Spatial Omics

Tweets about spatial biology including genomics, transcriptomics, proteomics, or other -omics in general. Some tweets about single-cell DNA or RNA sequencing.

[Zongming Ma @ZongmingMa]

Congrats to @ZhuBokai and the wonderful team! Ever feeling frustrated with annotating cells from a spatial-omics dataset with a small targeted panel? CellSNAP helps by leveraging info from cell location and tissue image via a parallel GNN architecture.

https://t.co/hcPEiDzqoo

[Eldad Shulman @ShulmanEldad]

Excited to share our AI research on brain tumor classification from H&E images, now published in @NatureMedicine! 🎉

Honored to be a co-first author with @danhtai_hoang. This work was co-led by @NCIEytanRuppin and @NCIKenAldape.
Check out our tweetorial:
#AI #DigitalPathology

[BGI Group @TheBgiGroup]

#BGI-Research's cutting-edge liver studies have been selected as the cover story for @NatureGenet . These two studies integrate scRNA-seq and Stereo-seq data to characterize molecular signatures and interactions of liver cell types across different states including homeostasis, damage, repair, and regeneration. https://t.co/PKPpHdFKwf

[Nature Methods @naturemethods]

Spatial Transition Tensor or STT, developed by Qing Nie and colleagues @UCI_CMCF is a method that connects messenger RNA splicing and cell state transitions across spatiotemporal dimensions.

https://t.co/8AaPzpUg0O

[antisense. @razoralign]

STT: Spatial transition tensor of single cells https://t.co/9ReuwPZqRm

[allen institute @AllenInstitute]

We've begun rolling out anatomical annotations to the Allen Brain Cell Atlas!

The first data set to support these annotations is the MERFISH Spatial Transcriptomics Dataset of a Single Adult Mouse Brain - registered to CCFv3. 🔗 https://t.co/lpzSg8hyjK

[Vipul Singhal @vipul1891]

Pleased to share our new Research highlights article, which summarizes some of the core features and applications of the BANKSY spatial omics algo. Viewable via: https://t.co/7mhwhrLKFl !

Thanks @NigelChouS @NatureRevGenet @shyam_lab @khchenlab @astar_gis!

[Vizgen @vizgen_inc]

🌏 The Asia Pacific Spatial Omics Technology Conference is happening next week in #Taipei. Don’t miss out on key presentations from @vizgen_inc! Visit us at Booth #4 to learn more & win fun prizes!

Register- https://t.co/UwpX3OpFJW

#SpatialOmics #MERSCOPEUltra #Vizgen

[Sizun Jiang @SizunJ]

Wanna annotate cells in your spatial-omics data but tired of just calling them by their general phenotypes? Hey we got the solution for you! See awesome thread by the hotshot @ZhuBokai, and working with maestros @ZongmingMa and @GarryPNolan

[Juhyun Kim @juhyunk_]

Spatial transition tensor of single cells https://t.co/ZeweIevsvv #journals #feedly

[Lukas Valihrach @LukasValihrach]

The multimodality cell segmentation challenge: toward universal solutions https://t.co/GuswTiFfsH

[Hao Yin @HaoYin20]

SpiDe-Sr
Spatial proteomic images denoising & super-resolution
#SpatialProteomics

⏫peak signal-to-noise ratio & cell extraction accuracy in #ImagingMassCytometry

"In denoising module training, a pair of sub-sampled images (g1(y), g2(y)) were generated from noise image y with the sub-sampler G......as the input and target to train the denoising network (Uθ)"

Also applicable to immunofluorescent images

vs SRCNN KernelGAN RCAN

@NatureComms 2024
https://t.co/NS95hV5HaM

[Nature Methods @naturemethods]

Is cell segmentation a solved problem? Maybe not yet, but the results of this multimodality cell segmentation challenge get us closer! (Spoiler, the winner is a generalist Transformer-based model). @BoWang87 https://t.co/uAHiTo97bY

[Xingzhao Wen @Irene_xzwen]

Thrilled to announce our paper in @Nature introducing MUSIC! For the first time, MUSIC enables simultaneous mapping of multiplexed chromatin interactions, RNA-chromatin interactions, RNA-RNA interactions & gene transcription at single-cell resolution. https://t.co/cPV68KxgC1

[Luciano Martelotto 🛠🧬💻🇦🇺 @LGMartelotto]

I'm behind @broadinstitute's benchmarking efforts led by Sami and team. While our preliminary work took a different approach and strategy, we ended up demonstrating the same findings.

Stay tuned. More on this soon.

https://t.co/ZgT135zVot

https://t.co/mT5jpbBgEF

[Hao Yin @HaoYin20]

DART-FISH
#SpatialTranscriptomics

Pad-lock probe
Rolony
RiboSoma for cell segmentation
Detect <1kb short RNA (able to probe pri-microRNAs?😁)

Very nice reading if interested in how to design/optimize imaging-based ST methods👍

121 genes for human Cortex
300 genes for human kidney (Look at the exquisite closely-apposed single-cell-resolved glomerular Endothelial-Mesangial-Podocyte niche!😍)

@KunZhangBioE @NatureComms 2024
https://t.co/xSD7vSvEaM

[Hao Yin @HaoYin20]

STCellbin

Use Nuclei+Cell Membrane/Wall stains to improve #CellSegmentation &amp; single-cell-resolved #SpatialTranscriptomics

Tailored for #StereoSeq, but likely implementable for other ST methods

Susanne Brix &amp; Xun Xu labs @GigaByteJournal 2024
https://t.co/TmbhT17bAb

[Ming "Tommy" Tang @tangming2005]

Starfysh ️ for spatial transcriptomic+histology analysis and multi-sample integration https://t.co/YcnrAuorvb

[Juhyun Kim @juhyunk_]

Spatial transcriptomics reveal neuron–astrocyte synergy in long-term memory https://t.co/7oGJ7aTo8c #journals #feedly

[Rong Fan @RongFan8]

🤩🤩🤩 Spatial Omics fans, I am super excited to share our latest manuscript!!! 🤩🤩🤩
#spatialomics #spatialbiology #singlecell

Spatially Exploring RNA Biology in Archival Formalin-Fixed Paraffin-Embedded Tissues
https://t.co/WB0qL6ZPOK