ArticleCytometry. Part A : the journal of the International Society for Analytical Cytology2022
MIRIAM: A machine and deep learning single-cell segmentation and quantification pipeline for multi-dimensional tissue images.
Article in Cytometry. Part A : the journal of the International Society for Analytical Cytology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
22 citing papers in PubMed, 32 citations in OpenAlex.
- Spotlight on challenges and novel methods in highly multiplexed tissue imaging-based spatial proteomics.Journal of translational medicine · 2026Review
- MacNet: a mobile attention classification network combining convolutional neural network and transformer for the differentiation of cervical cancer.Quantitative imaging in medicine and surgery · 2025Article
- Consensus tissue domain detection in spatial omics data using multiplex image labeling with regional morphology (MILWRM).Communications biology · 2024Article
- Identification and multimodal characterization of a specialized epithelial cell type associated with Crohn's disease.Nature communications · 2024Article
- Recent Advancements in Subcellular Proteomics: Growing Impact of Organellar Protein Niches on the Understanding of Cell Biology.Journal of proteome research · 2024Review
- GammaGateR: semi-automated marker gating for single-cell multiplexed imaging.Bioinformatics (Oxford, England) · 2024Article
- Article
- A Specialized Epithelial Cell Type Regulating Mucosal Immunity and Driving Human Crohn's Disease.bioRxiv : the preprint server for biology · 2023Article
- GammaGateR: semi-automated marker gating for single-cell multiplexed imaging.bioRxiv : the preprint server for biology · 2023Article
- Unleashing the potential of AI for pathology: challenges and recommendations.The Journal of pathology · 2023Review
- Topological-Preserving Membrane Skeleton Segmentation in Multiplex Immunofluorescence Imaging.Proceedings of SPIE--the International Society for Optical Engineering · 2023Article
- Influence of Cell-type Ratio on Spatially Resolved Single-cell Transcriptomes using the Tangram Algorithm: Based on Implementation on Single-Cell and MxIF Data.Proceedings of SPIE--the International Society for Optical Engineering · 2023Article
- Article
- YOUPI: Your powerful and intelligent tool for segmenting cells from imaging mass cytometry data.Frontiers in immunology · 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
- MIRIAM: A machine and deep learning single-cell segmentation and quantification pipeline for multi-dimensional tissue images.Cytometry. Part A : the journal of the International Society for Analytical Cytology · 2022Article
- Quantifying and correcting slide-to-slide variation in multiplexed immunofluorescence images.Bioinformatics (Oxford, England) · 2022Article
- mxnorm: An R Package to Normalize Multiplexed Imaging Data.Journal of open source software · 2022Article
- Cancer-Associated Fibroblasts and Squamous Epithelial Cells Constitute a Unique Microenvironment in a Mouse Model of Inflammation-Induced Colon Cancer.Frontiers in oncology · 2022Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
10 authors at 2 institutions in 1 country.
Funding
Abstract
Increasingly, highly multiplexed tissue imaging methods are used to profile protein expression at the single-cell level. However, a critical limitation is the lack of robust cell segmentation tools for tissue sections. We present Multiplexed Image Resegmentation of Internal Aberrant Membranes (MIRIAM) that combines (a) a pipeline for cell segmentation and quantification that incorporates machine learning-based pixel classification to define cellular compartments, (b) a novel method for extending incomplete cell membranes, and (c) a deep learning-based cell shape descriptor. Using human colonic adenomas as an example, we show that MIRIAM is superior to widely utilized segmentation methods and provides a pipeline that is broadly applicable to different imaging platforms and tissue types.
Indexed as
Identifiers
What OpenQuestion holds
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.