Moore, B. A. | Search bioRxiv

bioRxiv2025

A multi-modal whole-slide image processing pipeline for quantitative mapping of tissue architecture, histopathology, and tissue microenvironment

Multi-modal, multiscale imaging is crucial for quantitative high-content spatial profiling. We present an integrated image processing pipeline for comprehensive tissue analysis that combines quantitative phase microscopy for tissue architecture mapping, hyper-plex fluorescence imaging for immune microenvironment profiling, and whole-slide histopathology. This approach enables detailed morphological mapping of tissue architecture and cell morphology, while simultaneously linking them to the functional states of individual cells across the entire slide. By analyzing tissue biopsies from patients with ulcerative colitis, we demonstrate the potential of this pipeline for quantitative spatial analysis of molecular markers related to mucosal healing. Open-source and compatible with conventional microscopy systems, this pipeline provides a powerful tool for research and clinical applications through its comprehensive integration of quantitative, high-content, and histological imaging modalities.

bioinformatics↗

bioRxiv2019

A novel cellular structure in the photoreceptors of insectivorous birds

The keen visual systems of birds have been relatively well-studied. The foundations of avian vision rest on their cone and rod photoreceptors. Most birds use four cone photoreceptor types for color vision, a fifth cone for achromatic tasks, and a rod for low-light levels. The cones, along with their oil droplets, and rods are conserved across birds - with the exception of a few shifts in spectral sensitivity - despite taxonomic, behavioral and ecological differences. Here, however, we describe a novel photoreceptor in a group of New World flycatchers (Empidonax spp.) in which the traditional oil droplet is replaced with a complex of electron-dense megamitochondria surrounded by hundreds of small, orange oil droplets. These photoreceptors were unevenly distributed across the retina, being present in the central region (including in the fovea), but absent from the retinal periphery and the area temporalis. Many bird species have had their oil droplets and photoreceptors characterized, but only the two flycatchers described here (E. virescens and E. minimus) possess this unusual structure. We discuss the potential functional significance of the unique sub-cellular structure in these photoreceptors providing an additional visual channel for these small predatory songbirds.

zoology↗