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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…

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

I'm behind Broad Institute'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…

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

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). Bo Wang nature.com/articles/s4159…

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

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…

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

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 Nigel Chou Nature Reviews Genetics Shyam Prabhakar Lab Kok Hao Chen Lab A*STAR Genome Institute of Singapore (A*STAR GIS)!

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 Bokai Zhu, and working with maestros Zongming Ma and Garry P. Nolan

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. 🔗 knowledge.brain-map.org/abcatlas#AQEBW…

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

Spatial Transition Tensor or STT, developed by Qing Nie and colleagues Multiscale Cell Fate Research 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…

Congrats to Bokai Zhu 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…

🌏 The Asia Pacific Spatial Omics Technology Conference is happening next week in #Taipei. Don’t miss out on key presentations from Vizgen! Visit us at Booth #4 to learn more & win fun prizes! Register- hubs.ly/Q02wTDZD0 #SpatialOmics #MERSCOPEUltra #Vizgen

#BGI-Research's cutting-edge liver studies have been selected as the cover story for Nature Genetics . 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,

Excited to share our AI research on brain tumor classification from H&E images, now published in Nature Medicine! 🎉 Honored to be a co-first author with Danh-Tai Hoang. This work was co-led by @NCIEytanRuppin and @NCIKenAldape. Check out our tweetorial: #AI #DigitalPathology