Mukesh Varshney | Searcharxiv

arXiv2026

Lateral shearing optical diffraction tomography of brain organoid with reduced spatial coherence

Optical diffraction tomography (ODT) is a powerful technique for quantitative, label-free reconstruction of the three-dimensional refractive index (RI) distribution of biological samples. While ODT is well established for imaging thin, weakly scattering samples, it encounters significant challenges when applied to heterogeneous, strongly scattering thick samples such as tissues and organoids. In this work, a novel common-path interferometric approach to ODT is presented, specifically designed for the RI reconstruction of heterogeneous and highly scattering samples at high temporal stability. The proposed technique, termed lateral shearing (LS)-ODT, incorporates partial lateral shearing off-axis interferometry to suppress the effects of multiple scattering, similar to the mechanism in differential interference contrast (DIC) microscopy, which is widely used for imaging thick specimens. Additionally, the LS-ODT system uses dynamic speckle illumination to enhance both spatial phase and RI sensitivity compared to laser-based ODT systems. The effectiveness of this method is demonstrated through experiments on a cell phantom. Its robustness and accuracy are further validated across a wide range of samples, including mouse kidney tissue sections and brain organoids derived from human induced pluripotent stem cells (iPSCs), in both thin and thick sections. Furthermore, correlative fluorescence and RI tomography of the organoids highlights the potential of LS-ODT to enhance and support a broad spectrum of biomedical studies, particularly in the field of histology.

physics.optics↗

arXiv2025

High Space-bandwidth Product Label-free Examination of iPSC-derived Brain Organoids via Fourier Ptychographic Microscopy

Fourier ptychographic microscopy (FPM) is a promising quantitative phase imaging technique that enables high-resolution, label-free imaging over a large field-of-view. Here, we present the first application of FPM for the quantitative analysis of human brain organoid slices, providing a powerful, cost-effective, and label-free enhancement to the current gold-standard fluorescence microscopy. Brain organoids, prepared as thin (5 micrometer) slices, were imaged with a custom-built FPM system consisting of a standard light microscope (4x, 0.2 NA objective) and a 7x7 LED array. This configuration achieved a synthetic numerical aperture of 0.54 and a spatial resolution of approximately 488 nm across an area of 2.077 x 3.65 mm. Fluorescence microscopy was used in parallel for neurons, astrocytes, and nuclei labeling, providing rich fluorescence imaging. Moreover, we designed an automated method to merge classical resolution fluorescence images to visualize the whole brain organoid and align it with the numerically increased space-bandwidth product FPM image. The provided alignment method enables rich phase-fluorescence correlative imaging. Based on the segmentation performed on the stitched fluorescence images, we devised a quantitative phase analysis revealing a higher mean optical thickness of the nuclei versus astrocytes and neurons. Notably, nuclei located in neurogenic regions consistently exhibited significantly higher phase values (optical path difference) compared to nuclei elsewhere, suggesting cell-type-specific biophysical signatures. The label-free, quantitative, and high-throughput capabilities of the FPM approach demonstrated here make it a powerful and accessible tool for future structural and functional studies of whole-section brain organoid development and disease modeling studies.

physics.med-ph↗