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"/bil/data/50/51/505118bf1edfb3e6/702265/1296400318/merfish_output/1296400318_SISSeg_mousedevmodel_20241004", "title": "Developing mouse whole-brain transcriptomic cell type atlas - MERSCOPE v1: 1296400318", "socialmedia": "MERFISH imaging of 10 \u00b5m thick sections of P28 male C57BL/6J mouse brain that covers the entire brain. Individual sections are taken at 200 \u00b5m interval", "subject": "MERFISH, spatial transcriptomics, atlas, development, mouse, MERSCOPE", "subjectscheme": "", "rights": "Creative Commons Attribution 4.0 International (CC BY 4.0)", "rightsuri": "https://creativecommons.org/licenses/by/4.0/", "rightsidentifier": "CC-BY-4.0", "dataset_image": "", "generalmodality": "spatial transcriptomics", "technique": "MERFISH", "other": "", "abstract": "Spatial transcriptomics atlas of the entire brain of a developing mouse (P28). We profiled 500 genes which were selected to maximize our ability to relate each cell to one of the 5200 cell types defined in our RNAseq-based taxonomy. We image 10 \u00b5m section which were acquired at an interval of 200 \u00b5m. Individual cell were identified using cell segmentation algorithms to a total of ~6 million cells.  The MERFISH datasets not only provide the possibility for accurate spatial annotation of major cell types at subclass level, but also reveal very fine resolution spatial distinctions or gradients for cell types within each subclass.", "methods": "", "technicalinfo": "Dataset was resegmented using cellpose", "doi": "", "dataset_size": "8.131427418", "number_of_files": "7"}], "Tags": [], "Assets": [{"bildid": "ace-low-aim", "bildoi": "", "manifestfile": "/bil/pscstaff/icaoberg/bil-inventory/datasets/json/ace-low-aim.json", "brainpiroot": "", "brainpidata": []}], "Image": [{"xaxis": "left-to-right", "obliquexdim1": "", "obliquexdim2": "", "obliquexdim3": "", "yaxis": "left-to-right", "obliqueydim1": "", "obliqueydim2": "", "obliqueydim3": "", "zaxis": "posterior-to-anterior", "obliquezdim1": "", "obliquezdim2": "", "obliquezdim3": "", "landmarkname": "", "landmarkx": "", "landmarky": "", "landmarkz": "", "number": "NA", "displaycolor": "NA", "representation": "", "flurophore": "DAPI, NA", "stepsizex": "0.108", "stepsizey": "0.108", "stepsizez": "1.5", "stepsizet": "", "channels": "3.0", "slices": "7.0", "z": "1.0", "xsize": "", "ysize": "", "zsize": "", "gbytes": "", "files": "", "dimensionorder": ""}]}]}