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Stryker mouse visual cortex
Mouse Visual Cortex, supplied by Stryker, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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mouse visual cortex - by Bioz Stars, 2026-05

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starmap mouse visual cortex transcriptomics data (Dropbox Inc)

Dropbox Inc starmap mouse visual cortex transcriptomics data

a The first simulated dataset was created by shuffling L5/L4 and L5/L6 regions of a spatially resolved <t>STARmap</t> mouse visual cortex <t>transcriptomics</t> dataset, with Gaussian noise added to the expression values. We compared the best domain segmentation results from the six algorithms, noting that SpaceFlow, which operates on single omics, was contrasted with algorithms capable of integrating two omics. b We evaluated the Adjusted Rand Index (ARI) of domain segmentations produced by the six algorithms at different clustering resolutions using “leiden” method. c The distribution of modality weights for the two omics in COSMOS is shown. d UMAP visualizations of integrated embeddings from SpatialGlue, SpaMultiVAE, and COSMOS are presented. e The pseudo-spatiotemporal maps (pSM) generated by these three algorithms are illustrated. f–j Similar analyses were conducted on a second simulated dataset, created by shuffling EPL/MCL and EPL/GL regions of a spatially resolved Stereo-Seq mouse olfactory bulb dataset, with Gaussian noise added to the expression values. SpaMultiVAE was excluded from this comparison due to its instability in analyzing the sparse Stereo-Seq dataset. The full names of the abbreviations of brain regions are: hippocampus (HPC), corpus callosum (CC), layer 1 (L1), layer 2/3 (L2/3), layer 4 (L4), layer 5 (L5), layer 6 (L6), rostral migratory stream (RMS), granule cell layer (GCL), internal plexiform layer (IPL), mitral cell layer (MCL), external plexiform layer (EPL), glomerular layer (GL) and olfactory nerve layer (ONL). Source data are provided as a Source Data file.

Starmap Mouse Visual Cortex Transcriptomics Data, supplied by Dropbox Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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a The first simulated dataset was created by shuffling L5/L4 and L5/L6 regions of a spatially resolved STARmap mouse visual cortex transcriptomics dataset, with Gaussian noise added to the expression values. We compared the best domain segmentation results from the six algorithms, noting that SpaceFlow, which operates on single omics, was contrasted with algorithms capable of integrating two omics. b We evaluated the Adjusted Rand Index (ARI) of domain segmentations produced by the six algorithms at different clustering resolutions using “leiden” method. c The distribution of modality weights for the two omics in COSMOS is shown. d UMAP visualizations of integrated embeddings from SpatialGlue, SpaMultiVAE, and COSMOS are presented. e The pseudo-spatiotemporal maps (pSM) generated by these three algorithms are illustrated. f–j Similar analyses were conducted on a second simulated dataset, created by shuffling EPL/MCL and EPL/GL regions of a spatially resolved Stereo-Seq mouse olfactory bulb dataset, with Gaussian noise added to the expression values. SpaMultiVAE was excluded from this comparison due to its instability in analyzing the sparse Stereo-Seq dataset. The full names of the abbreviations of brain regions are: hippocampus (HPC), corpus callosum (CC), layer 1 (L1), layer 2/3 (L2/3), layer 4 (L4), layer 5 (L5), layer 6 (L6), rostral migratory stream (RMS), granule cell layer (GCL), internal plexiform layer (IPL), mitral cell layer (MCL), external plexiform layer (EPL), glomerular layer (GL) and olfactory nerve layer (ONL). Source data are provided as a Source Data file.

Journal: Nature Communications

Article Title: Cooperative integration of spatially resolved multi-omics data with COSMOS

doi: 10.1038/s41467-024-55204-y

Figure Lengend Snippet: a The first simulated dataset was created by shuffling L5/L4 and L5/L6 regions of a spatially resolved STARmap mouse visual cortex transcriptomics dataset, with Gaussian noise added to the expression values. We compared the best domain segmentation results from the six algorithms, noting that SpaceFlow, which operates on single omics, was contrasted with algorithms capable of integrating two omics. b We evaluated the Adjusted Rand Index (ARI) of domain segmentations produced by the six algorithms at different clustering resolutions using “leiden” method. c The distribution of modality weights for the two omics in COSMOS is shown. d UMAP visualizations of integrated embeddings from SpatialGlue, SpaMultiVAE, and COSMOS are presented. e The pseudo-spatiotemporal maps (pSM) generated by these three algorithms are illustrated. f–j Similar analyses were conducted on a second simulated dataset, created by shuffling EPL/MCL and EPL/GL regions of a spatially resolved Stereo-Seq mouse olfactory bulb dataset, with Gaussian noise added to the expression values. SpaMultiVAE was excluded from this comparison due to its instability in analyzing the sparse Stereo-Seq dataset. The full names of the abbreviations of brain regions are: hippocampus (HPC), corpus callosum (CC), layer 1 (L1), layer 2/3 (L2/3), layer 4 (L4), layer 5 (L5), layer 6 (L6), rostral migratory stream (RMS), granule cell layer (GCL), internal plexiform layer (IPL), mitral cell layer (MCL), external plexiform layer (EPL), glomerular layer (GL) and olfactory nerve layer (ONL). Source data are provided as a Source Data file.

Article Snippet: STARmap mouse visual cortex transcriptomics data is available at the Dropbox ( https://www.dropbox.com/sh/f7ebheru1lbz91s/AADm6D54GSEFXB1feRy6OSASa/visual_1020/20180505_BY3_1kgenes?dl=0&subfolder_nav_tracking=1 ).

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