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peer-review-methodology
Structured peer review of manuscripts and grants. 7-stage evaluation: initial assessment, section review, statistical rigor, reproducibility, figure integrity, ethics, writing. Covers CONSORT/STROBE/PRISMA and report structure. For evidence quality see scientific-critical-thinking; scoring see scholar-evaluation.
opencv-bioimage-analysis
Computer vision for bio-image preprocessing, feature detection, real-time microscopy. Color conversion, morphology, contour/blob detection, template matching, optical flow on fluorescence/brightfield. 10-100× faster than pure Python via C++. Use scikit-image for scientific morphometry/regionprops; OpenCV for real-time, video, classical feature extraction.
trackpy-particle-tracking
Python library for single-particle tracking (SPT) in video microscopy via the Crocker-Grier algorithm. Locate particles (fluorescent spots, colloids, vesicles, cells) per frame, link into trajectories, filter short tracks, and compute MSD for diffusion analysis. 2D/3D with subpixel accuracy; reads TIF stacks, AVI, image series via pims. Use for quantitative SPT and diffusion coefficient extraction
cnvkit-copy-number
Detect somatic CNVs from WES/WGS/targeted BAMs (CNVkit v0.9.x). Bin coverage in target/antitarget regions, normalize vs reference, segment with CBS/HMM, call amps/dels, scatter/diagram plots, purity/ploidy, VCF/SEG export. CLI plus Python API (cnvlib). Use GATK CNV for deep WGS with population controls; use CNVkit for targeted/exome where antitarget bins matter.
simpleitk-image-registration
Register, segment, filter, resample 3D medical images (MRI, CT, microscopy) via SimpleITK Python; DICOM, NIfTI, multi-modal. Rigid/affine/deformable registration, threshold/region-growing segmentation, Gaussian/morph filtering, label stats, format conversion. Use to align volumes across timepoints/modalities, segment fluorescence, or convert DICOM→NIfTI.
cellpose-cell-segmentation
DL cell/nucleus segmentation for fluorescence and brightfield microscopy. Pre-trained models (cyto3, nuclei, tissuenet) and a generalist flow-based algorithm segment cells without retraining. Outputs label masks for morphology and tracking. Use scikit-image watershed for rule-based; Cellpose when DL generalization across staining is needed.
write-content
Use when writing a complete SEO article. Includes the full anti-AI-slop ruleset (banned vocabulary, banned phrases, banned structural patterns) and voice rules. The agent researches the SERP itself if needed — no keyword data exports required.
page-audit
Use when auditing a specific page's SEO performance, content quality, and competitive position. The agent fetches the URL, Googles the primary keyword, reads the top 3 competitors, and produces a full 7-dimension audit — no exports, no analytics access required.
topic-cluster-planning
Use when planning a topic cluster (hub + spokes) for a new content area. The agent researches the space, identifies the hub topic, maps the spokes, and produces a specific content plan with internal linking strategy.
featured-snippet-optimizer
Use when you want to win a featured snippet for a keyword you already rank for. The agent checks the current snippet format, analyzes your content, and rewrites the relevant section to match what Google wants.
keyword-deep-dive
Use when planning to rank for a specific keyword. The agent Googles it, reads the top 10, classifies intent, reads the top 3 competitor pages, and produces a 90-day ranking plan with intent, SERP analysis, and content recommendations.
improve-content
Use when rewriting or refreshing an existing page that's underperforming. The agent fetches the URL, analyzes the current content, researches the SERP, and rewrites using the full anti-AI-slop ruleset — no data exports needed.