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3 results for “Visium HD”
Supplementary data for ENACT: End-to-End Analysis and Cell Type Annotation for Visium High Definition (HD) Slides
<p>This project contains the datasets used to evaluate and reproduce the results of ENACT (End-to-End Analysis and Cell Type<br>Annotation for Visium HD Slides). The dataset consists of:</p> <ul> <li>a sample Visium HD sample of human colorectal cancer, courtesy of 10X Genomics (<a href="https://www.10xgenomics.com/datasets/visium-hd-cytassist-gene-expression-libraries-of-human-crc">Visium HD Spatial Gene Expression Library, Human Colorectal Cancer (FFPE) - 10x Genomics</a>). All credit goes to 10X Genomics.</li> <li>configuration files to be used to reproduce the results provided in the ENACT publication, </li> <li>evaluation plots used in the ENACT publication, and</li> <li>results obtained after running ENACT on the human colorectal cancer sample using the four bin-to-cell assignment methods (naive, weighted_by_area, weighted_by_transcript, and weighted_by_cluster) and the three cell annotation methods (Sargent, CellAssign, CellTypist)</li> </ul> <p>Additionally, results from running ENACT on the following three public VisiumHD samples are provided to showcase ENACT’s tissue-agnostic nature:</p> <div> <div> <div> <ul> <li> <p><a href="https://www.10xgenomics.com/datasets/visium-hd-cytassist-gene-expression-human-lung-cancer-post-xenium-expt">Human Lung FFPE</a> sample from a subject with Adenocarcinoma (age and gender unspecified),</p> </li> <li> <p><a href="https://www.10xgenomics.com/datasets/visium-hd-cytassist-gene-expression-human-tonsil-fresh-frozen">Human Tonsil Fresh Frozen</a> sample from a 21 year old male subject with Reactive Follicular Hyperplasia,</p> </li> <li> <p><a href="https://www.10xgenomics.com/datasets/visium-hd-cytassist-gene-expression-human-breast-cancer-fresh-frozen">Human Breast Fresh Frozen</a> sample from a 58 year old female subject with Ductal Carcinoma in Situ (DCIS).</p> </li> </ul> </div> </div> </div> <p> </p>
Visium HD Human Colorectal Cancer (FFPE) data release pathologist annotation
<p>10X Genomics released a spatial <a href="https://www.10xgenomics.com/datasets/visium-hd-cytassist-gene-expression-libraries-of-human-crc">transcriptomic dataset of human colorectal cancer collected on the Visium HD platform. </a></p> <p>The dataset was divided into different spatial domains based on the accompanying HE stain and the expression of characteristic marker genes.</p> <p>The pathologist's annotation was added with the help of Napari and the Spatialdata python package.</p> <p>Every .csv file contains the Visium HD bin barcode and annotation for the respective level of binning.</p> <p>In addition the HE image was segmented and bins were assigned to Nuclei for a pseudo single cell resolution, as described <a href="https://www.10xgenomics.com/analysis-guides/segmentation-visium-hd">here.</a></p> <p>This work was carried out for the <a href="https://github.com/SpatialHackathon/SpaceHack2023">SpaceHack2023 project </a>and the data shared here is licensed CC0. </p> <p> </p>
Day2_Session2 - mini Visium HD
<p>Visium HD colorectal cancer dataset that was further subsetted based on the tissue positions parquest file. The first 1000 spatial array rows and columns were selected and the associated expression data was subsetted. In addition we selected 5,000 genes which were enriched for highly variable genes.</p>
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