ArticleCell genomics2023
A unified pipeline for FISH spatial transcriptomics.
Article in Cell genomics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- SCALPEL: A pipeline for processing large-scale spatial transcriptomics data.bioRxiv : the preprint server for biology · 2026Article
- GPU-accelerated, self-optimizing processing for 3D multiplexed iterative RNA-FISH experiments.bioRxiv : the preprint server for biology · 2025Article
- The emerging role of multiomics in aging research.Epigenomics · 2025Review
- Single-cell sequencing in diabetic retinopathy: progress and prospects.Journal of translational medicine · 2025Review
- Xenomake: a pipeline for processing and sorting xenograft reads from spatial transcriptomic experiments.Bioinformatics (Oxford, England) · 2024Article
- Article
- Sopa: a technology-invariant pipeline for analyses of image-based spatial omics.Nature communications · 2024Article
- Accurate single-molecule spot detection for image-based spatial transcriptomics with weakly supervised deep learning.Cell systems · 2024Article
- Spatial transcriptomics in development and disease.Molecular biomedicine · 2023Review
- MoleculeExperiment enables consistent infrastructure for molecule-resolved spatial omics data in bioconductor.Bioinformatics (Oxford, England) · 2023Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
High-throughput spatial transcriptomics has emerged as a powerful tool for investigating the spatial distribution of mRNA expression and its effects on cellular function. There is a lack of standardized tools for analyzing spatial transcriptomics data, leading many groups to write their own in-house tools that are often poorly documented and not generalizable. To address this, we have expanded and improved the starfish library and used those tools to create PIPEFISH, a semi-automated and generalizable pipeline that performs transcript annotation for fluorescence
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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.