ArticleCell systems2024
Accurate single-molecule spot detection for image-based spatial transcriptomics with weakly supervised deep learning.
Article in Cell systems, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- SpotMAX: A generalist framework for multidimensional automatic spot detection and quantification.Science advances · 2026Article
- Imaging-Based Spatial Transcriptomics: Data Interpretation Methods and Biomedical Applications.Biology · 2026Review
- Review
- Artificial Intelligence in Traditional Chinese Medicine: Unraveling Herbal Medicine's Mechanisms.Research (Washington, D.C.) · 2026Review
- Multiomic Detection of RNA, Protein, and Protein-Protein Proximity at Subcellular Resolution Using Automated Protease-Free RNAscope™ Workflows.Methods in molecular biology (Clifton, N.J.) · 2026Article
- AI/ML-Assisted Detection ofInternational journal of molecular sciences · 2025Article
- CellSAM: a foundation model for cell segmentation.Nature methods · 2025Article
- GPU-accelerated, self-optimizing processing for 3D multiplexed iterative RNA-FISH experiments.bioRxiv : the preprint server for biology · 2025Article
- Agentic Superoptimization of Bioimaging Analysis Workflows.... Conference on Language Modeling · 2025Article
- Automated classification of cellular expression in multiplexed imaging data with Nimbus.Nature methods · 2025Article
- TrueSpot: a robust automated tool for quantifying signal puncta in fluorescent imaging.Genome biology · 2025Article
- Spatial omics enters the microscopic realm: opportunities and challenges.Trends in genetics : TIG · 2025Review
- TrueSpot: A robust automated tool for quantifying signal puncta in fluorescent imaging.bioRxiv : the preprint server for biology · 2025Article
- Artificial intelligence in traditional Chinese medicine: advances in multi-metabolite multi-target interaction modeling.Frontiers in pharmacology · 2025Review
- Machine learning approaches for spatial omics data analysis in digital pathology: tools and applications in genitourinary oncology.Frontiers in oncology · 2024Review
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Authors and funding
11 authors.
Funding
Abstract
Image-based spatial transcriptomics methods enable transcriptome-scale gene expression measurements with spatial information but require complex, manually tuned analysis pipelines. We present Polaris, an analysis pipeline for image-based spatial transcriptomics that combines deep-learning models for cell segmentation and spot detection with a probabilistic gene decoder to quantify single-cell gene expression accurately. Polaris offers a unifying, turnkey solution for analyzing spatial transcriptomics data from multiplexed error-robust FISH (MERFISH), sequential fluorescence in situ hybridization (seqFISH), or in situ RNA sequencing (ISS) experiments. Polaris is available through the DeepCell software library (https://github.com/vanvalenlab/deepcell-spots) and https://www.deepcell.org.
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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.