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Use when working with HistoQC for digital pathology slide quality control, whole-slide image artifact screening, and cohort-level WSI QC triage. HistoQC runs configurable module pipelines on SVS and r
Use with AI
Install the MCP server or CLI to instantly fetch HistoQC documentation:
Install command
claude mcp add biocontext7 -- npx @biocontext7/mcpOr share this page: biocontext7.com/tools/histoqc
Use when preprocessing fMRI data with fMRIPrep. Covers BIDS-compliant preprocessing pipelines, fieldmap correction, ICA-AROMA denoising, confound extraction, surface and volume output spaces, FreeSurf
1 shared topic • 1 shared operation
Use when processing or analyzing Magnetic Resonance Spectroscopy (MRS) data with FSL MRS. Covers spectral fitting, basis set generation, preprocessing, quantification, and quality control of 1H-MRS an
1 shared topic • 1 shared operation
Giotto Suite — comprehensive R framework for spatial multi-omics analysis supporting 20+ spatial technologies (Visium, MERFISH, Xenium, CosMx, Slide-seq, seqFISH, CODEX, Stereo-seq). Technology-agnost
1 shared topic • 1 shared operation
Use when assessing MRI image quality, extracting Image Quality Metrics (IQMs), running quality control on BIDS neuroimaging datasets, or generating QC reports for T1w, T2w, or BOLD fMRI data. Covers M
1 shared topic • 1 shared operation
Orfeo ToolBox (OTB) is an open-source library for remote sensing image processing. It provides a wide range of state-of-the-art algorithms for high-resolution optical, multispectral, and radar images.
1 shared topic