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35 results for “codex”
Fluoro-Forest CODEX data for random Forest-based cell type annotation
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CODEX multiplexed imaging of immunotherapy in human and mouse melanomas
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OMAP-15 Human Intestine with CODEX
<p>Datasets are CODEX experiments performed on TMA ffpe sections (composed of human duodenum, proximal jejunum, 3 mid jejunum samples, ileum, ascending colon, and sigmoid colon samples) labeled with nuclear marker DAPI and anitbodies directed against the indicated markers in OMAP-15. Images were acquired with the Akoya Phenocycler. </p> <p>Markers not included in OMAP-15 are not representative images.</p> <p>See "S16-0513-B13-TMA_Scan1.qptiff" for all markers except SPIB. See "S7-B017-011624_Scan1.qptiff" for SPIB.</p>
CODEX multiplexed imaging cell datasets used for using STELLAR to transfer cell type annotations to other tissues and donors
<p>We performed CODEX (co-detection by indexing) multiplexed imaging on 24 sections of the human intestine from 3 donors (B004, B005, B006) using a panel of 47 oligonucleotide-barcoded antibodies. We also performed CODEX imaging on both human tonsil and Barrett's esophagus (BE) using a panel of 57 oligonucleotide-barcoded antibodies. Subsequently images underwent standard CODEX image processing (tile stitching, drift compensation, cycle concatenation, background subtraction, deconvolution, and determination of best focal plane), single cell segmentation, and column marker z-normalization by tissue. Output of this process were dataframes of 870,000 cells and 220,000 cells respectively with fluorescence values quantified from each marker.</p>
Piloting Copilot and Codex: Hot Temperature, Cold Prompts, or Black Magic? - Data
<p>Generated programs from <a href="https://arxiv.org/abs/2210.14699">Piloting Copilot and Codex: Hot Temperature, Cold Prompts, or Black Magic?</a></p>
One Health EJP MATRIX video about the One Health Surveillance CODEX: The Knowledge Integration Platform (OHS Codex/KIP)
<p>This video was recorded during the webinar about the <strong>One Health Surveillance CODEX: The Knowledge Integration Platform (OHS Codex/KIP) </strong>as part of the OHEJP MATRIX Webinar Series 2022 <em>Solutions for One Health Surveillance in Europe</em>. The webinar took place on November 10<sup>th</sup> from 14:00 to 15:15 CET and was hosted by the <a href="https://onehealthejp.eu/jip-matrix/">One Health EJP project MATRIX.</a></p> <p>The One Health Surveillance CODEX: The Knowledge Integration Platform (OHS Codex/KIP) is a community resource supporting the adoption of the OH paradigm. The OHS Codex/KIP comprises five high-level “action principles”, which respectively support: i) planning and management; ii) collaboration; iii) knowledge exchange; iv) data interoperability; v) reporting and dissemination. These principles are applicable to any sector-specific or cross sectorial surveillance activity.<br> Under each of these principles, the OHS Codex/KIP provides the users a collection of resources (e.g. tools, technical resources, guidance documents and experiences) that address specific OH-problems in the context of the corresponding principle. As an open community framework, it is continuously updated by and for the community. More information is available <a href="https://oh-surveillance-codex.readthedocs.io/en/latest/">here.</a></p> <p>The OHS Codex/KIP has been initially devolped in <a href="https://onehealthejp.eu/jip-orion/">One Health EJP ORION</a> and was expanded and promoted within <a href="https://onehealthejp.eu/jip-matrix/">One Health EJP MATRIX.</a></p> <p>The MATRIX and ORION projects are part of the One Health European Joint Programme (OHEJP).<br> They received funding from the European Union’s Horizon 2020 research and innovation programme under Grant Agreement No 773830.</p> <p>Leading MATRIX partner of the OHS Codex/KIP: German Federal Institute for Risk Assessment (BfR). Contact: Matthias Filter (Matthias.Filter@bfr.bund.de)</p> <p><em><strong>Webinar agenda:</strong></em></p> <p><strong>Welcome and general overview of the MATRIX solutions for One Health Surveillance</strong><br> Guido Benedetti, Statens Serum Institut (SSI), Denmark</p> <p><strong>One Health Surveillance CODEX: Knowledge Integration Platform – ORION perspective and MATRIX extension</strong><br> Matthias Filter, German Federal Institute for Risk Assessment (BfR), Germany</p> <p><strong>Live Demo and special features of the One Health Surveillance CODEX: Knowledge Integration Platform</strong><br> Yvonne Mensching, German Federal Institute for Risk Assessment (BfR), Germany</p>
CODEX multiplexed imaging cell datasets used for using STELLAR to transfer cell type annotations to other tissues and donors
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Processed CODEX multiplexed imaging data of cellular microenvironment around T cell stimulating hydrogels
<p>Our research used CODEX (Co-Detection by Indexing) multiplexed imaging to gain insights into the cellular microenvironment surrounding T cell stimulating hydrogels. These hydrogels were engineered with signals that could locally expand antigen-specific T cells for use in tumor immunotherapy. CODEX imaging involves an iterative process of annealing and stripping fluorophore-labeled oligonucleotide barcodes, complementing the barcodes attached to over 40 antibodies used for tissue staining. Subsequently, images underwent standard CODEX image processing (tile stitching, drift compensation, cycle concatenation, background subtraction, deconvolution, and determination of best focal plane), single cell segmentation, and column marker z-normalization by tissue.</p> <p>Our datasets comprise individual cells as rows, each characterized by 40+ antibody fluorescence values quantified from various markers evaluated for each study. These markers correspond to the antibodies targeting specific proteins within the tissue, quantified at the single-cell level. The values represent per-cell/area-averaged fluorescent intensities, z-normalized along each column. Each cell is mapped with its cell type, defined by x and y coordinates representing pixel locations in the original image. </p> <p>We then used this data to investigate how different proportions of the cell types change over time in response to the stimulating hydrogel injection with antigen-specific T cells. These data could be used to understand the cellular interactions, composition, and structure of T cell stimulating biomaterials for antigen-specific immunotherapy and with adoptive T cell transfer. These datasets offer valuable insights for researchers interested in engineering T cell stimulating microenvironments, immune responses, and therapeutic interventions such as T cell therapies.</p> <p>We investigate the dynamic interplay between immune responses, antigen-specific T cell interactions, and hydrogel environment in a murine melanoma model. We injected antigen-specific T cells with microparticle T cell stimulating hydrogels into mice subcutaneously. Injection sites were take out at different time points day=0 (just after injection), day=3, and day=9 (n=3-6 per time point). Our 51-plex CODEX antibody panel characterizes immune cell types, T cell phenotypes, and stromal cell types, resulting in a rich dataset of 241,685 cells across 51 marker channels.</p>
Organ Mapping Antibody Panel (OMAP) for Multiplexed Antibody-Based Imaging of Human Pancreas with CODEX
<p>Representative dataset using OMAP-13: Organ Mapping Antibody Panel (OMAP) for Multiplexed Antibody-Based Imaging of Human Pancreas with CODEX, v1.0. See https://humanatlas.io/omap.</p>
Codex: Study of Inodiftagene Vixteplasmid (BC-819) in Unresponsive NMIBC
ClinicalTrials.gov study NCT03719300. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Processed CODEX multiplexed imaging data of cellular microenvironment around T cell stimulating hydrogels
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Evaluation of a Diagnostic Software for Coronary Artery Disease Using Retrospective CCTA Data (CODEX-1 Study)
ClinicalTrials.gov study NCT06977295. IPD Sharing: YES. Countries: 3. Publications: 0.
the ANRS CO21 " Extreme " Cohort (CODEX)
ClinicalTrials.gov study NCT01520844. IPD Sharing: Not stated. Countries: 1. Publications: 0.
CODEX data for Triple Negative Breast Cancers React to Pembrolizumab and Radiation Therapy with Three Distinct Immunological Trajectories
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Sex-biased architecture guides T cell development through spatially defined niches - CODEX images
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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.