Spatial Omics

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. biorxiv.org/content/10.110…

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-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. bit.ly/3vKGd0D

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. nature.com/articles/s4159…

STT: Spatial transition tensor of single cells nature.com/articles/s4159…

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. 🔗 #AQEBWkkzUlIwRlhMM0hZWEdWRTJTNQACRllZNE9NMkxVNUowWU9GMDdEUgADAQEyTlFUSUU3VEFNUDhQUUFITzRQAAIBQzU3Qkw2Si02Mzg4NTAuNTQAAAQBAAKEpj0EgVyx0wOBCKuDgW6LTwQyTlFUSUU3VEFNUDhQUUFITzRQAAWBr6ZKgemsDoGggUeAktXoBgAHAAAFAAYBAQJGUzAwRFhWMFQ5UjFYOUZKNFFFAAN%2BAAAABAAACDRTVENTWkJYSFlPSTBKVVVBM00ACUxWREJKQVc4Qkk1WVNTMVFVQkcACgALAVRMT0tXQ0w5NVJVMDNEOVBFVEcAAjczR1ZURFhERUdFMjdNMlhKTVQAAwEEAQACIzAwMDAwMAADyAEABQEBAiMwMDAwMDAAA8gBAAAAAgEA" target="_blank" rel="nofollow noopener">knowledge.brain-map.org/abcatlas#AQEBW…

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: rdcu.be/dH1mz ! Thanks @NigelChouS @NatureRevGenet @shyam_lab @khchenlab @astar_gis!

🌏 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- hubs.ly/Q02wTDZD0 #SpatialOmics #MERSCOPEUltra #Vizgen

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

Spatial transition tensor of single cells nature.com/articles/s4159… #journals #feedly

The multimodality cell segmentation challenge: toward universal solutions nature.com/articles/s4159…

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 nature.com/articles/s4146…

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 nature.com/articles/s4159…

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. doi.org/10.1038/s41586…

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. biorxiv.org/content/10.110… biorxiv.org/content/10.110…

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 nature.com/articles/s4146…

STCellbin Use Nuclei+Cell Membrane/Wall stains to improve #CellSegmentation & single-cell-resolved #SpatialTranscriptomics Tailored for #StereoSeq, but likely implementable for other ST methods Susanne Brix & Xun Xu labs @GigaByteJournal 2024 gigabytejournal.com/articles/110

Starfysh ️ for spatial transcriptomic+histology analysis and multi-sample integration nature.com/articles/s4158…

Spatial transcriptomics reveal neuron–astrocyte synergy in long-term memory nature.com/articles/s4158… #journals #feedly

🤩🤩🤩 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 biorxiv.org/content/10.110…