Mikolaj Krysa | Searcharxiv

arXiv2026

The mixture of glycerin with tartrazine: a solution to reversibly increase tissue transparency for in vitro quantitative phase imaging

Thick tissue sections strongly scatter and absorb light, which limits transmission-based label-free examination via quantitative phase imaging (QPI) modalities. Here we introduce a simple, room-temperature optical clearing medium - glycerol and tartrazine solution (GTS; 60 percent glycerol, 10 percent tartrazine) - that increases the transparency of 50-80 micron murine liver and kidney slices while preserving tissue morphology and enabling rapid, label-free quantitative phase imaging. Using Fourier ptychographic microscopy (FPM) and lensless digital holographic microscopy with pixel super-resolution (LDHM-PSR), we demonstrate markedly improved high-throughput visualization of microstructural features after GTS immersion compared with phosphate-buffered saline (PBS). The improvement is confirmed quantitatively by a significant increase in the one-pixel-lag autocorrelation of phase-gradient values, indicating reduced scattering-driven phase artifacts and enhanced structural continuity in reconstructed phase maps. We further show that GTS is stable for months at room temperature, provides instant yet durable clearing that improves over time, and can be removed by brief PBS washing, enabling downstream multimodal analyses on the same specimen. Finally, we benchmark GTS against the state-of-the-art clearing agent Ce3D, highlighting GTS as a low-cost, safe, operationally straightforward alternative with strong potential for routine, high-throughput QPI-based histopathology workflows.

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↗