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Bin2cell reconstructs cells from high resolution Visium HD data

70
Citations
September 2, 2024
Published Date

Research Abstract & Technology Focus

Abstract

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.
reconstructs cells resolution visium
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stackexchange.com › answer
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What is free available libraries, packages or sdks out their to take 10m resolution imagery from sentinel 2 down to 5m resolution

With sufficiently good signal to noise and iff you know the point spread function of the imaging system very accurately then a super resolution of about 2-3x is theoretically possible with good dat...
stackexchange.com › answer
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Disassembly of VCVTSD2USI in 16bit mode

I've thrown together a small test to see which one it is. Bochs decodes 62 F1 7F 08 79 C0 as VCVTSD2USI EAX, XMM0 and emulates it accordingly. I also checked with qemu-system-i386 -enable-kvm -cpu ...
stackexchange.com › answer
0%

What is free available libraries, packages or sdks out their to take 10m resolution imagery from sentinel 2 down to 5m resolution

Wouldn't this be upscaling, not downscaling? Also, when you do this, you are basically making up detail so the resulting images should not be relied on for anything.
crossref.org › academic paper
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Cellpose-SAM: superhuman generalization for cellular segmentation

Modern algorithms for biological segmentation can match inter-human agreement in annotation quality. This however is not a performance bound: a hypothetical human-consensus segmentation could reduc...
stackexchange.com › answer
0%

What is free available libraries, packages or sdks out their to take 10m resolution imagery from sentinel 2 down to 5m resolution

Just about any image upscaling tool should be able to do the job, no? You're trying to upscale the image going from a 10 by 10 meter square per pixel, to a 5 by 5 meter square per pixel. You can si...

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What is the core focus of the research titled 'Bin2cell reconstructs cells from high resolution Visium HD data'?

This literature focuses on: Abstract 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 ar...

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How is the concept of 'Bin2cell reconstructs cells from high resolution Visium HD data' being discussed by engineers on StackExchange?

Yes, highly correlated activity was mapped. An entry titled 'What is free available libraries, packages or sdks out their to take 10m resolution imagery from sentinel 2 down to 5m resolution' discusses this: With sufficiently good signal to noise and iff you know the point spread function of the imaging system very accurately then a super resolution of ...

What other academic literature is closely related to 'Bin2cell reconstructs cells from high resolution Visium HD data'?

Yes, highly correlated activity was mapped. An entry titled 'Cellpose-SAM: superhuman generalization for cellular segmentation' discusses this: Modern algorithms for biological segmentation can match inter-human agreement in annotation quality. This however is not a performance bound: a hyp...

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