ArticleCytometry. Part A : the journal of the International Society for Analytical Cytology2021
Semi-automated background removal limits data loss and normalizes imaging mass cytometry data.
Article in Cytometry. Part A : the journal of the International Society for Analytical Cytology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed, 44 citations in OpenAlex.
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- Spotlight on challenges and novel methods in highly multiplexed tissue imaging-based spatial proteomics.Journal of translational medicine · 2026Review
- OpenIMC: an open-source platform for analyzing single-cell and spatial proteomics by imaging mass cytometry.BMC bioinformatics · 2026Article
- OpenIMC: an open-source platform for analyzing single-cell and spatial proteomics by imaging mass cytometry.Research square · 2026Article
- Article
- Myeloid-T cell proximity is prominent in healthy pregnancies with extreme fetal-maternal HLA incompatibility.iScience · 2026Article
- Imaging Mass Cytometry-Based Immune Profiling of Human Peyer's Patches in Patients with Crohn's Disease.European journal of immunology · 2025Article
- Sensitive detection of minimal residual disease and immunotherapy targets by multi-modal bone marrow analysis in high-risk neuroblastoma - a multi-center study.Journal of experimental & clinical cancer research : CR · 2025Article
- NK cell-macrophage interactions in granulomas correlate with limited tuberculosis pathology.PLoS pathogens · 2025Article
- Integrated workflow for analysis of immune enriched spatial proteomic data with IMmuneCite.Scientific reports · 2025Article
- From surfing to diving into the tumor microenvironment through multiparametric imaging mass cytometry.Frontiers in immunology · 2025Review
- Postbiotics: a perspective on their quantification.Frontiers in nutrition · 2025Article
- Immunological differences between monophasic and biphasic synovial sarcoma with implications for immunotherapy.Cancer immunology, immunotherapy : CII · 2024Article
- PENGUIN: A rapid and efficient image preprocessing tool for multiplexed spatial proteomics.Computational and structural biotechnology journal · 2024Article
- Activated HLA-DR+CD38+ Effector Th1/17 Cells Distinguish Crohn's Disease-associated Perianal Fistulas from Cryptoglandular Fistulas.Inflammatory bowel diseases · 2024Article
- Integration of mass cytometry and mass spectrometry imaging for spatially resolved single-cell metabolic profiling.Nature methods · 2024Article
- Enhanced immune responses are accompanied by increased MAGEA expression in osteosarcoma metastases.BMJ oncology · 2024Article
- A platform-independent framework for phenotyping of multiplex tissue imaging data.PLoS computational biology · 2023Article
- IMC-Denoise: a content aware denoising pipeline to enhance Imaging Mass Cytometry.Nature communications · 2023Article
- B cell immune profiles in dysbiotic vermiform appendixes of pancreatic cancer patients.Frontiers in immunology · 2023Article
Corrections and comments
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
Abstract
Imaging mass cytometry (IMC) allows the detection of multiple antigens (approximately 40 markers) combined with spatial information, making it a unique tool for the evaluation of complex biological systems. Due to its widespread availability and retained tissue morphology, formalin-fixed, paraffin-embedded (FFPE) tissues are often a material of choice for IMC studies. However, antibody performance and signal to noise ratios can differ considerably between FFPE tissues as a consequence of variations in tissue processing, including fixation. In contrast to batch effects caused by differences in the immunodetection procedure, variations in tissue processing are difficult to control. We investigated the effect of immunodetection-related signal intensity fluctuations on IMC analysis and phenotype identification, in a cohort of 12 colorectal cancer tissues. Furthermore, we explored different normalization strategies and propose a workflow to normalize IMC data by semi-automated background removal, using publicly available tools. This workflow can be directly applied to previously acquired datasets and considerably improves the quality of IMC data, thereby supporting the analysis and comparison of multiple samples.
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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.