arXiv subjects

John Peters

Publications and source records attributed to John Peters.

3 recordsLinked to original sources

arXiv2025

CHAMMI-75: Pre-training multi-channel models with heterogeneous microscopy images

Quantifying cell morphology using images and machine learning has proven to be a powerful tool to study the response of cells to treatments. However, models used to quantify cellular morphology are typically trained with a single microscopy imaging type. This results in specialized models that cannot be reused across biological studies because the technical specifications do not match (e.g., different number of channels). Here, we present CHAMMI-75, an open access dataset of heterogeneous, multi-channel microscopy images from 75 diverse biological studies. We curated this resource from publicly available sources to investigate cellular morphology models that are channel-adaptive and can process any microscopy image type. Our experiments show that training with CHAMMI-75 can improve performance in multi-channel bioimaging tasks primarily because of its high diversity in microscopy modalities. This work paves the way to create the next generation of cellular morphology models for biological studies.

cs.CV↗

arXiv2025

Progress and new challenges in image-based profiling

For over two decades, image-based profiling has revolutionized cell phenotype analysis. Image-based profiling processes rich, high-throughput, microscopy data into thousands of unbiased measurements that reveal phenotypic patterns powerful for drug discovery, functional genomics, and cell state classification. Here, we review the evolving computational landscape of image-based profiling, detailing the bioinformatics processes involved from feature extraction to normalization and batch correction. We discuss how deep learning has fundamentally reshaped the field. We examine key methodological advancements, such as single-cell analysis, the development of robust similarity metrics, and the expansion into new modalities like optical pooled screening, temporal imaging, and 3D organoid profiling. We also highlight the growth of public benchmarks and open-source software ecosystems as a key driver for fostering reproducibility and collaboration. Despite these advances, the field still faces substantial challenges, particularly in developing methods for emerging temporal and 3D data modalities, establishing robust quality control standards and workflows, and interpreting the processed features. By focusing on the technical evolution of image-based profiling rather than the wide-ranging biological applications, our aim with this review is to provide researchers with a roadmap for navigating the progress and new challenges in this rapidly advancing domain.

q-bio.QM↗

arXiv2022

Supercell low-level mesocyclones: Origins of inflow and vorticity

The development of low-level mesocyclones in supercell thunderstorms has often been explained via the development of storm-generated streamwise vorticity along a baroclinic gradient in the forward flank of supercells. However, the ambient streamwise vorticity of the environment (often quantified via storm-relative helicity), especially near the ground, is particularly skillful at discriminating between nontornadic and tornadic supercells. This study investigates whether the origins of the inflow air into supercell low-level mesocyclones, both horizontally and vertically, can help explain the dynamical role of environmental versus storm-generated vorticity in the development of low-level mesocyclone rotation. Simulations of supercells, initialized with wind profiles common to supercell environments observed in nature, show that the air bound for the low-level mesocyclone primarily originates from the undisturbed, ambient environment, rather than from along the forward flank, and from very close to the ground, often in the lowest 200 - 400 m of the atmosphere. Given that the near-ground environmental air comprises the bulk of the inflow into low-level mesocyclones, this likely explains the forecast skill of environmental streamwise vorticity in the lowest few hundred meters of the atmosphere. The low-level mesocyclone does not appear to require much augmentation from the development of additional horizontal vorticity in the forward flank. Instead, the dominant contributor to vertical vorticity within the low-level mesocyclone is from the environmental horizontal vorticity. This study hopefully clarifies the development of low-level mesocyclones in supercells.

physics.ao-ph↗