ArticleScientific data2019
Highly multiplexed immunofluorescence images and single-cell data of immune markers in tonsil and lung cancer.
Article in Scientific data, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed, 57 citations in OpenAlex.
- MIAAIM: Multi-omics image integration with dimensional reduction for tissue state mapping.PLoS computational biology · 2026Article
- Distinct Tumor-Immune Ecologies in Patients with Lung Cancer Predict Progression and Define a Clinical Biomarker of Therapy Response.Cancer research · 2026Article
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- Flexible and robust cell type annotation for highly multiplexed tissue images.bioRxiv : the preprint server for biology · 2024Article
- Spatial Morphoproteomic Features Predict Uniqueness of Immune Microarchitectures and Responses in Lymphoid Follicles.bioRxiv : the preprint server for biology · 2024Article
- Single-cell and spatial analyses reveal a tradeoff between murine mammary proliferation and lineage programs associated with endocrine cues.Cell reports · 2023Article
- DNA-barcoded signal amplification for imaging mass cytometry enables sensitive and highly multiplexed tissue imaging.Nature methods · 2023Article
- IMC-Denoise: a content aware denoising pipeline to enhance Imaging Mass Cytometry.Nature communications · 2023Article
- Topological-Preserving Membrane Skeleton Segmentation in Multiplex Immunofluorescence Imaging.Proceedings of SPIE--the International Society for Optical Engineering · 2023Article
- Statistical Analysis of Multiplex Immunofluorescence and Immunohistochemistry Imaging Data.Methods in molecular biology (Clifton, N.J.) · 2023Review
- MxIF Q-score: Biology-Informed Quality Assurance for Multiplexed Immunofluorescence Imaging.Medical optical imaging and virtual microscopy image analysis : first International Workshop, MOVI 2022, held in conjunction with MICCAI 2022, Singapore, September 18, 2022, Proceedings. MOVI (Workshop) (1st : 2022 : Singapore) · 2022Article
- Mistic: An open-source multiplexed image t-SNE viewer.Patterns (New York, N.Y.) · 2022Article
- A human breast atlas integrating single-cell proteomics and transcriptomics.Developmental cell · 2022Article
- Narrative online guides for the interpretation of digital-pathology images and tissue-atlas data.Nature biomedical engineering · 2022Review
- Whole-cell segmentation of tissue images with human-level performance using large-scale data annotation and deep learning.Nature biotechnology · 2022Article
- Spatial mapping of protein composition and tissue organization: a primer for multiplexed antibody-based imaging.Nature methods · 2022Review
- A community-based approach to image analysis of cells, tissues and tumors.Computerized medical imaging and graphics : the official journal of the Computerized Medical Imaging Society · 2022Review
- Reduction of autofluorescence in whole adult worms of Schistosoma japonicum for immunofluorescence assay.Parasites & vectors · 2021Article
- Artificial Intelligence and Cellular Segmentation in Tissue Microscopy Images.The American journal of pathology · 2021Review
Corrections and comments
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Authors and funding
12 authors at 3 institutions in 1 country.
Funding
Abstract
In this data descriptor, we document a dataset of multiplexed immunofluorescence images and derived single-cell measurements of immune lineage and other markers in formaldehyde-fixed and paraffin-embedded (FFPE) human tonsil and lung cancer tissue. We used tissue cyclic immunofluorescence (t-CyCIF) to generate fluorescence images which we artifact corrected using the BaSiC tool, stitched and registered using the ASHLAR algorithm, and segmented using ilastik software and MATLAB. We extracted single-cell features from these images using HistoCAT software. The resulting dataset can be visualized using image browsers and analyzed using high-dimensional, single-cell methods. This dataset is a valuable resource for biological discovery of the immune system in normal and diseased states as well as for the development of multiplexed image analysis and viewing tools.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.