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642 results for “Multiplexing”
Multiplexed histology of COVID-19 post-mortem lung samples - ACUTE CASE 2 FOV3
<p><strong>Image-based data set of a post-mortem lung sample from a COVID-19 donor (ACUTE CASE 2 FOV3)</strong></p> <p>Each image shows the same field of view (FOV), sequentially stained with the depicted fluorescence-labelled antibodies, including surface proteins, intracellular proteins and transcription factors. Images contain 2024 x 2024 pixels and are generated using an inverted wide-field fluorescence microscope with a 20x objective, a lateral resolution of 325 nm and an axial resolution above 5 µm. Images have been normalized and intensities adjusted.</p>
Multiplexed histology of COVID-19 post-mortem lung samples - ACUTE CASE 1 FOV2
<p><strong>Image-based data set of a post-mortem lung sample from a COVID-19 donor (ACUTE CASE 1 FOV2)</strong></p> <p>Each image shows the same field of view (FOV), sequentially stained with the depicted fluorescence-labelled antibodies, including surface proteins, intracellular proteins and transcription factors. Images contain 2024 x 2024 pixels and are generated using an inverted wide-field fluorescence microscope with a 20x objective, a lateral resolution of 325 nm and an axial resolution above 5 µm. Images have been normalized and intensities adjusted.</p>
Multiplexed histology of COVID-19 post-mortem lung samples - CONROL CASE 3 FOV1
<p><strong>Image-based data set of a post-mortem lung sample from a COVID-19 donor (CONTROL CASE 3 FOV1)</strong></p> <p>Each image shows the same field of view (FOV), sequentially stained with the depicted fluorescence-labelled antibodies, including surface proteins, intracellular proteins and transcription factors. Images contain 2024 x 2024 pixels and are generated using an inverted wide-field fluorescence microscope with a 20x objective, a lateral resolution of 325 nm and an axial resolution above 5 µm. Images have been normalized and intensities adjusted.</p>
Multiplexed histology of COVID-19 post-mortem lung samples - PROLONGED CASE 2 FOV2
<p><strong>Image-based data set of a post-mortem lung sample from a COVID-19 donor (PROLONGED CASE 2 FOV2)</strong></p> <p>Each image shows the same field of view (FOV), sequentially stained with the depicted fluorescence-labelled antibodies, including surface proteins, intracellular proteins and transcription factors. Images contain 2024 x 2024 pixels and are generated using an inverted wide-field fluorescence microscope with a 20x objective, a lateral resolution of 325 nm and an axial resolution above 5 µm. Images have been normalized and intensities adjusted.</p>
Multiplexed histology of COVID-19 post-mortem lung samples - ACUTE CASE 1 FOV1
<p><strong>Image-based data set of a post-mortem lung sample from a COVID-19 donor (ACUTE CASE 1 FOV1)</strong></p> <p>Each image shows the same field of view (FOV), sequentially stained with the depicted fluorescence-labelled antibodies, including surface proteins, intracellular proteins and transcription factors. Images contain 2024 x 2024 pixels and are generated using an inverted wide-field fluorescence microscope with a 20x objective, a lateral resolution of 325 nm and an axial resolution above 5 µm. Images have been normalized and intensities adjusted.</p>
Multiplexed histology of COVID-19 post-mortem lung samples - PROLONGED CASE 4 FOV1
<p><strong>Image-based data set of a post-mortem lung sample from a COVID-19 donor (PROLONGED CASE 4 FOV1)</strong></p> <p>Each image shows the same field of view (FOV), sequentially stained with the depicted fluorescence-labelled antibodies, including surface proteins, intracellular proteins and transcription factors. Images contain 2024 x 2024 pixels and are generated using an inverted wide-field fluorescence microscope with a 20x objective, a lateral resolution of 325 nm and an axial resolution above 5 µm. Images have been normalized and intensities adjusted.</p>
Multiplexed histology of COVID-19 post-mortem lung samples - CONTROL CASE 1 FOV3
<p><strong>Image-based data set of a post-mortem lung sample from a non-COVID-related pneumonia donor (CONTROL CASE 1 FOV3)</strong></p> <p>Each image shows the same field of view (FOV), sequentially stained with the depicted fluorescence-labelled antibodies, including surface proteins, intracellular proteins and transcription factors. Images contain 2024 x 2024 pixels and are generated using an inverted wide-field fluorescence microscope with a 20x objective, a lateral resolution of 325 nm and an axial resolution above 5 µm. Images have been normalized and intensities adjusted.</p>
Multiplexed histology of COVID-19 post-mortem lung samples - CHRONIC CASE 1 FOV3
<p><strong>Image-based data set of a post-mortem lung sample from a COVID-19 donor (CHRONIC CASE 1 FOV3)</strong></p> <p>Each image shows the same field of view (FOV), sequentially stained with the depicted fluorescence-labelled antibodies, including surface proteins, intracellular proteins and transcription factors. Images contain 2024 x 2024 pixels and are generated using an inverted wide-field fluorescence microscope with a 20x objective, a lateral resolution of 325 nm and an axial resolution above 5 µm. Images have been normalized and intensities adjusted.</p>
Multiplexed histology of COVID-19 post-mortem lung samples - PROLONGED CASE 3 FOV1
<p><strong>Image-based data set of a post-mortem lung sample from a COVID-19 donor (PROLONGED CASE 3 FOV1)</strong></p> <p>Each image shows the same field of view (FOV), sequentially stained with the depicted fluorescence-labelled antibodies, including surface proteins, intracellular proteins and transcription factors. Images contain 2024 x 2024 pixels and are generated using an inverted wide-field fluorescence microscope with a 20x objective, a lateral resolution of 325 nm and an axial resolution above 5 µm. Images have been normalized and intensities adjusted.</p>
Multiplexed histology of COVID-19 post-mortem lung samples - PROLONGED CASE 2 FOV1
<p><strong>Image-based data set of a post-mortem lung sample from a COVID-19 donor (PROLONGED CASE 2 FOV1)</strong></p> <p>Each image shows the same field of view (FOV), sequentially stained with the depicted fluorescence-labelled antibodies, including surface proteins, intracellular proteins and transcription factors. Images contain 2024 x 2024 pixels and are generated using an inverted wide-field fluorescence microscope with a 20x objective, a lateral resolution of 325 nm and an axial resolution above 5 µm. Images have been normalized and intensities adjusted.</p>
Multiplexed histology of COVID-19 post-mortem lung samples - ACUTE CASE 1 FOV2
<p><strong>Image-based data set of a post-mortem lung sample from a COVID-19 donor (ACUTE CASE 1 FOV2)</strong></p> <p>Each image shows the same field of view (FOV), sequentially stained with the depicted fluorescence-labelled antibodies, including surface proteins, intracellular proteins and transcription factors. Images contain 2024 x 2024 pixels and are generated using an inverted wide-field fluorescence microscope with a 20x objective, a lateral resolution of 325 nm and an axial resolution above 5 µm. Images have been normalized and intensities adjusted.</p>
Multiplexed histology of COVID-19 post-mortem lung samples - CONROL CASE 2 FOV2
<p><strong>Image-based data set of a post-mortem lung sample from a COVID-19 donor (CONTROL CASE 2 FOV2)</strong></p> <p>Each image shows the same field of view (FOV), sequentially stained with the depicted fluorescence-labelled antibodies, including surface proteins, intracellular proteins and transcription factors. Images contain 2024 x 2024 pixels and are generated using an inverted wide-field fluorescence microscope with a 20x objective, a lateral resolution of 325 nm and an axial resolution above 5 µm. Images have been normalized and intensities adjusted.</p>
Multiplexed histology of COVID-19 post-mortem lung samples - PROLONGED CASE 3 FOV2
<p><strong>Image-based data set of a post-mortem lung sample from a COVID-19 donor (PROLONGED CASE 3 FOV2)</strong></p> <p>Each image shows the same field of view (FOV), sequentially stained with the depicted fluorescence-labelled antibodies, including surface proteins, intracellular proteins and transcription factors. Images contain 2024 x 2024 pixels and are generated using an inverted wide-field fluorescence microscope with a 20x objective, a lateral resolution of 325 nm and an axial resolution above 5 µm. Images have been normalized and intensities adjusted.</p>
Ultrasensitive and multiplexed miRNA detection system with DNA-PAINT
<p>This dataset contains the raw data that were used for the publication entitled, "Ultrasensitive and multiplexed miRNA detection system with DNA-PAINT" published in Biosensors and Bioelectronics on 30 December 2023.</p>
Multiplexed histology of COVID-19 post-mortem lung samples - Single-cell Mean Fluorescence Intensities
<p>Data table containing single-cell mean fluorescence intensities (MFI) of all markers analyzed by multiplexed histology in all COVID-19 post-mortem lung samples and non-COVID-related pneumonia controls (14 lung samples, stratified based on disease duration into control, acute, chronic and prolonged). It contains information at the single-cell level about approx 50 proteins in around 40.000 lung cells.</p> <p>Data shown has been arcsin(h) transformed with a co-factor of 0.2. Additionally, cells expressing less than 0.15 MFI of all markers have been labeled as non-defined and excluded from the data set.</p> <p>Seurat package 4.0.0 was used in R to perform mean centering and scaling, followed by PCA, and reduced the dimensions of the data to the top 11 principal components. UMAP was initialized in this PCA space to visualize the data on reduced UMAP dimensions. The cells were clustered on PCA space using the SNN algorithm implemented as <em>FindNeighbors</em> and <em>FindClusters </em>with <em>n.epochs = 500</em> and default parameters (<em>res = 0.8</em>). We obtained 26 clusters that we merged to get relevant populations for our analysis based on canonical lineage markers. We ended up with 8 cell clusters that were manually annotated based on cell-type-specific markers found to be differentially expressed.</p> <p> </p> <p> </p>
Multiplexed histology of COVID-19 post-mortem lung samples - CHRONIC CASE 3 FOV1
<p><strong>Image-based data set of a post-mortem lung sample from a COVID-19 donor (CHRONIC CASE 3 FOV1)</strong></p> <p>Each image shows the same field of view (FOV), sequentially stained with the depicted fluorescence-labelled antibodies, including surface proteins, intracellular proteins and transcription factors. Images contain 2024 x 2024 pixels and are generated using an inverted wide-field fluorescence microscope with a 20x objective, a lateral resolution of 325 nm and an axial resolution above 5 µm. Images have been normalized and intensities adjusted.</p>
Multiplexed histology of COVID-19 post-mortem lung samples - CHRONIC CASE 3 FOV2
<p><strong>Image-based data set of a post-mortem lung sample from a COVID-19 donor (CHRONIC CASE 3 FOV2)</strong></p> <p>Each image shows the same field of view (FOV), sequentially stained with the depicted fluorescence-labelled antibodies, including surface proteins, intracellular proteins and transcription factors. Images contain 2024 x 2024 pixels and are generated using an inverted wide-field fluorescence microscope with a 20x objective, a lateral resolution of 325 nm and an axial resolution above 5 µm. Images have been normalized and intensities adjusted.</p>
OMAP-10: Multiplexed Antibody-Based Imaging of Human Palatine Tonsil with MACSima v1.0
<p> </p> <p>OMAP-10 was designed for MACSima (MACSima imaging cyclic staining) imaging of <em>paraformaldehyde</em> (PFA)-fixed human tonsil samples. The MACSima technology is described in detail in the following publication (<a href="https://doi.org/10.1038/s41598-022-05841-4">https://doi.org/10.1038/s41598-022-05841-4</a>). Most, but not all, antibodies in this panel are recombinant antibodies with a mutated human IgG1 constant region. The described mutation removes the Fc receptor binding capacity of human IgG1, eliminating the need for additional blocking steps and reducing non-specific binding of human antibodies on human tissues. Highly multiplexed imaging is achieved through cycles of immunolabeling with FITC, PE, and APC conjugated antibodies and photobleaching to eliminate fluorescence signal between imaging cycles. The panel contains 30 antibodies and the nuclear marker DAPI for image alignment and nuclear segmentation. This OMAP provides a spatial context for all anatomical structures and most cell types present in the ASCT+B tonsil table, v1.0 (submitted for review). OMAP-10 follows closely OMAP-1 described for human lymph nodes (<a href="https://hubmapconsortium.github.io/ccf-releases/v1.3/docs/omap/omap-1-human-lymph-node-ibex.html">https://hubmapconsortium.github.io/ccf-releases/v1.3/docs/omap/omap-1-human-lymph-node-ibex.html</a>). The initial dataset associated with OMAP-10 can be found in this dataset. All reagents were obtained from Miltenyi Biotec and have been rigorously tested through an internal quality control system to have minimal variation between lots. For this reason, lot information is not included in the table below. Analysis was performed by an accompanied software package MACSIQ View Analysis also described in the MACSima publication (<a href="https://doi.org/10.1038/s41598-022-05841-4">https://doi.org/10.1038/s41598-022-05841-4</a>). The plan was to also include the data analysis in the uploaded dataset. However mixing the original data with analyses data would lead to confusion. Therefore only the original image files are included here. This is in brief the image analysis pipeline: the software processes the raw images of the MACSima run, generates stitched images, and then allows downstream analysis including cell segmentation, cell gating, data normalization, dimension reduction plots (tSNE, UMAP), heat maps, distance analyses and cluster analyses, all of which are interactively linked together. The MACSima system is continuously evolving, and this is the first OMAP dataset generated by using the MACSima system (Instrument, Reagents and Software).</p> <p>The images enclosed are in OME-tif format (16 bit depth). The optical resolution is 0.17 micron/pixel. The imaged area size is 1.6 mm x 1.3 mm. This Data is currently under review by the OMAP community and changes are still possible in the follow up version. The image contains stichted images of 9 fields of view. The complete runtime on the MACSima for this image dataset was about 12 hours on the instrument. The OMAP description also links to the ASCT+B table for the palatine tonsil.</p> <p><strong>Anatomical Structures, Cell Types, plus Biomarkers (ASCT+B) table for Palatine Tonsil v1.0</strong></p> <p><strong>Description</strong></p> <p><a href="https://hubmapconsortium.github.io/ccf/pages/ccf-anatomical-structures.html">Anatomical Structures, Cell Types, plus Biomarkers (ASCT+B) tables</a> aim to capture the nested <em>part of</em> structure of anatomical human body parts, the typology of cells, and biomarkers used to identify cell types. The tables are authored and reviewed by an international team of experts. The Palatine Tonsil ASCT+B table is derived from published literature, public datasets, and unpublished studies from table authors. The Palatine Tonsil is part of the tonsiluar ring of Waldeyer network. In comparison to other Tonsils the Palatine Tonsil has an enlarged lymphoid tissue.</p> <p>The gene biomarkers are primarily derived from a preprint on an Atlas of Cells of the human tonsil (<a href="https://www.biorxiv.org/content/10.1101/2022.06.24.497299v1">Ramon Massoni-Badosa et al 2022</a>). The tonsil azimuth data set can be explored <a href="https://azimuth.hubmapconsortium.org/references/human_tonsil/">here</a> .Cell phenotypes, especially for antibody-based assays like the MACSima are very complex and in its first version, only the basic cell types are listed with many more to be included in the next iteration of the ASCT+B table. The correlation between protein detection and RNA expression data at the single cell level needs to be established. In total, this table reports 13 anatomical structures, 17 cell types, and 30 biomarkers. </p> <p>The following list contains the file name and the target name of the antibody used in a given staining:</p> <p>ACTIN_REAL650/ACTA2</p> <p>Bcl2_REA872/BCL2</p> <p>CD11c_REAL235/ITGAX</p> <p>CD138_REA929/SDC1</p> <p>CD15_VIMC6/FUT4</p> <p>CD19_REAL106/CD19</p> <p>CD1c_REA694/CD1C</p> <p>CD209_REAL1087/CD209</p> <p>CD20_REA1087/MS4A1</p> <p>CD21_REA940/CR2</p> <p>CD274_PDL1/CD274</p> <p>CD279_REAL531/PDCD1</p> <p>CD27_REA499/CD27</p> <p>CD39_REA739/ENTPD1</p> <p>CD3_REAL1097/CD3E</p> <p>CD44_REA690/CD44</p> <p>CD4_REA1307/CD4</p> <p>CD68_REA1306/CD68</p> <p>CD79a_REA1142/CD79A</p> <p>CD8_REA734/CD8A</p> <p>CollagenIV_REAL1212/COL4A1</p> <p>Cytokeratin_CK36H5/KRT7,KRT8,KRT18,KRT19</p> <p>FoxP3_REA1253/FOXP3</p> <p>HLADR_REAL550/HLA-DRA</p> <p>IgD_REA740/IGHD</p> <p>IgM_REAL689/IGHM</p> <p>Ki67_REA183/MKI67</p> <p>PlasmaCell_REA908/CKAP4</p> <p>Vimentin_REA409/VIM</p>
Multiplexed Staining Dataset - OMAP 5 - Liver-Lanthanides-conjugated antibodies and C60-secondary ion mass spectrometry imaging
<p>This dataset contains images of multiplexed antibody panel on a human pediatric liver section including the nuclear marker and antibodies conjugated with lanthanides tags. The dataset is one example of serial experiments of multiplexed antibody staining and imaging. The antibody panel targets the major cell types and tissue structures in the liver tissue. Data acquisition was performed using single multiplexing imaging by C60-secondary ion mass spectrometry.</p> <p> </p>
OMAP-8: Multiplexed Antibody-Based Imaging of Placenta with Imaging Mass Cytometry (IMC), v1.0
<p>OMAP-8 was designed for Imaging Mass Cytometry (IMC) (<a href="https://pubmed.ncbi.nlm.nih.gov/24584193/">https://pubmed.ncbi.nlm.nih.gov/24584193/</a>) of formalin-fixed paraffin-embedded (FFPE) human term-placenta samples. The tissue slides were prepared with a two-step antigen retrieval process (pH 6 and pH 9, as described <a href="https://dx.doi.org/10.17504/protocols.io.bpwumpew">https://dx.doi.org/10.17504/protocols.io.bpwumpew</a>). OMAP antibodies validated by immunohistochemistry and IMC were conjugated to polymers containing metal isotopes. Conjugated antibodies were used to stain processed human term-placenta tissue simultaneously. Regions of the processed tissue were then acquired on the imaging mass cytometer (Hyperion; Standard BioTools) by laser ablation and visualized. The panel contains 26 antibodies conjugated to unique metal isotopes and iridium marks the DNA. This OMAP provides a spatial context for key placenta cell types in the <a href="https://doi.org/10.48539/HBM446.WGLG.755">ASCT+B v.1.0 table</a>. Single-cell RNA sequencing data were used to guide marker selection for multiplexed tissue imaging. For example, ASCL2, HLA-G, PD-L1, CD68 and LYVE1 allow functionally specialized cell types to be visualized and quantified in the placenta. Note that one of our core antibodies is to LYVE1 but, unlike in other tissues where it is used to mark lymphatic vasculature, here we use it to mark the macrophage of the placenta (Hofbauer cells) – there should be no lymphatics in the placenta.</p>
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
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Annotated Behaviour and Observability Dataset (ABODe)
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DANDI Archive for NWB datasets
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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.