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33 results for “Imaging Mass Cytometry”
DNA-barcoded signal amplification for imaging mass cytometry enables sensitive and highly multiplexed tissue imaging
<p>Tiff images, single cell data, and cell masks for the publication "DNA-barcoded signal amplification for imaging mass cytometry enables sensitive and highly multiplexed tissue imaging". The code used to produce the results of this study is available at https://github.com/BodenmillerGroup/SABER-IMC_publication</p>
Imaging mass cytometry data from IDH wildtype glioblastomas
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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>
Characterization of the tumor-immune microenvironment in hepatocellular carcinoma patients undergoing immune checkpoint inhibitor therapy by highly multiplexed imaging mass cytometry
<p>Imaging mass cytometry data of 42 HCC patients that received immune checkpoint inhibtor therapy after tumor biopsy or resection. </p> <ul> <li>ICI_img_normalized: Preprocessed and normalized multistack .tiff images. Each stack represents one channel. Channel annotations are stored in the ICICohort_panel.csv file.</li> <li>ICI_cellmasks: Masks identifying individual cells on the images.</li> <li>ICI_stromamasks: Masks identifying stromal and parenchymal regions on the image.</li> <li>ICICohort_panel.csv: table containing channel information (metal tag and marker).</li> </ul> <p>Patient etadata may be found in the supplementary table 3 of DOI <a href="https://doi.org/10.1136/gutjnl-2024-332837" target="_blank" rel="noopener noreferrer">10.1136/gutjnl-2024-332837</a>.</p>
Imaging mass cytometry data: Diffuse large B-cell lymphoma lymph node section
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Imaging mass cytometry data: Head and neck squamous cell carcinoma tissue section
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Imaging Mass Cytometry: p161
<p>Imaging Mass Cytometry: p161</p> <p>Raw acquisitions for the paper:</p> <p><strong>A quantitative analysis of the interplay of environment, neighborhood, and cell state in 3D spheroids</strong></p> <p> Vito RT Zanotelli<br> Matthias Leutenegger<br> Xiao‐Kang Lun<br> Fanny Georgi<br> Natalie de Souza<br> Bernd Bodenmiller</p> <p><em>Mol Syst Biol. (2020) 16: e9798</em><br> <a href="https://doi.org/10.15252/msb.20209798">https://doi.org/10.15252/msb.20209798</a></p> <p><em>Please cite this article if you re-use any of the data or code.</em></p>
Results of IMC-Denoise: a content aware pipeline to enhance Imaging Mass Cytometry
<ul> <li>Generated training sets: <ul> <li>training_set_supp_table6.zip</li> <li>training_set_supp_table7.zip</li> <li>training_set_supp_table8.zip</li> <li>training_set_supp_table9.zip</li> <li>training_set_supp_table10.zip</li> <li>training_set_supp_table11.zip</li> </ul> </li> <li>Trained weights of experimental data: <ul> <li>training_result_supp_table7.zip</li> <li>training_result_supp_table8.zip</li> <li>training_result_supp_table9.zip</li> <li>training_result_supp_table10.zip</li> <li>training_result_supp_table11.zip</li> </ul> </li> <li>Simulation results: <ul> <li>Simulation_results.zip</li> </ul> </li> <li>Experimental results: <ul> <li>Human_bone_marrow_IMC_denoising_results.zip</li> <li>Human_breast_cancer_IMC_denoising_results.zip</li> <li>Human_pancreatic_cancer_IMC_denoising_results.zip</li> <li>MIBI_denoising_results.zip</li> </ul> </li> <li>Ilastik-processed or manual-labeled results: <ul> <li>DIMR_Ilastik_results.zip</li> <li>background_removal_results.zip</li> <li>manual_annotated_public_datasets.zip</li> </ul> </li> <li>Extracted single cell data and the corresponding phenotyping results from both DIMR and DeepSNiF-based segmented cell masks: <ul> <li>Single_cell_analysis.zip</li> </ul> </li> </ul>
Searching for Predictive Biomarkers of Efficacy in Small Cell Lung Cancer Patients Treated With Chemotherapy-immunotherapy Combination Using Imaging Mass Cytometry (HYPE)
ClinicalTrials.gov study NCT06558903. IPD Sharing: YES. Countries: 1. Publications: 0.
Interleukin-18 induced chromatin accessibility coupled to proteomic analysis by mass cytometry and ion beam imaging
GEO Series GSE124297. Homo sapiens. 8 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Using Mass Cytometry and In vivo Imaging to Study Emergency Repopulation of Immune Cells in Murine Liver
GEO Series GSE81645. Mus musculus. 12 samples. Type: Other.
Immunogenomics of colorectal cancer response to immune checkpoint blockade: Imaging Mass Cytometry
<p><strong>Immunogenomics of colorectal cancer response to immune checkpoint blockade</strong></p> <p>Imaging Mass Cytometry data supporting the paper: "Immunogenomics of colorectal cancer response to immune checkpoint blockade"</p> <p>The provided data includes:</p> <ul> <li>Sample metadata: Raw_txt_mcd_files.tar.gz/Metadata.csv</li> <li>Raw ablation data in .mcd or .txt format: Raw_txt_mcd_files.tar.gz</li> <li>Thresholded and cleaned tiff images:Cleaned_Tiff_Images.tar.gz</li> <li>Tissue/tumor/stroma masks: Masks.tar.gz</li> <li>Single-cell marker expression values and centroid coordinates: Single_Cell_Data.csv</li> </ul>
Multi-omics and imaging mass cytometry characterization of human kidneys to identify pathways and phenotypes associated with kidney damage
GEO Series GSE217427. Homo sapiens. 44 samples. Type: Expression profiling by high throughput sequencing.
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OpenNeuro
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