Biology subjects

Kosuri, P.

Publications and source records attributed to Kosuri, P..

2 recordsLinked to original sources

bioRxiv2025

BellaVista: Open-Source Visualization for Imaging-Based Spatial Transcriptomics

Imaging-based spatial transcriptomics can reveal gene expression in situ by locating and identifying individual RNA molecules at subcellular resolution. These datasets typically contain an abundance of information that when analyzed appropriately can reveal tissue organization across scales from molecules to entire organs. However, there is currently a lack of simple open-source tools that facilitate visualization, quality control, and custom spatial analysis. Here we introduce BellaVista, a lightweight open-source tool for interactive visualization and exploration of imaging-based spatial transcriptomics data. BellaVista natively supports data from Xenium (10x Genomics), MERSCOPE (Vizgen), and custom MERFISH platforms. By providing a simple means for simultaneous visualization of images, transcripts, and cell segmentation boundaries, we anticipate that BellaVista will accelerate accessibility, exploration and discovery in the rapidly expanding field of spatial biology. BellaVista is available at https://github.com/pkosurilab/BellaVista.

bioinformatics↗

bioRxiv2023

NanoNERF: A nanoscale NERF blaster replica made of DNA

We used DNA origami to create NanoNERF, the worlds smallest NERF blaster replica (Figure 1). We based our design on the NERF model Maverick Rev-6, and scaled the dimensions down three million times. NanoNERF is planar and measures [~]100 nm in length, with a length-to-width ratio closely resembling the original toy. Here, we describe the design, prototyping, and validation pipeline used to create the NanoNERF. We also discuss potential applications to motivate the creation of future nanoscale blasters with a firing functionality. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=41 SRC="FIGDIR/small/560388v3_fig1.gif" ALT="Figure 1"> View larger version (25K): org.highwire.dtl.DTLVardef@1d7619forg.highwire.dtl.DTLVardef@14a16dforg.highwire.dtl.DTLVardef@123b531org.highwire.dtl.DTLVardef@14cb703_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 1:C_FLOATNO A nanoscale replica of the NERF Maverick Rev-6 a) Original NERF Maverick Rev-6 toy, b) rendering of the NanoNERF structure in oxView. Gray lines represent individual DNA strands. NanoNERF length: 100 nm; width of barrel: 35 nm; thickness: 2 nm; c) Scan of a NanoNERF blaster acquired in an Atomic Force Microscope. C_FIG

biophysics↗