SUMMARY: Visium HD by 10X Genomics is the first commercially available platform capable of capturing full scale transcriptomic data paired with a reference morphology image from archived FFPE blocks at sub-cellular resolution. However, aggregation of capture regions to single cells poses challenges. Bin2cell reconstructs cells from the highest resolution data (2 μm bins) by leveraging morphology image segmentation and gene expression information. It is compatible with established Python single cell and spatial transcriptomics software, and operates efficiently in a matter of minutes without requiring a GPU. We demonstrate improvements in downstream analysis when using the reconstructed cells over default 8 μm bins on mouse brain and human colorectal cancer data. AVAILABILITY AND IMPLEMENTATION: Bin2cell is available at https://github.com/Teichlab/bin2cell, along with documentation and usage examples, and can be installed from pip. Probe design functionality is available at https://github.com/Teichlab/gene2probe.

We present the WarpEngine, an architecture designed for real-time imaged-based rendering of natural scenes from arbitrary viewpoints. The modeling primitives are real-world images with per-pixel depth. Currently they are acquired and stored off-line; in the near future real-time depth-image acquisition will be possible, the WarpEngine is designed to render in immediate mode from such data sources.The depth-image resolution is locally adapted by interpolation to match the resolution of the output image. 3D warping can occur either before or after the interpolation; the resulting warped/interpolated samples are forward-mapped into a warp buffer, with the precise locations recorded using an offset. Warping processors are integrated on-chip with the warp buffer, allowing efficient, scalable implementation of very high performance systems. Each chip will be able to process 100 million samples per second and provide 4.8GigaBytes per second of bandwidth to the warp buffer.The WarpEngine is significantly less complex than our previous efforts, incorporating only a single ASIC design. Small configurations can be packaged as a PC add-in card, while larger deskside configurations will provide HDTV resolutions at 50 Hz, enabling radical new applications such as 3D television.WarpEngine will be highly programmable, facilitating use as a test-bed for experimental IBR algorithms.