18 skills · sorted by relevance
Inspect and transform local DICOM medical imaging files, including metadata, image frames, and compression formats. Generate technical inventories and preview images, check installed codecs, and review pseudonymized derivatives without treating those checks as proof of de-identification.
Organize MRI, EEG, and other biomedical research data using BIDS, a shared standard for filenames, folders, and metadata. Query datasets, check compliance, convert DICOM files, and prepare metadata or processed outputs for analysis and sharing.
Python library for working with DICOM (Digital Imaging and Communications in Medicine) files. Use this skill when reading, writing, or modifying medical imaging data in DICOM format, extracting pixel data from medical images (CT, MRI, X-ray, ultrasound), anonymizing DICOM files, working with DICOM metadata and tags, converting DICOM images to other formats, handling compressed DICOM data, or processing medical imaging datasets. Applies to tasks involving medical image analysis, PACS systems, radiology workflows, and healthcare imaging applications.
The English summary is being prepared. Showing the original description.
Read, write, and manipulate medical imaging data (DICOM, NIfTI, NRRD) in MATLAB. Covers Image Processing Toolbox functions (dicomreadVolume, niftiread, dicomContours, dicomanon) and Medical Imaging Toolbox enhanced APIs (medicalVolume, medicalImage, medicalref3d, extractSlice, updateOrientation). Use when reading medical files, listing DICOM series, extracting spatial referencing, changing orientation, working with RT structures, or anonymizing DICOM data. Some features require Medical Imaging Toolbox — see skill body and references for details.
The English summary is being prepared. Showing the original description.
Find and download public cancer imaging data from NCI Imaging Data Commons. Select CT, MR, PET, or pathology datasets using metadata, view images in a browser, and check licenses and citations before using the data.
Query and download NCI Imaging Data Commons (IDC) cancer radiology and pathology datasets via the idc-index Python client. No authentication required: the parquet index ships inside the pip wheel, SQL runs locally via DuckDB, and DICOM downloads stream from public S3/GCS buckets through s5cmd. Use sql_query() for DuckDB cohort selection, get_collections/get_patients/get_dicom_studies/get_dicom_series for hierarchical browsing, download_from_selection() for downloads, and get_viewer_URL() for OHIF/Slim links. Use pydicom-medical-imaging for local DICOM reading; histolab for whole-slide pathology preprocessing.
The English summary is being prepared. Showing the original description.
Used for converting one CT DICOM series folder to a HU NIfTI volume with affine evidence. Not for multi-frame DICOM or clinical use.
The English summary is being prepared. Showing the original description.
Pure Python DICOM for medical imaging (CT, MRI, X-ray, ultrasound). Read/write DICOM, pixels as NumPy, edit tags, windowing (VOI LUT), PHI anonymization, build DICOM, series→3D volumes. Use histolab for WSI pathology; nibabel for NIfTI.
The English summary is being prepared. Showing the original description.
Used for extracting selected metadata from one DICOM file and flagging standard-tag PHI presence. Not for anonymization or clinical use.
The English summary is being prepared. Showing the original description.
Used for header-only preflight of one DICOM series folder before conversion or inference. Not for de-identification or clinical clearance.
The English summary is being prepared. Showing the original description.
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.
The English summary is being prepared. Showing the original description.
Support authorized external security reconnaissance, the discovery of exposed systems and information. The skill provides search queries, probe references, secret detection patterns, and scoring guidance to help identify assets and organize findings with evidence and confidence levels.
Computational pathology toolkit for analyzing whole-slide images (WSI) and multiparametric imaging data. Use this skill when working with histopathology slides, H&E stained images, multiplex immunofluorescence (CODEX, Vectra), spatial proteomics, nucleus detection/segmentation, tissue graph construction, or training ML models on pathology data. Supports 160+ slide formats including Aperio SVS, NDPI, DICOM, OME-TIFF for digital pathology workflows.
The English summary is being prepared. Showing the original description.
Load this first for any task involving images, pictures, photos, scans, frames, volumes, or visual data — including reading, writing, filtering, enhancing, denoising, sharpening, deblurring, thresholding, segmenting, masking, detecting, finding or counting objects, removing backgrounds, measuring, comparing, registering, stitching, aligning, cropping, resizing, transforming, or analyzing. Use for image I/O (TIFF, PNG, JPEG, RAW, HDR), histograms, edge detection, color processing, morphology, geometric transforms, deep learning for images, quality assessment, and 3-D volume processing. Also triggers when users describe image problems (dark, noisy, blurry, low contrast, uneven lighting, hazy, color cast) or data exploration tasks (folder of images, characterize data, understand format). Handles microscopy (cells, particles) and general scientific imaging. Routes to sibling skills for medical imaging (DICOM, NIfTI), hyperspectral data, and visual inspection.
The English summary is being prepared. Showing the original description.
Expert knowledge for Azure Health Data Services development including troubleshooting, best practices, decision making, architecture & design patterns, limits & quotas, security, configuration, integrations & coding patterns, and deployment. Use when using FHIR/DICOM APIs, bulk export/import, de-identification, change feeds, or Synapse/Data Factory, and other Azure Health Data Services related development tasks. Not for Azure Health Bot (use azure-health-bot), Azure Data Factory (use azure-data-factory), Azure Synapse Analytics (use azure-synapse-analytics), Azure Machine Learning (use azure-machine-learning).
The English summary is being prepared. Showing the original description.
Use when preparing a medical-imaging dataset (DICOM/NIfTI) for modelling. Profiles spacing, orientation, intensity, label integrity, foreground fraction and target volume, gates them against the plan, then plans and audits preprocessing and augmentation for leakage.
The English summary is being prepared. Showing the original description.
Think and work like an expert Biomedical Imaging Scientist. Use when a task calls for Biomedical Imaging Scientist judgment. Reasons from contrast mechanisms, the resolution-SNR-scan-time triangle, and measurement reliability through DICOM/BIDS pipelines, QIBA profiles, phantom QC (ACR, NEMA IQ, Catphan), and blinded central reads (RECIST, RANO, PERCIST) while treating motion, partial volume effects, and cross-scanner harmonization drift as first-class failure modes.
The English summary is being prepared. Showing the original description.
Use this skill when working with Brain Imaging Data Structure (BIDS) datasets: organizing neuroscience and biomedical data (MRI, EEG, MEG, iEEG, PET, microscopy, NIRS, motion capture, EMG, MR spectroscopy, behavioral), querying BIDS layouts, validating compliance, converting DICOM to BIDS, writing metadata sidecars, or creating BIDS derivatives.
The English summary is being prepared. Showing the original description.