{"slug":"jaechang-hits-opencv-bioimage-analysis","name":"opencv-bioimage-analysis","description":"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.","long_description":"---\nname: \"opencv-bioimage-analysis\"\ndescription: \"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.\"\nlicense: \"Apache-2.0\"\n---\n\n# OpenCV — Bio-image Computer Vision\n\n## Overview\n\nOpenCV (cv2) provides optimized C++-backed image processing routines for preprocessing, segmentation, feature extraction, and video analysis of biological images. In life sciences, OpenCV is used for fluorescence image enhancement (background subtraction, CLAHE), morphological segmentation (watershed, contour detection), brightfield cell detection, and real-time microscopy stream processing. Unlike scikit-image (which emphasizes scientific measurement), OpenCV prioritizes computational speed and video support — making it ideal for preprocessing pipelines and real-time imaging applications.\n\n## When to Use\n\n- Preprocessing fluorescence or brightfield images: background subtraction, CLAHE, Gaussian/median blur\n- Detecting cell contours, blobs, or edges without deep learning (classical methods)\n- Processing video streams from live-cell imaging microscopes in real-time\n- Template matching for finding repeated structures (organelles, crystals, patterns)\n- Applying morphological operations (erosion, dilation, opening, closing) for mask refinement\n- Computing optical flow between video frames for cell tracking\n- Use **scikit-image** instead for scientific morphometry, regionprops, and scientific image I/O (TIFF metadata)\n- Use **Cellpose** or **StarDist** instead for deep-learning cell segmentation on fluorescence images\n\n## Prerequisites\n\n- **Python packages**: `opencv-python`, `numpy`, `matplotlib`\n- **Optional**: `opencv-contrib-python` for extra modules (SIFT, SURF, optical flow)\n\n```bash\n# Install OpenCV\npip install opencv-python\n\n# Install with extra contributed modules (SIFT, SURF, etc.)\npip install opencv-contrib-python\n\n# Verify\npython -c \"import cv2; print(cv2.__version__)\"\n# 4.10.0\n```\n\n## Quick Start\n\n```python\nimport cv2\nimport numpy as np\n\n# Read and display image info\nimg = cv2.imread(\"cells.tif\", cv2.IMREAD_GRAYSCALE)\nprint(f\"Shape: {img.shape}, dtype: {img.dtype}\")\nprint(f\"Min: {img.min()}, Max: {img.max()}\")\n\n# Apply Gaussian blur and threshold\nblurred = cv2.GaussianBlur(img, (5, 5), 0)\n_, binary = cv2.threshold(blurred, 0, 255, cv2.THRESH_BINARY + cv2.THRESH_OTSU)\nprint(f\"Cells detected (rough): {np.sum(binary > 0)} foreground pixels\")\n```\n\n## Core API\n\n### Module 1: Image I/O and Color Space Conversion\n\nRead, write, and convert images between color spaces.\n\n```python\nimport cv2\nimport numpy as np\n\n# Read image (GRAYSCALE, COLOR, or UNCHANGED for 16-bit)\nimg_gray  = cv2.imread(\"cells.tif\", cv2.IMREAD_GRAYSCALE)   # uint8\nimg_color = cv2.imread(\"rgb.tif\", cv2.IMREAD_COLOR)         # BGR order!\nimg_16bit = cv2.imread(\"16bit.tif\", cv2.IMREAD_UNCHANGED)   # uint16\n\nprint(f\"Grayscale shape: {img_gray.shape}, dtype: {img_gray.dtype}\")\nprint(f\"Color shape:     {img_color.shape}\")\n\n# Color space conversions\nimg_rgb  = cv2.cvtColor(img_color, cv2.COLOR_BGR2RGB)   # BGR → RGB\nimg_hsv  = cv2.cvtColor(img_color, cv2.COLOR_BGR2HSV)   # BGR → HSV\nimg_gray2 = cv2.cvtColor(img_color, cv2.COLOR_BGR2GRAY) # BGR → gray\n\n# Write image\ncv2.imwrite(\"output.png\", img_gray)\ncv2.imwrite(\"output_16bit.tif\", img_16bit)\nprint(\"Images written.\")\n```\n\n### Module 2: Filtering and Enhancement\n\nApply filters and contrast enhancement for image preprocessing.\n\n```python\nimport cv2\nimport numpy as np\n\nimg = cv2.imread(\"cells.tif\", cv2.IMREAD_GRAYSCALE)\n\n# Gaussian blur (noise reduction)\nblurred = cv2.GaussianBlur(img, (7, 7), sigmaX=1.5)\n\n# Median blur (salt-and-pepper noise)\nmedian = cv2.medianBlur(img, 5)\n\n# CLAHE: Contrast Limited Adaptive Histogram Equalization (for microscopy)\nclahe = cv2.createCLAHE(clipLimit=2.0, tileGridSize=(8, 8))\nclahe_img = clahe.apply(img)\n\n# Top-hat filter for bright spots on dark background\nkernel = cv2.getStructuringElement(cv2.MORPH_ELLIPSE, (15, 15))\ntophat = cv2.morphologyEx(img, cv2.MORPH_TOPHAT, kernel)\n\nprint(f\"CLAHE range: [{clahe_img.min()}, {clahe_img.max()}]\")\ncv2.imwrite(\"clahe_enhanced.tif\", clahe_img)\n```\n\n### Module 3: Thresholding and Binary Segmentation\n\nConvert grayscale images to binary masks using various thresholding methods.\n\n```python\nimport cv2\nimport numpy as np\n\nimg = cv2.imread(\"nuclei.tif\", cv2.IMREAD_GRAYSCALE)\n\n# Otsu's thresholding (automatic threshold selection)\nthresh_val, otsu_mask = cv2.threshold(img, 0, 255,\n                                      cv2.THRESH_BINARY + cv2.THRESH_OTSU)\nprint(f\"Otsu threshold: {thresh_val:.0f}\")\n\n# Adaptive thresholding (handles uneven illumination)\nadaptive = cv2.adaptiveThreshold(\n    img, 255,\n    cv2.ADAPTIVE_THRESH_GAUSSIAN_C,\n    cv2.THRESH_BINARY,\n    blockSize=11,     # neighborhood size (odd)\n    C=2,              # constant subtracted from mean\n)\n\n# For 16-bit images: normalize first\nimg_16 = cv2.imread(\"16bit_nuclei.tif\", cv2.IMREAD_UNCHANGED)\nimg_8 = cv2.normalize(img_16, None, 0, 255, cv2.NORM_MINMAX, dtype=cv2.CV_8U)\n_, mask_16 = cv2.threshold(img_8, 0, 255, cv2.THRESH_BINARY + cv2.THRESH_OTSU)\n\nprint(f\"Otsu mask foreground: {mask_16.sum() / 255} pixels\")\n```\n\n### Module 4: Contour Detection and Measurement\n\nFind and measure cell contours from binary masks.\n\n```python\nimport cv2\nimport numpy as np\nimport pandas as pd\n\nimg = cv2.imread(\"cells.tif\", cv2.IMREAD_GRAYSCALE)\nblurred = cv2.GaussianBlur(img, (5, 5), 0)\n_, binary = cv2.threshold(blurred, 0, 255, cv2.THRESH_BINARY + cv2.THRESH_OTSU)\n\n# Remove small objects with morphological opening\nkernel = np.ones((3, 3), np.uint8)\ncleaned = cv2.morphologyEx(binary, cv2.MORPH_OPEN, kernel, iterations=2)\n\n# Find contours\ncontours, hierarchy = cv2.findContours(cleaned, cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_SIMPLE)\nprint(f\"Objects detected: {len(contours)}\")\n\n# Measure each contour\nrecords = []\nfor i, cnt in enumerate(contours):\n    area = cv2.contourArea(cnt)\n    if area < 50: continue  # skip tiny objects\n    perimeter = cv2.arcLength(cnt, True)\n    x, y, w, h = cv2.boundingRect(cnt)\n    (cx, cy), radius = cv2.minEnclosingCircle(cnt)\n    records.append({\"cell_id\": i, \"area\": area, \"perimeter\": perimeter,\n                     \"x\": x, \"y\": y, \"w\": w, \"h\": h, \"radius\": radius})\n\ndf = pd.DataFrame(records)\nprint(f\"Cells > 50 px²: {len(df)}\")\nprint(df[[\"area\", \"perimeter\", \"radius\"]].describe())\n```\n\n### Module 5: Morphological Operations for Mask Refinement\n\nRefine segmentation masks with morphological operations.\n\n```python\nimport cv2\nimport numpy as np\n\n# Load binary mask (from thresholding or Cellpose)\nmask = cv2.imread(\"rough_mask.png\", cv2.IMREAD_GRAYSCALE)\n_, mask = cv2.threshold(mask, 127, 255, cv2.THRESH_BINARY)\n\n# Structural elements\nellipse = cv2.getStructuringElement(cv2.MORPH_ELLIPSE, (7, 7))\nrect    = cv2.getStructuringElement(cv2.MORPH_RECT, (5, 5))\n\n# Opening: remove small bright noise\nopened = cv2.morphologyEx(mask, cv2.MORPH_OPEN, ellipse, iterations=1)\n\n# Closing: fill small holes inside cells\nclosed = cv2.morphologyEx(opened, cv2.MORPH_CLOSE, ellipse, iterations=2)\n\n# Dilation: expand cell boundaries slightly\ndilated = cv2.dilate(closed, ellipse, iterations=1)\n\n# Distance transform for watershed seed generation\ndist = cv2.distanceTransform(closed, cv2.DIST_L2, 5)\n_, seeds = cv2.threshold(dist, 0.5 * dist.max(), 255, 0)\nseeds = seeds.astype(np.uint8)\nprint(f\"Potential cell centers: {cv2.connectedComponents(seeds)[0] - 1}\")\n```\n\n### Module 6: Video Processing for Live-Cell Imaging\n\nProcess video streams from time-lapse microscopy.\n\n```python\nimport cv2\nimport numpy as np\n\n# Process a time-lapse video file\ncap = cv2.VideoCapture(\"timelapse.avi\")\nfps = cap.get(cv2.CAP_PROP_FPS)\nn_frames = int(cap.get(cv2.CAP_PROP_FRAME_COUNT))\nprint(f\"Video: {n_frames} frames at {fps} FPS\")\n\n# Background subtraction (remove static background)\nbg_subtractor = cv2.createBackgroundSubtractorMOG2(\n    history=50, varThreshold=25, detectShadows=False\n)\n\nframe_counts = []\nframe_idx = 0\nwhile cap.isOpened():\n    ret, frame = cap.read()\n    if not ret: break\n    \n    gray = cv2.cvtColor(frame, cv2.COLOR_BGR2GRAY)\n    fg_mask = bg_subtractor.apply(gray)\n    \n    # Count moving objects in this frame\n    contours, _ = cv2.findContours(fg_mask, cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_SIMPLE)\n    moving = [c for c in contours if cv2.contourArea(c) > 100]\n    frame_counts.append(len(moving))\n    frame_idx += 1\n\ncap.release()\nprint(f\"Processed {frame_idx} frames. Mean moving objects: {np.mean(frame_counts):.1f}\")\n```\n\n## Key Parameters\n\n| Parameter | Module | Default | Effect |\n|-----------|--------|---------|--------|\n| `sigmaX` | `GaussianBlur` | auto from ksize | Gaussian standard deviation; larger = more smoothing |\n| `clipLimit` | `createCLAHE` | `40.0` | Maximum contrast amplification; 2.0–4.0 for microscopy |\n| `tileGridSize` | `createCLAHE` | `(8,8)` | Tile size for local histogram equalization |\n| `blockSize` | `adaptiveThreshold` | required | Neighborhood size for adaptive threshold (must be odd, ≥ 3) |\n| `C` | `adaptiveThreshold` | required | Constant subtracted from mean; positive to subtract |\n| `iterations` | `morphologyEx` | `1` | Number of erosion/dilation cycles; higher = stronger effect |\n| `history` | `BackgroundSubtractorMOG2` | `500` | Frames to model background; lower = faster adaptation |\n| `varThreshold` | `BackgroundSubtractorMOG2` | `16` | Pixel variance threshold; higher = less sensitive |\n| `minArea` | contour filter | — | Minimum `cv2.contourArea(cnt)` to keep; filter noise |\n| `cv2.IMREAD_UNCHANGED` | `imread` | — | Preserve bit-depth (16-bit, 32-bit); required for scientific images |\n\n## Common Workflows\n\n### Workflow 1: Fluorescence Nucleus Detection Pipeline\n\n```python\nimport cv2\nimport numpy as np\nimport pandas as pd\n\ndef detect_nuclei(image_path: str, min_area: int = 200) -> pd.DataFrame:\n    \"\"\"Detect DAPI-stained nuclei from a fluorescence image.\"\"\"\n    img = cv2.imread(image_path, cv2.IMREAD_UNCHANGED)\n    \n    # Normalize 16-bit to 8-bit\n    if img.dtype == np.uint16:\n        img = cv2.normalize(img, None, 0, 255, cv2.NORM_MINMAX, dtype=cv2.CV_8U)\n    \n    # Preprocess: CLAHE → Gaussian blur\n    clahe = cv2.createCLAHE(clipLimit=2.0, tileGridSize=(8, 8))\n    enhanced = clahe.apply(img)\n    blurred = cv2.GaussianBlur(enhanced, (5, 5), 1.5)\n    \n    # Segment: Otsu threshold → morphological opening\n    _, binary = cv2.threshold(blurred, 0, 255, cv2.THRESH_BINARY + cv2.THRESH_OTSU)\n    kernel = cv2.getStructuringElement(cv2.MORPH_ELLIPSE, (5, 5))\n    cleaned = cv2.morphologyEx(binary, cv2.MORPH_OPEN, kernel, iterations=1)\n    \n    # Find and measure contours\n    contours, _ = cv2.findContours(cleaned, cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_SIMPLE)\n    records = []\n    for cnt in contours:\n        area = cv2.contourArea(cnt)\n        if area < min_area: continue\n        M = cv2.moments(cnt)\n        if M[\"m00\"] == 0: continue\n        cx = int(M[\"m10\"] / M[\"m00\"])\n        cy = int(M[\"m01\"] / M[\"m00\"])\n        records.append({\"area\": area, \"cx\": cx, \"cy\": cy,\n                         \"perimeter\": cv2.arcLength(cnt, True)})\n    \n    return pd.DataFrame(records)\n\ndf = detect_nuclei(\"dapi.tif\", min_area=300)\nprint(f\"Nuclei detected: {len(df)}\")\nprint(df.describe())\n```\n\n### Workflow 2: Batch Process Image Directory\n\n```python\nimport cv2\nimport numpy as np\nimport pandas as pd\nfrom pathlib import Path\n\ndef process_image(path: str) -> dict:\n    img = cv2.imread(path, cv2.IMREAD_GRAYSCALE)\n    if img is None:\n        return {}\n    blurred = cv2.GaussianBlur(img, (5, 5), 0)\n    _, binary = cv2.threshold(blurred, 0, 255, cv2.THRESH_BINARY + cv2.THRESH_OTSU)\n    contours, _ = cv2.findContours(binary, cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_SIMPLE)\n    cells = [c for c in contou","tagline":"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 morpho","category":"design-creative","tags":["agent-skill"],"author":"jaechang-hits","verified":false,"attribution":{"status":"registry_indexed","statusLabel":"Registry indexed","shortLabel":"REGISTRY INDEXED","sourceLabel":"github fast track","sourceDetail":"jaechang-hits/SciAgent-Skills","creatorName":"jaechang-hits","creatorUrl":"https://github.com/jaechang-hits","sourceUrl":"https://github.com/jaechang-hits/SciAgent-Skills/tree/main/skills/cell-biology/opencv-bioimage-analysis","indexedBy":"OpenAgentSkill community index","claimUrl":"https://www.openagentskill.com/skills/jaechang-hits-opencv-bioimage-analysis#claim-this-skill","claimCta":"Claim this skill","trustNote":"This listing was indexed from public sources and is not marked official until a maintainer claim is approved.","publicNote":"Attribution links to the public repository or creator profile. Creators can claim the listing to update ownership signals."},"stats":{"stars":359,"forks":35,"verified_installs":0,"successful_runs":0,"total_outcomes":0,"rating":0,"review_count":0,"quality_score":40.99},"quality":{"score":72,"tier":"strong","label":"Strong","summary":"Solid option that is likely worth shortlisting for production workflows.","signals":[{"label":"GitHub stars","value":"359","tone":"neutral"},{"label":"Freshness","value":"7d ago","tone":"positive"},{"label":"Install ready","value":"Yes","tone":"positive"},{"label":"License","value":"Apache-2.0","tone":"neutral"}],"warnings":[]},"trust":{"version":"trust-score-v5","score":67,"base_score":75,"outcome_confidence":0,"tier":"review","label":"Sandbox only","summary":"Useful candidate with missing or mixed trust signals. 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issue activity unavailable in current metadata","Dependency/runtime risk: command execution surface, external package install surface","Permission surface: shell or command execution, filesystem or document access"],"backward_compatible":{"trust_score_v4":{"version":"trust-score-v4","score":75,"tier":"strong","label":"Strong shortlist","summary":"Good trust signals with a few areas worth checking before rollout."}}},"trust_score_v5":{"version":"trust-score-v5","score":67,"base_score":75,"outcome_confidence":0,"tier":"review","label":"Sandbox only","summary":"Useful candidate with missing or mixed trust signals. Keep it in an isolated workspace until the outcome loop proves task fit.","recommendedAction":"Run only in a sandbox and compare close alternatives before using it for real work.","decision":{"install_policy":"human_review_before_install","auto_install_allowed":false,"human_review_required":true,"sandbox_first":true,"agent_action":"Compare alternatives before installing.","reasoning":["67/100 Trust Score v5","75/100 Trust Score v4 baseline","Needs more real agent outcomes before unattended install","Install path is available","Review before production"],"review_required_when":["The workspace contains production secrets, payments, private customer data, or irreversible actions.","The install command requests shell, network, credential, database, or broad filesystem access.","Outcome evidence is missing, recently failed, or required human review.","Production credentials, payments, or irreversible account changes without explicit human review","Sensitive private data before reviewing repository code, license, and permission surface","Automatic installation in a production workspace"]},"dimensions":[{"id":"github_adoption","label":"GitHub adoption","score":62,"weight":0.13,"status":"info","detail":"359 GitHub stars"},{"id":"repo_activity","label":"Stars/forks activity","score":57,"weight":0.08,"status":"warn","detail":"359 stars, 35 forks; issue activity unavailable in current metadata"},{"id":"maintenance","label":"Recent maintenance","score":100,"weight":0.14,"status":"pass","detail":"7d since push"},{"id":"license","label":"License clarity","score":86,"weight":0.09,"status":"pass","detail":"Apache-2.0"},{"id":"documentation","label":"README/SKILL.md completeness","score":86,"weight":0.14,"status":"pass","detail":"Metadata includes enough usage and workflow context"},{"id":"dependency_risk","label":"Dependency/runtime risk","score":54,"weight":0.12,"status":"warn","detail":"command execution surface, external package install surface"},{"id":"installability","label":"Install availability","score":92,"weight":0.1,"status":"pass","detail":"npx skills add jaechang-hits/SciAgent-Skills --skill opencv-bioimage-analysis"},{"id":"install_safety","label":"Install command safety","score":92,"weight":0.1,"status":"pass","detail":"standard package or runtime install path"},{"id":"permission_surface","label":"Permission surface","score":48,"weight":0.07,"status":"warn","detail":"shell or command execution, filesystem or document access"},{"id":"repository","label":"Repository evidence","score":86,"weight":0.04,"status":"pass","detail":"https://github.com/jaechang-hits/SciAgent-Skills/tree/main/skills/cell-biology/opencv-bioimage-analysis"},{"id":"review_status","label":"Review status","score":88,"weight":0.05,"status":"pass","detail":"AI review data available"},{"id":"agent_outcomes","label":"Agent Proven outcomes","score":54,"weight":0.13,"status":"info","detail":"No agent outcome data yet"}],"checks":[{"status":"info","label":"GitHub adoption","detail":"359 GitHub stars"},{"status":"warn","label":"Stars/forks activity","detail":"359 stars, 35 forks; issue activity unavailable in current metadata"},{"status":"pass","label":"Recent maintenance","detail":"7d since push"},{"status":"pass","label":"License clarity","detail":"Apache-2.0"},{"status":"pass","label":"README/SKILL.md completeness","detail":"Metadata includes enough usage and workflow context"},{"status":"warn","label":"Dependency/runtime risk","detail":"command execution surface, external package install surface"},{"status":"pass","label":"Install availability","detail":"npx skills add jaechang-hits/SciAgent-Skills --skill opencv-bioimage-analysis"},{"status":"pass","label":"Install command safety","detail":"standard package or runtime install path"},{"status":"warn","label":"Permission surface","detail":"shell or command execution, filesystem or document access"},{"status":"pass","label":"Repository evidence","detail":"https://github.com/jaechang-hits/SciAgent-Skills/tree/main/skills/cell-biology/opencv-bioimage-analysis"},{"status":"pass","label":"Review status","detail":"AI review data available"},{"status":"info","label":"Agent Proven outcomes","detail":"No agent outcome data yet"},{"status":"warn","label":"Ownership","detail":"No approved owner claim yet"},{"status":"info","label":"OpenAgentSkill usage","detail":"No local usage activity yet"},{"status":"info","label":"Agent outcomes","detail":"No agent outcome data yet"}],"strengths":["AI review approved","Install path is available","Repository evidence is available","Recently maintained repository","Install command has no obvious high-risk pattern","Outcome loop is ready but needs first real agent run"],"warnings":["Quality score needs review","Permission surface needs review: shell or command execution, filesystem or document access","Stars/forks activity: 359 stars, 35 forks; issue activity unavailable in current metadata","Dependency/runtime risk: command execution surface, external package install surface","Permission surface: shell or command execution, filesystem or document access","No real agent outcome reports yet","Human review required before unattended installation"],"evidence":{"stars":"359 GitHub stars","repoActivity":"359 stars, 35 forks","lastPushed":"7d since push","license":"Apache-2.0","repository":"https://github.com/jaechang-hits/SciAgent-Skills/tree/main/skills/cell-biology/opencv-bioimage-analysis","install":"npx skills add jaechang-hits/SciAgent-Skills --skill opencv-bioimage-analysis","installSafety":"standard package or runtime install path","permissionSurface":"shell or command execution, filesystem or document access","documentation":"Strong README/SKILL.md context","agentOutcomes":"No agent outcome data yet","agentProvenScore":0,"outcomeConfidence":"0%","installPolicy":"human_review_before_install"},"installReadiness":{"ready":true,"command":"npx skills add jaechang-hits/SciAgent-Skills --skill opencv-bioimage-analysis","policy":"human_review_before_install","label":"Human review before install","notes":["Install path is available","Repository evidence is available","License is declared","No Agent Proven outcome evidence yet","7d since push","Trust Score v5 requires review or sandbox-only use before install."]},"agentCompatibility":["Codex","Claude Code","Cursor","OpenAgentSkill CLI"],"riskSummary":{"level":"medium","label":"Review before production","notes":["Quality score needs review","Permission surface needs review: shell or command execution, filesystem or document access","Stars/forks activity: 359 stars, 35 forks; issue activity unavailable in current metadata","Dependency/runtime risk: command execution surface, external package install surface","Permission surface: shell or command execution, filesystem or document access"]},"outcomeEvidence":{"total":0,"successes":0,"failures":0,"notRelevant":0,"successRate":null,"installAttempts":0,"riskBlocked":0,"setupRequired":0,"installSuccessRate":null,"avgOutputQuality":null,"avgTimeToUsefulMs":null,"productionOutcomes":0,"humanReviewRequired":0,"recentSuccessRate":null,"recentFailureRate":null,"uniqueAgents":0,"agentProvenScore":0,"agentProvenLabel":"Needs first agent run","lastOutcomeAt":null,"label":"No agent outcome data yet"},"autoInstall":{"allowed":false,"sandboxRequired":true,"policy":"human_review_before_install","reason":"Compare alternatives before installing."},"outcome_loop":{"version":"openagentskill-agent-outcome-v4","required_after_install":true,"endpoint":"/api/agent/outcome","method":"POST","event_id_source":"feedback.event_id, install_receipt.resolve_event_id, or decision_packet.outcome_feedback.event_id","expected_outcomes":["success","failed","not_relevant","blocked_by_risk","setup_required"],"required_fields":["event_id","skill_slug","task"],"quality_fields":["task_success","output_quality","error_type","human_review_required","used_in_production","workspace","evidence_url","time_to_useful_ms","source_version"],"ranking_inputs_updated":["Trust Score v5 outcome confidence","Agent Proven Score","Resolve ranking task-fit evidence","Skill detail machine-readable metadata","Outcome leaderboard"]},"agent_contract":{"suited_tasks":["design-creative","agent-skill"],"suited_agents":["Codex","Claude Code","Cursor","OpenAgentSkill CLI"],"install_command":"npx skills add jaechang-hits/SciAgent-Skills --skill opencv-bioimage-analysis","trust_score":67,"trust_version":"trust-score-v5","risk_level":"medium","do_not_use_when":["Production credentials, payments, or irreversible account changes without explicit human review","Sensitive private data before reviewing repository code, license, and permission surface","Automatic installation in a production workspace"],"before_install":["Read the audit page and machine-readable metadata.","Confirm the install command, license, and permission surface fit the workspace.","Get explicit human approval or choose an alternative before installing."],"after_run":["Report the outcome to /api/agent/outcome using the resolve event id.","Include output_quality, workspace, human_review_required, and evidence_url when available.","Re-resolve before broad production rollout."]},"bestFor":["design-creative","agent-skill"],"doNotUseFor":["Production credentials, payments, or irreversible account changes without explicit human review","Sensitive private data before reviewing repository code, license, and permission surface","Automatic installation in a production workspace"],"knownRisks":["Quality score needs review","Permission surface needs review: shell or command execution, filesystem or document access","Stars/forks activity: 359 stars, 35 forks; issue activity unavailable in current metadata","Dependency/runtime risk: command execution surface, external package install surface","Permission surface: shell or command execution, filesystem or document access"],"backward_compatible":{"trust_score_v4":{"version":"trust-score-v4","score":75,"tier":"strong","label":"Strong shortlist","summary":"Good trust signals with a few areas worth checking before rollout."}}},"trust_score_v4":{"version":"trust-score-v4","score":75,"tier":"strong","label":"Strong shortlist","summary":"Good trust signals with a few areas worth checking before rollout.","recommendedAction":"Test in a sandbox workflow and compare its install path with close alternatives.","dimensions":[{"id":"github_adoption","label":"GitHub adoption","score":62,"weight":0.13,"status":"info","detail":"359 GitHub stars"},{"id":"repo_activity","label":"Stars/forks activity","score":57,"weight":0.08,"status":"warn","detail":"359 stars, 35 forks; issue activity unavailable in current metadata"},{"id":"maintenance","label":"Recent maintenance","score":100,"weight":0.14,"status":"pass","detail":"7d since push"},{"id":"license","label":"License clarity","score":86,"weight":0.09,"status":"pass","detail":"Apache-2.0"},{"id":"documentation","label":"README/SKILL.md completeness","score":86,"weight":0.14,"status":"pass","detail":"Metadata includes enough usage and workflow context"},{"id":"dependency_risk","label":"Dependency/runtime risk","score":54,"weight":0.12,"status":"warn","detail":"command execution surface, external package install surface"},{"id":"installability","label":"Install availability","score":92,"weight":0.1,"status":"pass","detail":"npx skills add jaechang-hits/SciAgent-Skills --skill opencv-bioimage-analysis"},{"id":"install_safety","label":"Install command safety","score":92,"weight":0.1,"status":"pass","detail":"standard package or runtime install path"},{"id":"permission_surface","label":"Permission surface","score":48,"weight":0.07,"status":"warn","detail":"shell or command execution, filesystem or document access"},{"id":"repository","label":"Repository evidence","score":86,"weight":0.04,"status":"pass","detail":"https://github.com/jaechang-hits/SciAgent-Skills/tree/main/skills/cell-biology/opencv-bioimage-analysis"},{"id":"review_status","label":"Review status","score":88,"weight":0.05,"status":"pass","detail":"AI review data available"},{"id":"agent_outcomes","label":"Agent Proven outcomes","score":54,"weight":0.13,"status":"info","detail":"No agent outcome data yet"}],"checks":[{"status":"info","label":"GitHub adoption","detail":"359 GitHub stars"},{"status":"warn","label":"Stars/forks activity","detail":"359 stars, 35 forks; issue activity unavailable in current metadata"},{"status":"pass","label":"Recent maintenance","detail":"7d since push"},{"status":"pass","label":"License clarity","detail":"Apache-2.0"},{"status":"pass","label":"README/SKILL.md completeness","detail":"Metadata includes enough usage and workflow context"},{"status":"warn","label":"Dependency/runtime risk","detail":"command execution surface, external package install surface"},{"status":"pass","label":"Install availability","detail":"npx skills add jaechang-hits/SciAgent-Skills --skill opencv-bioimage-analysis"},{"status":"pass","label":"Install command safety","detail":"standard package or runtime install path"},{"status":"warn","label":"Permission surface","detail":"shell or command execution, filesystem or document access"},{"status":"pass","label":"Repository evidence","detail":"https://github.com/jaechang-hits/SciAgent-Skills/tree/main/skills/cell-biology/opencv-bioimage-analysis"},{"status":"pass","label":"Review status","detail":"AI review data available"},{"status":"info","label":"Agent Proven outcomes","detail":"No agent outcome data yet"},{"status":"warn","label":"Ownership","detail":"No approved owner claim yet"},{"status":"info","label":"OpenAgentSkill usage","detail":"No local usage activity yet"},{"status":"info","label":"Agent outcomes","detail":"No agent outcome data yet"}],"strengths":["AI review approved","Install path is available","Repository evidence is available","Recently maintained repository","Install command has no obvious high-risk pattern"],"warnings":["Quality score needs review","Permission surface needs review: shell or command execution, filesystem or document access","Stars/forks activity: 359 stars, 35 forks; issue activity unavailable in current metadata","Dependency/runtime risk: command execution surface, external package install surface","Permission surface: shell or command execution, filesystem or document access"],"evidence":{"stars":"359 GitHub stars","repoActivity":"359 stars, 35 forks","lastPushed":"7d since push","license":"Apache-2.0","repository":"https://github.com/jaechang-hits/SciAgent-Skills/tree/main/skills/cell-biology/opencv-bioimage-analysis","install":"npx skills add jaechang-hits/SciAgent-Skills --skill opencv-bioimage-analysis","installSafety":"standard package or runtime install path","permissionSurface":"shell or command execution, filesystem or document access","documentation":"Strong README/SKILL.md context","agentOutcomes":"No agent outcome data yet"},"installReadiness":{"ready":true,"command":"npx skills add jaechang-hits/SciAgent-Skills --skill opencv-bioimage-analysis","policy":"human_review_before_install","label":"Human review before install","notes":["Install path is available","Repository evidence is available","License is declared","No Agent Proven outcome evidence yet","7d since push"]},"agentCompatibility":["Codex","Claude Code","Cursor","OpenAgentSkill CLI"],"riskSummary":{"level":"medium","label":"Review before production","notes":["Quality score needs review","Permission surface needs review: shell or command execution, filesystem or document access","Stars/forks activity: 359 stars, 35 forks; issue activity unavailable in current metadata","Dependency/runtime risk: command execution surface, external package install surface","Permission surface: shell or command execution, filesystem or document access"]},"outcomeEvidence":{"total":0,"successes":0,"failures":0,"notRelevant":0,"successRate":null,"installAttempts":0,"riskBlocked":0,"setupRequired":0,"installSuccessRate":null,"avgOutputQuality":null,"avgTimeToUsefulMs":null,"productionOutcomes":0,"humanReviewRequired":0,"recentSuccessRate":null,"recentFailureRate":null,"uniqueAgents":0,"agentProvenScore":0,"agentProvenLabel":"Needs first agent run","lastOutcomeAt":null,"label":"No agent outcome data yet"},"autoInstall":{"allowed":false,"sandboxRequired":true,"policy":"human_review_before_install","reason":"Human review or sandbox validation is required before automatic installation."},"bestFor":["design-creative","agent-skill"],"doNotUseFor":["Production credentials, payments, or irreversible account changes without explicit human review","Sensitive private data before reviewing repository code, license, and permission surface","Automatic installation in a production workspace"],"knownRisks":["Quality score needs review","Permission surface needs review: shell or command execution, filesystem or document access","Stars/forks activity: 359 stars, 35 forks; issue activity unavailable in current metadata","Dependency/runtime risk: command execution surface, external package install surface","Permission surface: shell or command execution, filesystem or document access"]},"agent_proven":{"version":"agent-proven-v1","score":0,"tier":"unproven","label":"Needs first agent run","summary":"No agent outcome reports yet. Use Resolve, run one narrow sandbox task, then report the result.","metrics":{"totalOutcomes":0,"successfulOutcomes":0,"failedOutcomes":0,"installAttempts":0,"installSuccessRate":null,"successRate":null,"recentSuccessRate":null,"recentFailureRate":null,"riskBlocked":0,"setupRequired":0,"notRelevant":0,"avgOutputQuality":null,"avgTimeToUsefulMs":null,"productionOutcomes":0,"humanReviewRequired":0,"uniqueAgents":0,"lastOutcomeAt":null},"signals":[],"penalties":["No real agent outcome evidence yet"]},"outcome_stats":null,"safety":{"score":52,"level":"avoid_auto_install","label":"Avoid automatic install","safety_tier":{"tier":"experimental","label":"Experimental","badge":"EXPERIMENTAL","summary":"Sparse or mixed signals. Useful for discovery, but not for autonomous installation.","recommended_action":"Test manually in an isolated workspace and compare against safer alternatives.","auto_install_policy":"review","reasons":["High-risk permission hints: Shell or command execution","52/100 agent safety score"]},"auto_install_allowed":false,"human_review_required":true,"blocked":false,"audit_risk":"needs_review","permission_hints":[{"id":"shell","label":"Shell or command execution","reason":"Skill metadata references terminal, CLI, shell, subprocess, or command execution workflows.","severity":"high"},{"id":"network","label":"Network access","reason":"Skill likely fetches remote pages, APIs, repositories, or external services.","severity":"medium"},{"id":"filesystem","label":"Filesystem access","reason":"Skill may read or write project files, documents, generated artifacts, or local workspace state.","severity":"medium"}],"policy_warnings":["High-risk permission hints: Shell or command execution","Dependency or permission surface needs review"],"constraints_applied":{"max_risk":"medium","needs_install_command":true,"min_stars":0}},"safety_gate":{"tier":"experimental","label":"Experimental","badge":"EXPERIMENTAL","auto_install_policy":"review","auto_install_allowed":false,"blocked":false,"human_review_required":true,"recommended_action":"Test manually in an isolated workspace and compare against safer alternatives.","reasons":["High-risk permission hints: Shell or command execution","52/100 agent safety score"]},"eval":{"version":"openagentskill-skill-eval-v1","status":"failed","score":71,"risk_level":"high","decision":{"recommendation":"do_not_auto_install","reason":"Permission surface: shell or command execution, filesystem or document access","auto_install_allowed":false,"policy":"block","human_review_required":true},"blockers":["Permission surface: shell or command execution, filesystem or document access"],"warnings":["Trust score: Good trust signals with a few areas worth checking before rollout.","Audit score: Needs review","Agent safety gate: Sparse or mixed signals. Useful for discovery, but not for autonomous installation.","High-risk permission hints: Shell or command execution","Dependency or permission surface needs review","Permission surface may require sandboxing","Quality score needs review","Permission surface needs review: shell or command execution, filesystem or document access","Stars/forks activity: 359 stars, 35 forks; issue activity unavailable in current metadata","Dependency/runtime risk: command execution surface, external package install surface","Permission surface: shell or command execution, filesystem or document access"],"validation_plan":["Inspect repository, README/SKILL.md, license, and recent commits before production use.","Install in an isolated workspace or sandbox with no production secrets available.","Run the smallest representative task and record files touched, commands run, network access, and outputs.","Compare the selected skill against at least one alternative when the eval status is review or failed.","Promote only after the agent reports a successful verification result and unresolved warnings are accepted."],"checks":[{"id":"task_fit","label":"Task fit","status":"pass","score":84,"required_for_auto_install":true,"detail":"Task wording matches this skill metadata.","evidence":["Evaluate opencv-bioimage-analysis before installing it in an agent workflow","design-creative","Multimodal media workflows; Claude Code teams; builders willing to evaluate younger projects"]},{"id":"install_path","label":"Install path","status":"pass","score":92,"required_for_auto_install":true,"detail":"Install handoff is available.","evidence":["npx skills add jaechang-hits/SciAgent-Skills --skill opencv-bioimage-analysis"]},{"id":"install_safety","label":"Install command safety","status":"pass","score":92,"required_for_auto_install":true,"detail":"standard package or runtime install path","evidence":["npx skills add jaechang-hits/SciAgent-Skills --skill opencv-bioimage-analysis"]},{"id":"trust_score","label":"Trust score","status":"warn","score":75,"required_for_auto_install":true,"detail":"Good trust signals with a few areas worth checking before rollout.","evidence":["Strong shortlist","359 GitHub stars","Apache-2.0"]},{"id":"audit_score","label":"Audit score","status":"warn","score":80,"required_for_auto_install":true,"detail":"Needs review","evidence":["Dependency or permission surface needs review"]},{"id":"agent_safety_gate","label":"Agent safety gate","status":"warn","score":52,"required_for_auto_install":true,"detail":"Sparse or mixed signals. Useful for discovery, but not for autonomous installation.","evidence":["Test manually in an isolated workspace and compare against safer alternatives.","High-risk permission hints: Shell or command execution"]},{"id":"readme_skillmd_completeness","label":"README/SKILL.md completeness","status":"pass","score":86,"required_for_auto_install":false,"detail":"Metadata includes enough usage and workflow context","evidence":["Strong README/SKILL.md context"]},{"id":"license_clarity","label":"License clarity","status":"pass","score":86,"required_for_auto_install":true,"detail":"Apache-2.0","evidence":["Apache-2.0"]},{"id":"recent_maintenance","label":"Recent maintenance","status":"pass","score":100,"required_for_auto_install":false,"detail":"7d since push","evidence":["7d since push"]},{"id":"permission_surface","label":"Permission surface","status":"fail","score":48,"required_for_auto_install":true,"detail":"shell or command execution, filesystem or document access","evidence":["Shell or command execution: high","Network access: medium","Filesystem access: medium"]},{"id":"alternatives","label":"Alternatives available","status":"info","score":55,"required_for_auto_install":false,"detail":"No close alternatives were found in the current shortlist.","evidence":[]}],"endpoints":{"web":"https://www.openagentskill.com/skills/jaechang-hits-opencv-bioimage-analysis/evals","api":"/api/agent/evals?slug=jaechang-hits-opencv-bioimage-analysis","text":"/api/agent/evals?slug=jaechang-hits-opencv-bioimage-analysis&format=text"}},"agent_readable_metadata":{"version":"openagentskill-agent-metadata-v2","skill":{"slug":"jaechang-hits-opencv-bioimage-analysis","name":"opencv-bioimage-analysis","description":"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.","category":"design-creative","url":"https://www.openagentskill.com/skills/jaechang-hits-opencv-bioimage-analysis","repository":"https://github.com/jaechang-hits/SciAgent-Skills/tree/main/skills/cell-biology/opencv-bioimage-analysis","github_repo":"jaechang-hits/SciAgent-Skills"},"suited_tasks":["Multimodal media workflows","Claude Code teams","builders willing to evaluate younger projects","Read media metadata","Convert formats","Summarize visual or audio content","Navigate local resources","Run repeatable desktop actions"],"suited_agents":["Codex","Claude Code","Cursor","OpenAgentSkill CLI","CLI"],"install":{"command":"npx skills add jaechang-hits/SciAgent-Skills --skill opencv-bioimage-analysis","ready":true,"targets":[{"id":"openagentskill-cli","label":"CLI","kind":"command","value":"npx --yes https://github.com/Leon-Drq/openagentskill/releases/download/cli-v0.3.0/openagentskill-0.3.0.tgz add jaechang-hits-opencv-bioimage-analysis"},{"id":"codex","label":"Codex","kind":"agent-prompt","value":"Install the \"opencv-bioimage-analysis\" agent skill from https://github.com/jaechang-hits/SciAgent-Skills/tree/main/skills/cell-biology/opencv-bioimage-analysis. Read its SKILL.md or equivalent instructions first, install only the files needed for this workspace, and summarize any required setup before using it. Skill purpose: 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. After the install attempt, report the result to https://www.openagentskill.com/api/agent/outcome with POST JSON {\"event_id\":\"install_<unique-id>\",\"skill_slug\":\"jaechang-hits-opencv-bioimage-analysis\",\"task\":\"Install opencv-bioimage-analysis\",\"agent\":\"codex\",\"outcome\":\"success\",\"install_used\":true}. Replace event_id with a unique value and outcome with success or failed. Report success only after the skill is installed and a minimal verification passes."},{"id":"claude-code","label":"Claude Code","kind":"agent-prompt","value":"Add \"opencv-bioimage-analysis\" as a Claude Code skill from https://github.com/jaechang-hits/SciAgent-Skills/tree/main/skills/cell-biology/opencv-bioimage-analysis. Inspect the skill instructions, place the reusable skill files in the appropriate local skills location for this project, and report the activation steps. Skill purpose: 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. After the install attempt, report the result to https://www.openagentskill.com/api/agent/outcome with POST JSON {\"event_id\":\"install_<unique-id>\",\"skill_slug\":\"jaechang-hits-opencv-bioimage-analysis\",\"task\":\"Install opencv-bioimage-analysis\",\"agent\":\"claude-code\",\"outcome\":\"success\",\"install_used\":true}. Replace event_id with a unique value and outcome with success or failed. Report success only after the skill is installed and a minimal verification passes."},{"id":"cursor","label":"Cursor","kind":"agent-prompt","value":"Turn \"opencv-bioimage-analysis\" from https://github.com/jaechang-hits/SciAgent-Skills/tree/main/skills/cell-biology/opencv-bioimage-analysis into a reusable Cursor project rule or agent instruction. Preserve the core workflow, adapt paths to this repo, and keep the rule scoped to tasks where it is relevant. Skill purpose: 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. After the install attempt, report the result to https://www.openagentskill.com/api/agent/outcome with POST JSON {\"event_id\":\"install_<unique-id>\",\"skill_slug\":\"jaechang-hits-opencv-bioimage-analysis\",\"task\":\"Install opencv-bioimage-analysis\",\"agent\":\"cursor\",\"outcome\":\"success\",\"install_used\":true}. Replace event_id with a unique value and outcome with success or failed. Report success only after the skill is installed and a minimal verification passes."}],"handoff_url":"https://www.openagentskill.com/api/skills/jaechang-hits-opencv-bioimage-analysis/install","manifest_url":"https://www.openagentskill.com/api/registry/manifest/jaechang-hits-opencv-bioimage-analysis"},"trust":{"score":75,"label":"Strong shortlist","version":"trust-score-v4","install_policy":"human_review_before_install","evidence":{"stars":"359 GitHub stars","repoActivity":"359 stars, 35 forks","lastPushed":"7d since push","license":"Apache-2.0","repository":"https://github.com/jaechang-hits/SciAgent-Skills/tree/main/skills/cell-biology/opencv-bioimage-analysis","install":"npx skills add jaechang-hits/SciAgent-Skills --skill opencv-bioimage-analysis","installSafety":"standard package or runtime install path","permissionSurface":"shell or command execution, filesystem or document access","documentation":"Strong README/SKILL.md context","agentOutcomes":"No agent outcome data yet"},"outcome_evidence":{"total":0,"successes":0,"failures":0,"not_relevant":0,"success_rate":null,"recent_success_rate":null,"recent_failure_rate":null,"install_attempts":0,"install_success_rate":null,"risk_blocked":0,"setup_required":0,"avg_output_quality":null,"production_outcomes":0,"last_outcome_at":null,"label":"No agent outcome data yet"},"auto_install":{"allowed":false,"sandbox_required":true,"reason":"Human review or sandbox validation is required before automatic installation."},"best_for":["design-creative","agent-skill"],"known_risks":["Quality score needs review","Permission surface needs review: shell or command execution, filesystem or document access","Stars/forks activity: 359 stars, 35 forks; issue activity unavailable in current metadata","Dependency/runtime risk: command execution surface, external package install surface","Permission surface: shell or command execution, filesystem or document access"]},"agent_proven":{"version":"agent-proven-v1","score":0,"tier":"unproven","label":"Needs first agent run","summary":"No agent outcome reports yet. Use Resolve, run one narrow sandbox task, then report the result.","metrics":{"totalOutcomes":0,"successfulOutcomes":0,"failedOutcomes":0,"installAttempts":0,"installSuccessRate":null,"successRate":null,"recentSuccessRate":null,"recentFailureRate":null,"riskBlocked":0,"setupRequired":0,"notRelevant":0,"avgOutputQuality":null,"avgTimeToUsefulMs":null,"productionOutcomes":0,"humanReviewRequired":0,"uniqueAgents":0,"lastOutcomeAt":null},"signals":[],"penalties":["No real agent outcome evidence yet"]},"audit":{"score":80,"risk_level":"needs_review","risk_label":"Needs review","warnings":["Dependency or permission surface needs review","Permission surface may require sandboxing","Quality score needs review","Permission surface needs review: shell or command execution, filesystem or document access","Stars/forks activity: 359 stars, 35 forks; issue activity unavailable in current metadata","Dependency/runtime risk: command execution surface, external package install surface","Permission surface: shell or command execution, filesystem or document access"]},"safety_gate":{"tier":"experimental","label":"Experimental","auto_install_policy":"review","auto_install_allowed":false,"human_review_required":true,"blocked":false,"recommended_action":"Test manually in an isolated workspace and compare against safer alternatives."},"quality":{"score":72,"label":"Strong"},"supply":{"track":"Design and creative production","scenario":"Multimodal media","maintenance":"7d since push","risk":"Needs review"},"alternative_skills":[],"do_not_use_when":["teams that need a vendor-supported SLA","high-compliance environments without internal security review","No OpenAgentSkill engagement data yet","High-risk permission hints: Shell or command execution","Dependency or permission surface needs review","Permission surface may require sandboxing","Quality score needs review","Permission surface needs review: shell or command execution, filesystem or document access"],"agent_contract":{"task_input":"Use opencv-bioimage-analysis in an agent workflow","recommended_action":"Test manually in an isolated workspace and compare against safer alternatives.","install_policy":"review","minimum_review_before_use":["Trust: 75/100 Strong shortlist","Audit: 80/100 Needs review","Safety: 52/100 Avoid automatic install","Review repository, license, install command, and permission surface before production use."],"expected_agent_output":{"selected_skill":"jaechang-hits-opencv-bioimage-analysis (opencv-bioimage-analysis)","install_command":"npx skills add jaechang-hits/SciAgent-Skills --skill opencv-bioimage-analysis","risk_summary":"Needs review; Experimental; Review before production","verification_result":"Report the smallest successful task, files touched, warnings, and any missing setup."}},"outcome_feedback":{"endpoint":"https://www.openagentskill.com/api/agent/outcome","method":"POST","requires_resolve_event_id":true,"event_id_source":"Use install_receipt.outcome_feedback.event_id or feedback.event_id returned by /api/agent/resolve for the current task.","expected_outcomes":["success","failed","not_relevant","blocked_by_risk","setup_required"],"payload_template":{"event_id":"<install_receipt.outcome_feedback.event_id or feedback.event_id from /api/agent/resolve>","skill_slug":"jaechang-hits-opencv-bioimage-analysis","task":"Use opencv-bioimage-analysis in an agent workflow","agent":"codex","outcome":"success","install_used":true,"risk_blocked":false,"setup_required":false,"task_success":true,"output_quality":4,"error_type":null,"human_review_required":false,"workspace":"sandbox","time_to_useful_ms":120000,"notes":"Report the smallest successful task, setup friction, files touched, and risk notes."}},"endpoints":{"web":"https://www.openagentskill.com/skills/jaechang-hits-opencv-bioimage-analysis","api":"https://www.openagentskill.com/api/agent/skills/jaechang-hits-opencv-bioimage-analysis","audit":"https://www.openagentskill.com/skills/jaechang-hits-opencv-bioimage-analysis/audit","eval":"https://www.openagentskill.com/api/agent/evals?slug=jaechang-hits-opencv-bioimage-analysis&task=Use%20opencv-bioimage-analysis%20in%20an%20agent%20workflow&max_risk=medium","resolve":"https://www.openagentskill.com/api/agent/resolve?task=Use%20opencv-bioimage-analysis%20in%20an%20agent%20workflow&agent=codex&max_risk=medium","receipt":"https://www.openagentskill.com/api/agent/receipt?task=Use%20opencv-bioimage-analysis%20in%20an%20agent%20workflow&agent=codex&max_risk=medium&format=text","install":"https://www.openagentskill.com/api/skills/jaechang-hits-opencv-bioimage-analysis/install","manifest":"https://www.openagentskill.com/api/registry/manifest/jaechang-hits-opencv-bioimage-analysis"}},"machine_metadata":{"version":"openagentskill-agent-metadata-v2","skill":{"slug":"jaechang-hits-opencv-bioimage-analysis","name":"opencv-bioimage-analysis","description":"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.","category":"design-creative","url":"https://www.openagentskill.com/skills/jaechang-hits-opencv-bioimage-analysis","repository":"https://github.com/jaechang-hits/SciAgent-Skills/tree/main/skills/cell-biology/opencv-bioimage-analysis","github_repo":"jaechang-hits/SciAgent-Skills"},"suited_tasks":["Multimodal media workflows","Claude Code teams","builders willing to evaluate younger projects","Read media metadata","Convert formats","Summarize visual or audio content","Navigate local resources","Run repeatable desktop actions"],"suited_agents":["Codex","Claude Code","Cursor","OpenAgentSkill CLI","CLI"],"install":{"command":"npx skills add jaechang-hits/SciAgent-Skills --skill opencv-bioimage-analysis","ready":true,"targets":[{"id":"openagentskill-cli","label":"CLI","kind":"command","value":"npx --yes https://github.com/Leon-Drq/openagentskill/releases/download/cli-v0.3.0/openagentskill-0.3.0.tgz add jaechang-hits-opencv-bioimage-analysis"},{"id":"codex","label":"Codex","kind":"agent-prompt","value":"Install the \"opencv-bioimage-analysis\" agent skill from https://github.com/jaechang-hits/SciAgent-Skills/tree/main/skills/cell-biology/opencv-bioimage-analysis. Read its SKILL.md or equivalent instructions first, install only the files needed for this workspace, and summarize any required setup before using it. Skill purpose: 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. After the install attempt, report the result to https://www.openagentskill.com/api/agent/outcome with POST JSON {\"event_id\":\"install_<unique-id>\",\"skill_slug\":\"jaechang-hits-opencv-bioimage-analysis\",\"task\":\"Install opencv-bioimage-analysis\",\"agent\":\"codex\",\"outcome\":\"success\",\"install_used\":true}. Replace event_id with a unique value and outcome with success or failed. Report success only after the skill is installed and a minimal verification passes."},{"id":"claude-code","label":"Claude Code","kind":"agent-prompt","value":"Add \"opencv-bioimage-analysis\" as a Claude Code skill from https://github.com/jaechang-hits/SciAgent-Skills/tree/main/skills/cell-biology/opencv-bioimage-analysis. Inspect the skill instructions, place the reusable skill files in the appropriate local skills location for this project, and report the activation steps. Skill purpose: 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. After the install attempt, report the result to https://www.openagentskill.com/api/agent/outcome with POST JSON {\"event_id\":\"install_<unique-id>\",\"skill_slug\":\"jaechang-hits-opencv-bioimage-analysis\",\"task\":\"Install opencv-bioimage-analysis\",\"agent\":\"claude-code\",\"outcome\":\"success\",\"install_used\":true}. Replace event_id with a unique value and outcome with success or failed. Report success only after the skill is installed and a minimal verification passes."},{"id":"cursor","label":"Cursor","kind":"agent-prompt","value":"Turn \"opencv-bioimage-analysis\" from https://github.com/jaechang-hits/SciAgent-Skills/tree/main/skills/cell-biology/opencv-bioimage-analysis into a reusable Cursor project rule or agent instruction. Preserve the core workflow, adapt paths to this repo, and keep the rule scoped to tasks where it is relevant. Skill purpose: 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. After the install attempt, report the result to https://www.openagentskill.com/api/agent/outcome with POST JSON {\"event_id\":\"install_<unique-id>\",\"skill_slug\":\"jaechang-hits-opencv-bioimage-analysis\",\"task\":\"Install opencv-bioimage-analysis\",\"agent\":\"cursor\",\"outcome\":\"success\",\"install_used\":true}. Replace event_id with a unique value and outcome with success or failed. Report success only after the skill is installed and a minimal verification passes."}],"handoff_url":"https://www.openagentskill.com/api/skills/jaechang-hits-opencv-bioimage-analysis/install","manifest_url":"https://www.openagentskill.com/api/registry/manifest/jaechang-hits-opencv-bioimage-analysis"},"trust":{"score":75,"label":"Strong shortlist","version":"trust-score-v4","install_policy":"human_review_before_install","evidence":{"stars":"359 GitHub stars","repoActivity":"359 stars, 35 forks","lastPushed":"7d since push","license":"Apache-2.0","repository":"https://github.com/jaechang-hits/SciAgent-Skills/tree/main/skills/cell-biology/opencv-bioimage-analysis","install":"npx skills add jaechang-hits/SciAgent-Skills --skill opencv-bioimage-analysis","installSafety":"standard package or runtime install path","permissionSurface":"shell or command execution, filesystem or document access","documentation":"Strong README/SKILL.md context","agentOutcomes":"No agent outcome data yet"},"outcome_evidence":{"total":0,"successes":0,"failures":0,"not_relevant":0,"success_rate":null,"recent_success_rate":null,"recent_failure_rate":null,"install_attempts":0,"install_success_rate":null,"risk_blocked":0,"setup_required":0,"avg_output_quality":null,"production_outcomes":0,"last_outcome_at":null,"label":"No agent outcome data yet"},"auto_install":{"allowed":false,"sandbox_required":true,"reason":"Human review or sandbox validation is required before automatic installation."},"best_for":["design-creative","agent-skill"],"known_risks":["Quality score needs review","Permission surface needs review: shell or command execution, filesystem or document access","Stars/forks activity: 359 stars, 35 forks; issue activity unavailable in current metadata","Dependency/runtime risk: command execution surface, external package install surface","Permission surface: shell or command execution, filesystem or document access"]},"agent_proven":{"version":"agent-proven-v1","score":0,"tier":"unproven","label":"Needs first agent run","summary":"No agent outcome reports yet. Use Resolve, run one narrow sandbox task, then report the result.","metrics":{"totalOutcomes":0,"successfulOutcomes":0,"failedOutcomes":0,"installAttempts":0,"installSuccessRate":null,"successRate":null,"recentSuccessRate":null,"recentFailureRate":null,"riskBlocked":0,"setupRequired":0,"notRelevant":0,"avgOutputQuality":null,"avgTimeToUsefulMs":null,"productionOutcomes":0,"humanReviewRequired":0,"uniqueAgents":0,"lastOutcomeAt":null},"signals":[],"penalties":["No real agent outcome evidence yet"]},"audit":{"score":80,"risk_level":"needs_review","risk_label":"Needs review","warnings":["Dependency or permission surface needs review","Permission surface may require sandboxing","Quality score needs review","Permission surface needs review: shell or command execution, filesystem or document access","Stars/forks activity: 359 stars, 35 forks; issue activity unavailable in current metadata","Dependency/runtime risk: command execution surface, external package install surface","Permission surface: shell or command execution, filesystem or document access"]},"safety_gate":{"tier":"experimental","label":"Experimental","auto_install_policy":"review","auto_install_allowed":false,"human_review_required":true,"blocked":false,"recommended_action":"Test manually in an isolated workspace and compare against safer alternatives."},"quality":{"score":72,"label":"Strong"},"supply":{"track":"Design and creative production","scenario":"Multimodal media","maintenance":"7d since push","risk":"Needs review"},"alternative_skills":[],"do_not_use_when":["teams that need a vendor-supported SLA","high-compliance environments without internal security review","No OpenAgentSkill engagement data yet","High-risk permission hints: Shell or command execution","Dependency or permission surface needs review","Permission surface may require sandboxing","Quality score needs review","Permission surface needs review: shell or command execution, filesystem or document access"],"agent_contract":{"task_input":"Use opencv-bioimage-analysis in an agent workflow","recommended_action":"Test manually in an isolated workspace and compare against safer alternatives.","install_policy":"review","minimum_review_before_use":["Trust: 75/100 Strong shortlist","Audit: 80/100 Needs review","Safety: 52/100 Avoid automatic install","Review repository, license, install command, and permission surface before production use."],"expected_agent_output":{"selected_skill":"jaechang-hits-opencv-bioimage-analysis (opencv-bioimage-analysis)","install_command":"npx skills add jaechang-hits/SciAgent-Skills --skill opencv-bioimage-analysis","risk_summary":"Needs review; Experimental; Review before production","verification_result":"Report the smallest successful task, files touched, warnings, and any missing setup."}},"outcome_feedback":{"endpoint":"https://www.openagentskill.com/api/agent/outcome","method":"POST","requires_resolve_event_id":true,"event_id_source":"Use install_receipt.outcome_feedback.event_id or feedback.event_id returned by /api/agent/resolve for the current task.","expected_outcomes":["success","failed","not_relevant","blocked_by_risk","setup_required"],"payload_template":{"event_id":"<install_receipt.outcome_feedback.event_id or feedback.event_id from /api/agent/resolve>","skill_slug":"jaechang-hits-opencv-bioimage-analysis","task":"Use opencv-bioimage-analysis in an agent workflow","agent":"codex","outcome":"success","install_used":true,"risk_blocked":false,"setup_required":false,"task_success":true,"output_quality":4,"error_type":null,"human_review_required":false,"workspace":"sandbox","time_to_useful_ms":120000,"notes":"Report the smallest successful task, setup friction, files touched, and risk notes."}},"endpoints":{"web":"https://www.openagentskill.com/skills/jaechang-hits-opencv-bioimage-analysis","api":"https://www.openagentskill.com/api/agent/skills/jaechang-hits-opencv-bioimage-analysis","audit":"https://www.openagentskill.com/skills/jaechang-hits-opencv-bioimage-analysis/audit","eval":"https://www.openagentskill.com/api/agent/evals?slug=jaechang-hits-opencv-bioimage-analysis&task=Use%20opencv-bioimage-analysis%20in%20an%20agent%20workflow&max_risk=medium","resolve":"https://www.openagentskill.com/api/agent/resolve?task=Use%20opencv-bioimage-analysis%20in%20an%20agent%20workflow&agent=codex&max_risk=medium","receipt":"https://www.openagentskill.com/api/agent/receipt?task=Use%20opencv-bioimage-analysis%20in%20an%20agent%20workflow&agent=codex&max_risk=medium&format=text","install":"https://www.openagentskill.com/api/skills/jaechang-hits-opencv-bioimage-analysis/install","manifest":"https://www.openagentskill.com/api/registry/manifest/jaechang-hits-opencv-bioimage-analysis"}},"supply_profile":{"track":{"slug":"design","label":"Design and creative production","shortLabel":"Design","description":"Design assets, images, video, audio, multimodal media, presentation, and creative production skills."},"scenario":{"label":"Multimodal media","description":"I need my agent to process images, video, or audio and extract useful information.","useCases":[{"slug":"multimodal-media","title":"Multimodal media"},{"slug":"local-desktop","title":"Local desktop"},{"slug":"browser-automation","title":"Browser automation"}]},"applicableAgents":["Claude Code","CLI","Codex","Cursor"],"install":{"ready":true,"command":"npx skills add jaechang-hits/SciAgent-Skills --skill opencv-bioimage-analysis","primaryTarget":"CLI","targetCount":4},"githubQuality":{"stars":359,"starsLabel":"359","forks":35,"license":"Apache-2.0","qualityScore":72,"trustScore":75,"auditScore":80},"maintenance":{"status":"fresh","label":"7d since push","daysSincePush":7,"lastPushedAt":"2026-08-29T00:42:20+00:00"},"risk":{"level":"needs_review","label":"Needs review","requiresReview":true,"notes":["Dependency or permission surface needs review","Permission surface may require sandboxing","Quality score needs review","Permission surface needs review: shell or command execution, filesystem or document access","Stars/forks activity: 359 stars, 35 forks; issue activity unavailable in current metadata"]},"coverageTags":["Design","Multimodal media","design-creative","agent-skill"]},"audit":{"audit_score":80,"risk_level":"needs_review","risk_label":"Needs review","quality_score":72,"trust_score":75,"maintenance_score":100,"security_score":79,"install_score":92,"warnings":["Dependency or permission surface needs review","Permission surface may require sandboxing","Quality score needs review","Permission surface needs review: shell or command execution, filesystem or document access","Stars/forks activity: 359 stars, 35 forks; issue activity unavailable in current metadata","Dependency/runtime risk: command execution surface, external package install surface","Permission surface: shell or command execution, filesystem or document access"]},"quality_signals":{"model":"v2","star_score":17.89,"usage_score":0,"review_score":5.1,"metadata_score":3,"freshness_score":15},"platforms":["Claude Code"],"use_cases":[{"slug":"multimodal-media","title":"Multimodal media","url":"https://www.openagentskill.com/use-cases/multimodal-media"},{"slug":"local-desktop","title":"Local desktop","url":"https://www.openagentskill.com/use-cases/local-desktop"},{"slug":"browser-automation","title":"Browser automation","url":"https://www.openagentskill.com/use-cases/browser-automation"},{"slug":"workflow-automation","title":"Workflow automation","url":"https://www.openagentskill.com/use-cases/workflow-automation"}],"stacks":[{"slug":"browser-qa-agent","title":"Browser QA agent","url":"https://www.openagentskill.com/collections/browser-qa-agent"},{"slug":"frontend-product-ui","title":"Frontend and UI","url":"https://www.openagentskill.com/collections/frontend-product-ui"},{"slug":"content-growth-agent","title":"Content growth agent","url":"https://www.openagentskill.com/collections/content-growth-agent"}],"install":"npx skills add jaechang-hits/SciAgent-Skills --skill opencv-bioimage-analysis","install_targets":[{"id":"openagentskill-cli","label":"CLI","title":"OpenAgentSkill CLI","kind":"command","value":"npx --yes https://github.com/Leon-Drq/openagentskill/releases/download/cli-v0.3.0/openagentskill-0.3.0.tgz add jaechang-hits-opencv-bioimage-analysis","description":"Resolve policy, run the source installer safely, and report a verified install receipt.","copyLabel":"Copy command"},{"id":"codex","label":"Codex","title":"Codex install prompt","kind":"agent-prompt","value":"Install the \"opencv-bioimage-analysis\" agent skill from https://github.com/jaechang-hits/SciAgent-Skills/tree/main/skills/cell-biology/opencv-bioimage-analysis. Read its SKILL.md or equivalent instructions first, install only the files needed for this workspace, and summarize any required setup before using it. Skill purpose: 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. After the install attempt, report the result to https://www.openagentskill.com/api/agent/outcome with POST JSON {\"event_id\":\"install_<unique-id>\",\"skill_slug\":\"jaechang-hits-opencv-bioimage-analysis\",\"task\":\"Install opencv-bioimage-analysis\",\"agent\":\"codex\",\"outcome\":\"success\",\"install_used\":true}. Replace event_id with a unique value and outcome with success or failed. Report success only after the skill is installed and a minimal verification passes.","description":"Give Codex a repo-aware install prompt when the skill is not available through a local CLI.","copyLabel":"Copy prompt"},{"id":"claude-code","label":"Claude Code","title":"Claude Code skill prompt","kind":"agent-prompt","value":"Add \"opencv-bioimage-analysis\" as a Claude Code skill from https://github.com/jaechang-hits/SciAgent-Skills/tree/main/skills/cell-biology/opencv-bioimage-analysis. Inspect the skill instructions, place the reusable skill files in the appropriate local skills location for this project, and report the activation steps. Skill purpose: 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. After the install attempt, report the result to https://www.openagentskill.com/api/agent/outcome with POST JSON {\"event_id\":\"install_<unique-id>\",\"skill_slug\":\"jaechang-hits-opencv-bioimage-analysis\",\"task\":\"Install opencv-bioimage-analysis\",\"agent\":\"claude-code\",\"outcome\":\"success\",\"install_used\":true}. Replace event_id with a unique value and outcome with success or failed. Report success only after the skill is installed and a minimal verification passes.","description":"Use this prompt to ask Claude Code to add the skill and explain the local activation steps.","copyLabel":"Copy prompt"},{"id":"cursor","label":"Cursor","title":"Cursor rule prompt","kind":"agent-prompt","value":"Turn \"opencv-bioimage-analysis\" from https://github.com/jaechang-hits/SciAgent-Skills/tree/main/skills/cell-biology/opencv-bioimage-analysis into a reusable Cursor project rule or agent instruction. Preserve the core workflow, adapt paths to this repo, and keep the rule scoped to tasks where it is relevant. Skill purpose: 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. After the install attempt, report the result to https://www.openagentskill.com/api/agent/outcome with POST JSON {\"event_id\":\"install_<unique-id>\",\"skill_slug\":\"jaechang-hits-opencv-bioimage-analysis\",\"task\":\"Install opencv-bioimage-analysis\",\"agent\":\"cursor\",\"outcome\":\"success\",\"install_used\":true}. Replace event_id with a unique value and outcome with success or failed. Report success only after the skill is installed and a minimal verification passes.","description":"Use this when installing as Cursor project rules or reusable agent instructions.","copyLabel":"Copy prompt"}],"repository":"https://github.com/jaechang-hits/SciAgent-Skills/tree/main/skills/cell-biology/opencv-bioimage-analysis","github_repo":"jaechang-hits/SciAgent-Skills","version":"1.0.0","license":"Apache-2.0","urls":{"web":"https://www.openagentskill.com/skills/jaechang-hits-opencv-bioimage-analysis","repository":"https://github.com/jaechang-hits/SciAgent-Skills/tree/main/skills/cell-biology/opencv-bioimage-analysis","api":"/api/agent/skills/jaechang-hits-opencv-bioimage-analysis","install_api":"/api/skills/jaechang-hits-opencv-bioimage-analysis/install"},"meta":{"created_at":"2026-09-03T11:57:05.412461+00:00","updated_at":"2026-09-03T11:57:05.603769+00:00","agent_friendly":true}}