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86 results for “Xenium”
Example Analysis Output of Xenium Breast Cancer Data
<p>This is an example CartoStore dataset from Xenium Breast Cancer Analysis.</p> <p>Outputs generated from XeniumRanger and FICTURE are combined in this repository. </p> <p>Please refer to https://github.com/seqscope/cartloader for more details. </p>
Intermediate files used for generating co-register result on the Xenium Breast Cancer Dataset with Giotto Suite
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Xenium benchmarking- xenium formatted to AnnData 1 (mouse_brain)
<p>This repository contains Xenium datasets formated to AnnData format for benchmarking the characteristics and performance of Xenium (Marco Salas et al., 2024). Please visit https://github.com/Moldia/Xenium_benchmarking to obtain further information about the datasets. On summary, AnnData contains the expression of profiled cells with some metadata, including spatial position. In adata.obs['spots'] we also include the position of decoded reads as well as some additional metadata and quality. </p> <p> </p> <p>This repository is the part 1/4 of all repositories containing the datasets used in the study already formated to AnnData</p>
Xenium Cloud Optimized Geotiff Test
<p>Test dataset for Cloud Optimized Geotiff</p>
Example dataset to run end-to-end pipeline (Xenium benchmarking)
<p>This repository contains an. This example dataset is a reduced form of the one shared by Kukanja, Langseth et al. 2024. (<a title="Persistent link using digital object identifier" href="https://doi.org/10.1016/j.cell.2024.02.030" target="_blank" rel="noreferrer noopener">https://doi.org/10.1016/j.cell.2024.02.030</a>) and represents a human section of spinal chord (inactive lession of Multiple schlerosis) profiled with Xenium. Please refer to the original publication for further information.</p> <p>This dataset is expected to be used as an input for the end-to-end pipeline built in the context of Marco Salas et al. 2024 (Xenium benchkmarking). </p>
Xenium benchmarking- xenium formatted to AnnData 2 (human breast datasets)
<p>This repository contains Xenium datasets formated to AnnData format for benchmarking the characteristics and performance of Xenium (Marco Salas et al., 2024). Please visit https://github.com/Moldia/Xenium_benchmarking to obtain further information about the datasets. On summary, AnnData contains the expression of profiled cells with some metadata, including spatial position. In adata.obs['spots'] we also include the position of decoded reads as well as some additional metadata and quality. </p> <p> </p> <p>This repository is the part 2/4 of all repositories containing the datasets used in the study already formated to AnnData</p>
Xenium benchmarking- xenium formatted to AnnData 3 (miscellaneous)
<p>This repository contains Xenium datasets formated to AnnData format for benchmarking the characteristics and performance of Xenium (Marco Salas et al., 2024). Please visit https://github.com/Moldia/Xenium_benchmarking to obtain further information about the datasets. On summary, AnnData contains the expression of profiled cells with some metadata, including spatial position. In adata.obs['spots'] we also include the position of decoded reads as well as some additional metadata and quality. </p> <p> </p> <p>This repository is the part 3/4 of all repositories containing the datasets used in the study already formated to AnnData</p>
Xenium Breast Cancer Gene Count
<p>Xenium Breast Cancer Gene Count (JSON format)</p>
Xenium Breast Cancer Factor Analysis
<p>Xenium Breast Cancer Factor Analysis (TSV format)</p>
10x Xenium GeoJSON
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Example Analysis Output of Xenium Mouse Brain Data
<p>This is an example analysis output data from Xenium Mouse Brain Data Analysis</p>
PMTiles for xenium histology (H&E)
<p>PMTiles for xenium histology (H&E)</p>
Xenium Full SGE dataset in Flatgeobuf format
<p>Xenium Full SGE dataset in Flatgeobuf format</p>
Xenium datasets for Garma et al 2024 (Caudate and putamen human)-1
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Xenium datasets for Garma et al 2024 (Caudate and putamen human)-3
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Xenium datasets for Garma et al 2024 (Caudate and putamen human)-4
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Xenium datasets for Garma et al 2024 (Caudate and putamen human)-2
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Mouse Skin Xenium In Situ Spatial Gene Expression
GEO Series GSE276273. Mus musculus. 2 samples. Type: Other.
Growth of the maternal intestine during pregnancy and lactation [Xenium]
GEO Series GSE285027. Mus musculus. 12 samples. Type: Other.
Genetically Engineered Brain Organoids Recapitulate Spatial and Developmental States of Glioblastoma Progression [Xenium Spatial Transcriptomics]
GEO Series GSE283497. Homo sapiens. 6 samples. Type: Other.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.