103 件 ・ 関連度順
概要と使いどころ
Battle-tested PyTorch training recipes for all domains — LLMs, vision, diffusion, medical imaging, protein/drug discovery, spatial omics, genomics. Covers training loops, optimizer selection (AdamW, Muon), LR scheduling, mixed precision, debugging, and systematic experimentation. Use when training or fine-tuning neural networks, debugging loss spikes or OOM, choosing architectures, or optimizing GPU throughput.
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Compare cell-type composition and spatial features across conditions in IMC/MIBI cohorts with the patient as the experimental unit, covering pseudoreplication, per-patient aggregation, mixed models, compositional (Dirichlet/scCODA) differential abundance, diffcyt, per-image-to-patient spatial differential testing (SpaceANOVA), batch covariates, and FDR. Use when testing whether a cell type or spatial niche differs between groups, avoiding cell-level pseudoreplication, choosing a differential-abundance method, or correctly powering an IMC cohort comparison.
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Tracks ctDNA across serial liquid-biopsy timepoints for molecular residual disease (MRD) and treatment-response monitoring, treating MRD as a binary integrated detection call across the patient's full variant set (with a defined LoD95 and per-sample specificity) rather than a per-timepoint VAF threshold, and handling undetectable samples as left-censored at the per-sample limit of detection rather than true zeros. Covers tumor-informed bespoke vs tumor-naive design, landmark vs surveillance sampling, molecular-response definitions and their non-standardization, censoring-aware clearance kinetics, and the multiple-testing structure of repeated surveillance. Use when monitoring ctDNA during therapy, calling molecular relapse before imaging, or estimating clearance half-life from serial samples.
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Analyze spatial cell-cell interactions, neighborhoods, and niches in IMC/MIBI data with squidpy and imcRtools, covering neighborhood-enrichment permutation nulls, the abundance-vs-density confound, inhomogeneous Ripley's K, cellular-neighborhood discovery, graph-construction (contact vs proximity), and edge effects. Use when testing whether cell types co-locate, choosing a spatial null, building a neighbor graph, discovering tissue niches, or deciding whether a spatial pattern is real or a density/segmentation artifact.
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Quality control for IMC/MIBI data across pixel, channel, image, slide, and batch levels, covering Poisson-count SNR (cell-level Gaussian-mixture and empty-channel comparison), spillover-matrix QC (the three physical sources), drift and the missing EQ-bead analog, acquisition artifacts, and sample-of-origin batch effects. Use when deciding whether to keep or drop a channel, ROI, or slide, distinguishing a dim antibody from a failed one, reading a spillover matrix, or diagnosing batch-driven clustering before analysis.
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Interactive cell annotation and image QC for IMC/MIBI using napari, napari-imc, Mantis Viewer, and cytomapper, covering the pixels-to-cell-table bridge, overlaying masks to catch segmentation/spillover artifacts, inter-annotator variability as the accuracy ceiling, contrast-as-threshold, and building class-balanced ground-truth label sets. Use when manually labeling cells, generating training data for a classifier, QC-ing segmentation on the image, confirming clusters are spatially real, or choosing an annotation viewer.
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Segment single cells from multiplexed IMC/MIBI tissue images using Mesmer/DeepCell, Cellpose, or ilastik+CellProfiler, covering whole-cell vs nuclear segmentation, the summed-membrane-channel decision, nuclear-expansion bias, lateral spillover, resolution-floor parameters, and downstream-proxy evaluation. Use when delineating cells after preprocessing, choosing a segmentation model, building a cell mask for quantification, diagnosing impossible double-positive populations, or troubleshooting over/under-segmentation.
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lisaClust provides a series of functions to identify and visualise regions of tissue where spatial associations between cell-types is similar. This package can be used to provide a high-level summary of cell-type colocalization in multiplexed imaging data that has been segmented at a single-cell resolution.
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WSI processing for digital pathology. Tissue detection, tile extraction (random, grid, score-based), filter pipelines for H&E/IHC. For dataset prep, tile-based DL, slide QC. Use pathml for multiplexed imaging.
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Renamed to /model-assessment in v6 (removed in v7).
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Use when a trained medical-imaging model needs its documentation. Fills a Model Card and a Datasheet for its dataset from facts you supply, adds a METRIC-informed data-quality pass and gates that no required section is empty. Never invents numbers, provenance or licence.
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Use when validating or evaluating a trained medical-imaging model. Audits split leakage and validation design, computes task-correct held-out metrics (Dice + HD95, AUROC + AUPRC, FROC, calibration), and covers uncertainty/OOD and Grad-CAM explainability, each with a gate.
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Use when designing or auditing how an LLM or multimodal LLM is evaluated on a clinical task (report generation, VQA, text extraction). Covers reference standard, clinical-efficacy metrics beyond BLEU/ROUGE, hallucination, contamination and prompt sensitivity. Imaging models are /model-assessment.
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Use when choosing the model for a medical-imaging study. Picks a paper-grounded architecture family (CNN/ViT, U-Net/nnU-Net, detection, SAM/foundation, GNN), then vets the concrete repo or checkpoint for licence, version pin, weight provenance and benchmark overlap.
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Use when you need a runnable PyTorch training repo for a medical-imaging task (segmentation, classification, detection, synthesis, self-supervised, or fine-tuning a pretrained backbone). Emits a patient-level seed-locked split, train/evaluate scripts, config and a Methods stub.
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Route DLTK 0.2.1 medical-imaging workflows across legacy TensorFlow 1.x data, models, Estimators, and deployment utilities.
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Guides Attention-Gated Networks PyTorch medical imaging workflows for ultrasound classification, attention-gated U-Net segmentation, data layout, CUDA setup, and visualization helpers.
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Apply the bioengineering, mechanobiology, and lymphatic transport reasoning of J. Brandon Dixon, professor of mechanical and biomedical engineering at Georgia Institute of Technology. Reach for this skill whenever analyzing lymphatic biomechanics, active vessel contractility versus passive drainage, peristaltic fluid transport, microfluidic organ-on-a-chip design, preclinical lymphedema models, non-invasive functional imaging, targeted nanomedicine delivery, or automated disease staging. Use this skill to critique bioengineering assumptions, guide quantitative protocol design, evaluate biomechanical pump failure, and formulate interdisciplinary biomedical solutions.
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Think and work like an expert Geological Oceanographer. Use when a task calls for Geological Oceanographer judgment. Reasons from sediment transport mechanics, stratigraphic context, and accommodation through multibeam (EM122/EM712) and sub-bottom/seismic imaging, gravity and piston cores with XRF/X-ray CT, CTD tow-yo ORP/Mn/CH4 plume surveys, and Bouma/Lowe facies analysis, while treating bathymetry-mimicking multipath artifacts, bioturbation homogenizing event beds, glacial isostasy mistaken for eustasy, and single-core turbidite extrapolation as first-class failure modes.
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Think and work like an expert Developmental Biologist. Use when a task calls for Developmental Biologist judgment. Reasons from stage, positional information, gene regulatory networks, and tissue mechanics through morphology-based staging (Carnegie/HH/Theiler/NF/hpf), French-flag morphogen logic, light-sheet 4D imaging, lineage tracing, and ARRIVE/MDAR/REMBI reporting while treating developmental delay, CRISPR F0 mosaicism, morpholino p53 toxicity, and conflated fate-versus-lineage claims as first-class failure modes.
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Think and work like an expert Biological Oceanographer. Use when a task calls for Biological Oceanographer judgment. Reasons from light-nutrient-grazing coupling, the microbial loop, and size-structured export through CTD/MOCNESS sampling, 14C and O2/Ar production with 234Th export flux, imaging and flow cytometry enumeration, and SILVA/PR2 metabarcoding while treating spatial patchiness, diel-migration tow aliasing, CDOM-biased chlorophyll algorithms, and eDNA-detection-as-abundance as first-class failure modes.
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Think and work like an expert Cell Biologist. Use when a task calls for Cell Biologist judgment. Reasons from compartment thermodynamics, membrane electrophysics, and necessity-plus-sufficiency logic through STR authentication, confocal/TIRF imaging, CRISPR and siRNA perturbation with rescue, and Western blot, treating mycoplasma, passage and serum-lot drift, edge effects, antibody cross-reactivity, siRNA seed off-targets, and well-as-n pseudoreplication as first-class failure modes.
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Think and work like an expert Atomic, Molecular & Optical Physicist. Use when a task calls for Atomic, Molecular & Optical Physicist judgment. Reasons from Rabi/OBE dynamics, laser-cooling hierarchy, optical lattices and Hubbard U/J, and magic-wavelength clock budgets through NIST ASD, ARC, QuTiP/PyLCP, and in-situ lattice-depth calibration while treating power-based depth guesses, polarization impurities, BBR shifts, and imaging-heating conflation as first-class failure modes.
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Cell segmentation from multiplexed tissue images. Covers deep learning (Cellpose, Mesmer) and classical approaches for nuclear and whole-cell segmentation. Use when extracting single-cell data from IMC or MIBI images after preprocessing.
日本語の概要は準備中です。原文の説明を表示しています。