Spot-Based Global Registration for Subpixel Stitching of Single-Molecule Resolution Images for Tissue-Scale Spatial Transcriptomics.

Single-molecule imaging at the tissue scale has revolutionized our understanding of biology by providing unprecedented insight into the molecular expression of individual cells and their spatial organization within tissues. However, achieving precise image stitching at the single-molecule level remains a challenge, primarily due to heterogeneous background signals and dim labeling signals in single-molecule images. This paper introduces Spot-Based Global Registration (SBGR), a novel strategy that shifts the focus from raw images to identified molecular spots for high-resolution image alignment. The use of spot-based data enables straightforward and robust evaluation of the credibility of estimated translations and stitching performance. The method outperforms existing image-based stitching methods, achieving subpixel accuracy (83 ± 36 nm) with exceptional consistency. Furthermore, SBGR incorporates a mechanism to surgically remove duplicate spots in overlapping regions, maximizing information recovery from duplicate measurements. In conclusion, SBGR emerges as a robust and accurate solution for stitching single-molecule resolution images in tissue-scale spatial transcriptomics, offering versatility and potential for high-resolution spatial analysis.

Intracellular Spatial Transcriptomic Analysis Toolkit (InSTAnT).

Imaging-based spatial transcriptomics technologies such as MERFISH offer snapshots of cellular processes in unprecedented detail, but new analytic tools are needed to realize their full potential. We present InSTAnT, a computational toolkit for extracting molecular relationships from spatial transcriptomics data at the intra-cellular resolution. InSTAnT detects gene pairs and modules with interesting patterns of mutual co-localization within and across cells, using specialized statistical tests and graph mining. We showcase the toolkit on datasets profiling a human cancer cell line and hypothalamic preoptic region of mouse brain. We performed rigorous statistical assessment of discovered co-localization patterns, found supporting evidence from databases and RNA interactions, and identified subcellular domains associated with RNA-colocalization. We identified several novel cell type-specific gene co-localizations in the brain. Intra-cellular spatial patterns discovered by InSTAnT mirror diverse molecular relationships, including RNA interactions and shared sub-cellular localization or function, providing a rich compendium of testable hypotheses regarding molecular functions.

Controllable modulation of precursor reactivity using chemical additives for systematic synthesis of high-quality quantum dots.

The optical and electronic performance of quantum dots (QDs) are affected by their size distribution and structural quality. Although the synthetic strategies for size control are well established and widely applicable to various QD systems, the structural characteristics of QDs, such as morphology and crystallinity, are tuned mostly by trial and error in a material-specific manner. Here, we show that reaction temperature and precursor reactivity, the two parameters governing the surface-reaction kinetics during growth, govern the structural quality of QDs. For conventional precursors, their reactivity is determined by their chemical structure. Therefore, a variation of precursor reactivity requires the synthesis of different precursor molecules. As a result, existing precursor selections often have significant gaps in reactivity or require synthesis of precursor libraries comprising a large number of variants. We designed a sulfur precursor employing a boron-sulfur bond, which enables controllable modulation of their reactivity using commercially available Lewis bases. This precursor chemistry allows systematic optimization of the reaction temperature and precursor reactivity using a single precursor and grows high-quality QDs from cores of various sizes and materials. This work provides critical insights into the nanoparticle growth process and precursor designs, enabling the systematic preparation of high-quality QD of any sizes and materials.

Rapid, multiplexed detection of biomolecules using electrically distinct hydrogel beads.

Rapid, low-cost, and multiplexed biomolecule detection is an important goal in the development of effective molecular diagnostics. Our recent work has demonstrated a microfluidic biochip device that can electrically quantitate a protein target with high sensitivity. This platform detects and quantifies a target analyte by counting and capturing micron-sized beads in response to an immunoassay on the bead surface. Existing microparticles limit the technique to the detection of a single protein target and lack the magnetic properties required for separation of the microparticles for direct measurements from whole blood. Here, we report new precisely engineered microparticles that achieve electrical multiplexing and adapt this platform for low-cost and label-free multiplexed electrical detection of biomolecules. Droplet microfluidic synthesis yielded highly-monodisperse populations of magnetic hydrogel beads (MHBs) with the necessary properties for multiplexing the electrical Coulter counting on chip. Each bead population was designed to contain a different amount of the hydrogel material, resulting in a unique electrical impedance signature during Coulter counting, thereby enabling unique identification of each bead. These monodisperse bead populations span a narrow range of sizes ensuring that all can be captured sensitively and selectively under simultaneously flow. Incorporating these newly synthesized beads, we demonstrate versatile and multiplexed biomolecule detection of proteins or DNA targets. This development of multiplexed beads for the electrical detection of biomolecules, provides a critical advancement towards multiplexing the Coulter counting approach and the development of a low cost point-of-care diagnostic sensor.

Nanowire Lasers of Formamidinium Lead Halide Perovskites and Their Stabilized Alloys with Improved Stability.

The excellent intrinsic optoelectronic properties of methylammonium lead halide perovskites (MAPbX3, X = Br, I), such as high photoluminescence quantum efficiency, long carrier lifetime, and high gain coupled with the facile solution growth of nanowires make them promising new materials for ultralow-threshold nanowire lasers. However, their photo and thermal stabilities need to be improved for practical applications. Herein, we report a low-temperature solution growth of single crystal nanowires of formamidinium lead halide perovskites (FAPbX3) that feature red-shifted emission and better thermal stability compared to MAPbX3. We demonstrate optically pumped room-temperature near-infrared (∼820 nm) and green lasing (∼560 nm) from FAPbI3 (and MABr-stabilized FAPbI3) and FAPbBr3 nanowires with low lasing thresholds of several microjoules per square centimeter and high quality factors of about 1500-2300. More remarkably, the FAPbI3 and MABr-stabilized FAPbI3 nanowires display durable room-temperature lasing under ∼10(8) shots of sustained illumination of 402 nm pulsed laser excitation (150 fs, 250 kHz), substantially exceeding the stability of MAPbI3 (∼10(7) laser shots). We further demonstrate tunable nanowire lasers in wider wavelength region from FA-based lead halide perovskite alloys (FA,MA)PbI3 and (FA,MA)Pb(I,Br)3 through cation and anion substitutions. The results suggest that formamidinium lead halide perovskite nanostructures could be more promising and stable materials for the development of light-emitting diodes and continuous-wave lasers.