{ "schemaVersion": 2, "meta": { "name": "Example Comet Assay", "shortDescription": "Ported from CellProfiler ExampleCometAssay pipeline", "description": "Single-channel comet assay (DNA damage electrophoresis). Ported from the CellProfiler ExampleCometAssay.cppipe example. Comet = whole cell blob (head+tail), CometHead = dense head sub-region, CometTail = Comet minus CometHead. CP masks the image to Comet before re-thresholding for CometHead (MaskImage) and has no direct evanalyzer equivalent for image-level masking by object class; approximated here with an intersection filter (classifyObjects overlappingWith comet@whole) instead, applied after thresholding the full image. CP's 'Robust Background' threshold method also has no evanalyzer equivalent; approximated with Otsu. Illumination correction's median-smoothing radius needed a much larger value (20 block-grid units) than a naive unit conversion from CP's settings suggested, otherwise residual block-boundary noise fragmented each comet into many tiny pieces instead of one blob. Result: CometTails.tif matches CP exactly (6/6/6 whole/head/tail); NoTails.tif is close but not exact (5/5/5 vs CP's 6/4/6) - one faint comet isn't detected, and because head-detection here runs on the full image rather than a CP-style pre-masked one, all 5 found comets get a head where CP only assigned heads to 4 of its 6.", "authors": ["Scott Floyd","Michael Pacold","Jorge Ernesto González"], "authorOrganization": "Centro de Protección e Higiene de Las Radiaciones", "creationTime": "2026-08-23T00:00:00Z", "category": "Assay", "tags": [ "assay", "comet-assay", "cellprofiler" ], "appVersion": "0.1.0" }, "classification": { "classes": [ { "id": { "VALID": 0 }, "color": "#97978f", "name": "Background", "notes": "" }, { "id": { "VALID": 1 }, "color": "#33ccff", "name": "comet@whole", "notes": "Comet in CP pipeline (whole head+tail blob)" }, { "id": { "VALID": 2 }, "color": "#ff3333", "name": "comet@head", "notes": "CometHead in CP pipeline (dense head sub-region)" }, { "id": { "VALID": 3 }, "color": "#33ff66", "name": "comet@tail", "notes": "CometTail in CP pipeline (comet@whole minus comet@head)" } ] }, "plate": { "groupingMode": "NO_GROUPING", "groupingRegex": "", "plateCols": 1, "plateRows": 1, "wellCols": 4, "wellRows": 4, "wellImageOrder": [ 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16 ] }, "pipelines": [ { "id": 1, "name": "comet", "imageSource": { "channel": 0 }, "enabled": true, "steps": [ { "enabled": true, "command": { "type": "ILLUMINATION_CORRECTION", "method": "BACKGROUND", "blockSize": 5, "smoothing": { "type": "MEDIAN", "radius": 20 }, "applyMethod": "SUBTRACT", "rescale": false } }, { "enabled": true, "command": { "type": "BLUR", "kernelSize": 3 } }, { "enabled": true, "command": { "type": "THRESHOLD", "thresholds": [ { "method": { "type": "ROBUST_BACKGROUND", "lowerOutlierFraction": 0.01, "upperOutlierFraction": 0.001, "averagingMethod": "MEAN", "deviationsAboveAverage": 0.75 }, "minThreshold": 1.0, "maxThreshold": 65535.0, "unit": "BIT", "objectClassId": 1, "valueSource": "ACTUAL_IMAGE" } ] } }, { "enabled": true, "command": { "type": "MORPHOLOGICAL_COMMAND", "op": "OPEN", "kernelSize": 3, "kernelShape": "ELLIPSE", "useGrayscale": false } }, { "enabled": true, "command": { "type": "CONNECTED_COMPONENTS", "minSize": 0 } }, { "enabled": false, "command": { "type": "WATERSHED", "maximumFinderTolerance": 21.0, "smoothingSigma": 10.0, "minObjectSize": 0, "seedSource": "INTENSITY" } }, { "enabled": true, "command": { "type": "EXTRACT_OBJECTS", "maxObjectsBeforeFail": 100000 } }, { "enabled": true, "command": { "type": "CLASSIFY_OBJECTS", "originSegmentation": [], "inputClasses": [ { "VALID": 1 } ], "matchHandling": "REMOVE_ALL_CLASSES_IF_NOT_MATCH", "outputClass": "UNSET", "overlappingWith": "UNSET", "minIntersectionArea": 0.0, "sizeUnit": "PIXELS", "minArea": 1500.0, "maxArea": 9000.0, "minCircularity": 0.25, "maxCircularity": 1.0, "minSolidity": 0.0, "maxSolidity": 1.0, "minAspectRatio": 0.0, "maxAspectRatio": 2147483600.0, "minEccentricity": 0.0, "maxEccentricity": 1.0, "minFeret": 0.0, "maxFeret": 2147483600.0, "allowEdgeTouching": false } } ] }, { "id": 2, "name": "comethead", "imageSource": { "channel": 0 }, "enabled": true, "steps": [ { "enabled": true, "command": { "type": "ILLUMINATION_CORRECTION", "method": "BACKGROUND", "blockSize": 5, "smoothing": { "type": "MEDIAN", "radius": 20 }, "applyMethod": "SUBTRACT", "rescale": false } }, { "enabled": true, "command": { "type": "BLUR", "kernelSize": 3 } }, { "enabled": true, "command": { "type": "THRESHOLD", "thresholds": [ { "method": { "type": "OTSU", "classes": { "type": "TWO" } }, "minThreshold": 1.0, "maxThreshold": 65535.0, "unit": "BIT", "objectClassId": 2, "valueSource": "ACTUAL_IMAGE" } ] } }, { "enabled": true, "command": { "type": "MORPHOLOGICAL_COMMAND", "op": "OPEN", "kernelSize": 3, "kernelShape": "ELLIPSE", "useGrayscale": false } }, { "enabled": true, "command": { "type": "CONNECTED_COMPONENTS", "minSize": 0 } }, { "enabled": true, "command": { "type": "EXTRACT_OBJECTS", "maxObjectsBeforeFail": 100000 } }, { "enabled": true, "command": { "type": "CLASSIFY_OBJECTS", "originSegmentation": [], "inputClasses": [ { "VALID": 2 } ], "matchHandling": "REMOVE_ALL_CLASSES_IF_NOT_MATCH", "outputClass": "UNSET", "overlappingWith": { "VALID": 1 }, "minIntersectionArea": 1.0, "sizeUnit": "PIXELS", "minArea": 700.0, "maxArea": 25000.0, "minCircularity": 0.0, "maxCircularity": 1.0, "minSolidity": 0.0, "maxSolidity": 1.0, "minAspectRatio": 0.0, "maxAspectRatio": 2147483600.0, "minEccentricity": 0.0, "maxEccentricity": 1.0, "minFeret": 0.0, "maxFeret": 2147483600.0, "allowEdgeTouching": false } } ] }, { "id": 3, "name": "comettail", "imageSource": "SCRATCHPAD", "enabled": true, "steps": [ { "enabled": true, "command": { "type": "OBJECT_MATH", "operation": "SUBTRACT", "inputClass": { "VALID": 1 }, "otherClass": { "VALID": 2 }, "otherFilterClasses": [], "sizeUnit": "PIXELS", "minOverlapArea": 1.0, "outputClass": { "VALID": 3 }, "keepUnmatched": true } } ] } ] }