due to the use of inappropriate performance assessment metrics and the absence of multiple comparison corrections in studies involving 3D-DXA. Despite these limitations, 3D-DXA has received regulatory approval in various countries, potentially compromising the accuracy of clinical diagnoses and treatment decisions. By highlighting these issues, this article aims to inform clinicians, researchers, and regulatory bodies about the significant limitations of 3D-DXA. It underscores the urgent need for a reevaluation of its use in research and clinical settings to prevent misinterpretation of results and to ensure patient safety.
Thomas A Baycroft; S. Lalitha; A. H. M. J. Triaud; A. C. M. Correia
Science Advances · DOI ↗
One notable example of exoplanet diversity is the population of circumbinary planets, which orbit around both stars of a binary star system. There are, so far, only 16 known circumbinary exoplanets, all of which lie in the same orbital plane as the host binary. Suggestions indicate that circumbinary planets could also exist on orbits highly inclined to the binary, close to 90°, polar orbits. No such planets have been found yet, but polar circumbinary gas and debris discs have been observed, and if these were to form planets, then those would be left on a polar orbit. We report strong evidence for a polar circumbinary exoplanet, which orbits a close pair of brown dwarfs that are on an eccentric orbit. We use radial velocities to measure a retrograde apsidal precession for the binary and show that this can only be attributed to the presence of a polar planet.
Michael J. Wilensky; Melis O Irfan; Philip Bull
Accurate models of Galactic synchrotron emission are critical for our understanding of astrophysics and cosmology. For example, this emission is a bright foreground in observations of the redshifted 21-cm line and the Cosmic Microwave Background. It also serves as a probe of the astrophysical properties of our Galaxy such as its magnetic field. Galactic synchrotron emission is often modeled by anchoring to the 408 MHz Haslam map. While the map has been extensively analyzed over the past few decades and several of its known issues have been corrected, there are still uncertainties regarding the absolute calibration of the flux scale that are made apparent when compared to other maps of diffuse radio emission.