{"channelImages":{"list":[{"importKeyword":"_REF","name":"RFP"},{"importKeyword":"","name":"YFP"}]},"template":{"transformations":{"list":[{"pluginName":"RemoveDeadPixels","params":[{"Local Threshold":20.0},{"Frame Radius":4}],"inputChannel":[1]},{"pluginName":"RemoveDeadPixels","params":[{"Local Threshold":35.0},{"Frame Radius":1}],"inputChannel":[1]},{"pluginName":"RemoveStripesSignalExclusion","params":[{"Channel for Signal Exclusion":[0]},{"Signal Exclusion Threshold":{"pluginName":"BackgroundFit","params":[{"Sigma factor":5.0}]}},{"Second Signal Exclusion":{"action":"false"}},{"Add global mean (avoid negative values)":{"action":"false","params":[{"Set Negative values to Zero":"false"}]}}],"inputChannel":[0]},{"pluginName":"RemoveStripesSignalExclusion","params":[{"Channel for Signal Exclusion":[0]},{"Signal Exclusion Threshold":{"pluginName":"BackgroundFit","params":[{"Sigma factor":5.0}]}},{"Second Signal Exclusion":{"action":"true","params":[{"Channel for Signal Exclusion 2":[1]},{"Signal Exclusion Threshold 2":{"pluginName":"BackgroundFit","params":[{"Sigma factor":10.0}]}}]}},{"Add global mean (avoid negative values)":{"action":"false","params":[{"Set Negative values to Zero":"false"}]}}],"inputChannel":[1]},{"pluginName":"SaturateHistogramHyperfluoBacteria","params":[{"Maximum Saturated Signal Amount Proportion":0.02},{"Minimum Signal Ratio":10}],"inputChannel":[0]},{"pluginName":"AutoRotationXY","params":[{"Search method":"Fluo Microchannel"},{"Minimal Angle for search":-10.0},{"Maximal Angle for search":10.0},{"Angular Precision of first seach":0.5},{"Angular Precision":0.05},{"Interpolation":"BSPLINE5"},{"Number of frame":10},{"Remove Incomplete rows and columns":"false"},{"Maintain Maximum Value":"true"},{"Pre-Filters":{"list":[]}}],"inputChannel":[0]},{"pluginName":"AutoFlipY","params":[{"Method":{"action":"Bacteria Fluo: Upper Half of Image"}}],"inputChannel":[0]},{"pluginName":"CropMicrochannelsFluo2D","params":[{"Channel Height":350},{"Crop Margin":45},{"Object Size Filter":200},{"Intensity Threshold":{"pluginName":"BackgroundFit","params":[{"Sigma factor":10.0}]}},{"Filling proportion of Microchannel":0.5},{"Bound constraint":[{"X start":0},{"X stop (0 for image width)":0},{"Y start":0},{"Y stop (0 for image heigth)":0}]}],"inputChannel":[0]},{"pluginName":"TypeConverter","params":[{"Method":{"action":"LIMIT_TO_16","params":[{"Add value":1000}]}}]}]},"trimFramesEnd":0,"frameDuration":120.0,"trimFramesStart":0,"useImageScale":"Use Image Calibration","scaleXY":1,"scaleZ":1},"bestFocusPlane":[{"Channel":[0]},{"Algorithm":{"pluginName":"SelectBestFocusPlane","params":[{"Gradient Scale":3},{"Signal Exclusion Threshold":{"pluginName":"BackgroundThresholder","params":[{"Sigma factor":2.5},{"Final Sigma factor":3.0},{"Iteration number":3},{"Starting value":{"pluginName":"no selection"}}]}}]}}],"imagePath":[],"outputPath":[null],"structures":{"list":[{"name":"Microchannel","channelImage":[0],"manualSegmenter":{"pluginName":"no selection"},"segmentationParent":[],"parentStructure":[],"allowSplit":"no","allowMerge":"no","objectSplitter":{"pluginName":"no selection"},"processingScheme":{"pluginName":"SegmentAndTrack","params":[{"Pre-Filters":{"list":[]}},{"Track Pre-Filters":{"list":[]}},{"Tracker":{"pluginName":"MicrochannelTracker","params":[{"Segmentation algorithm":{"pluginName":"MicrochannelFluo2D","params":[{"Microchannel Height":430},{"Microchannel Width":60},{"y-shift (start of microchannel)":20},{"Threshold":{"pluginName":"BackgroundFit","params":[{"Sigma factor":10.0}]}},{"Microchannel filling proportion":0.3},{"Min. Object Size":200}]}},{"Maximal Distance for Gap-Closing procedure":40},{"Maximal Distance Factor for Frame-to-Frame Tracking":0.5},{"Normalize Y-shifts":{"action":"true","params":[{"Y-shift Quantile":0.05}]}},{"Normalize Widths":{"action":"true","params":[{"With Quantile":0.9}]}},{"Allow Gaps":"true"}]}},{"Post-Filters":{"list":[]}},{"Track Post-Filters":{"list":[{"pluginName":"RemoveMicrochannelsTouchingBackgroundOnSides","params":[{"Background":[2]},{"X margin":8}]},{"pluginName":"RemoveMicrochannelsWithOverexpression","params":[{"Intensity Quantile":99.0},{"Inter-Quartile Factor":5.0},{"Remove Method":"Trim Track"}]},{"pluginName":"TrackLengthFilter","params":[{"Minimum Length":5},{"Maximum Length":0},{"Merge Policy":"ALWAYS_MERGE"}]},{"pluginName":"RemoveTracksStartingAfterFrame","params":[{"Maximum starting frame":0},{"Merge Policy":"ALWAYS_MERGE"}]}]}}]}},{"name":"Bacteria","channelImage":[0],"manualSegmenter":{"pluginName":"no selection"},"segmentationParent":[0],"parentStructure":[0],"allowSplit":"yes","allowMerge":"no","objectSplitter":{"pluginName":"no selection"},"processingScheme":{"pluginName":"SegmentAndTrack","params":[{"Pre-Filters":{"list":[]}},{"Track Pre-Filters":{"list":[]}},{"Tracker":{"pluginName":"BacteriaClosedMicrochannelTrackerLocalCorrections","params":[{"Segmentation algorithm":{"pluginName":"BacteriaIntensity","params":[{"Sigma\/Mu thld for void channels":0.085},{"Edge Map":{"list":[{"pluginName":"ImageFeature","params":[{"Feature":{"action":"Gaussian Smooth","params":[{"Scale":{"scaleXY":1.5,"scaleZ":1.0,"useImageCalibration":"true"}}]}}]},{"pluginName":"Sigma","params":[{"Radius":{"scaleXY":2.0,"scaleZ":1.0,"useImageCalibration":"true"}},{"Median Filtering Radius":{"scaleXY":0.0,"scaleZ":1.0,"useImageCalibration":"true"}}]}]}},{"Foreground Selection Method":{"action":"EDGE_FUSION","params":[{"Background Edge Fusion Threshold":2},{"Foreground Edge Fusion Threshold":0.2},{"Background Threshold":{"action":"ROOT_BRANCH","params":[{"Method":{"pluginName":"BackgroundFit","params":[{"Sigma factor":10.0}]}}]}}]}},{"Hessian scale":4},{"Split Threshold":0.3},{"Smooth scale":2},{"Local Threshold Factor":1.25},{"Minimum Region Size":100}]}},{"Feature used for Size":"Size"},{"Minimum size Ratio":0.8},{"Maximum Size Ratio":1.5},{"Correction: operation cost limit":0.25},{"Correction: cumulative cost limit":1.25},{"End of channel contact Threshold":0.45}]}},{"Post-Filters":{"list":[]}},{"Track Post-Filters":{"list":[{"pluginName":"SegmentationPostFilter","params":[{"Delete method":"Prune Track"},{"Merge Policy":"MERGE_TRACKS_SIZE_COND"},{"Filter":{"list":[{"pluginName":"RemoveEndofChannelBacteria","params":[{"Do not remove if only one object":"true"},{"Contact Proportion":0.9},{"Minimum Size":300},{"Contact with Sides Proportion":0.6}]}]}}]},{"pluginName":"RemoveTrackByFeature","params":[{"Feature":{"pluginName":"Size","params":[{"Scale":"Pixel"}]}},{"Statistics":{"action":"Quantile","params":[{"Quantile":0.25}]}},{"Threshold":150.0},{"Keep over threshold":"true"},{"Merge Policy":"MERGE_TRACKS_SIZE_COND"}]}]}}]}},{"name":"Mutation","channelImage":[1],"manualSegmenter":{"pluginName":"no selection"},"segmentationParent":[1],"parentStructure":[0],"allowSplit":"no","allowMerge":"no","objectSplitter":{"pluginName":"no selection"},"processingScheme":{"pluginName":"SegmentAndTrack","params":[{"Pre-Filters":{"list":[{"pluginName":"BandPass","params":[{"Remove structures under size (pixels)":0.0},{"Remove structures over size (pixels)":7.0},{"Remove Stripes":{"action":"None","params":[]}}]}]}},{"Track Pre-Filters":{"list":[]}},{"Tracker":{"pluginName":"MutationTrackerSpine","params":[{"Segmentation algorithm":{"pluginName":"MutationSegmenter","params":[{"Scale":{"list":[2.5]}},{"Smooth scale":2},{"Min. Spot Size (Voxels)":5},{"Threshold for Seeds":3.0},{"Threshold for propagation":2.75},{"Intensity Threshold for Seeds":2.0}]}},{"Compartiment Structure":[1]},{"Projection type":"PROPORTIONAL"},{"Maximum Linking Distance (FTF)":0.75},{"Maximum Linking Distance":0.75},{"Maximum frame gap":3},{"Gap Distance Penalty":0.15},{"Alternative Distance":0.77},{"Spot Quality Threshold":3.122}]}},{"Post-Filters":{"list":[{"pluginName":"FeatureFilter","params":[{"Feature":{"pluginName":"Quality"}},{"Threshold":2.2},{"Keep over threshold":"true"},{"Strict comparison with threshold":"true"}]}]}},{"Track Post-Filters":{"list":[]}}]}}]},"importMethod":{"action":"One File Per Channel And Position"},"positions":{"list":[]},"measurements":{"list":[{"pluginName":"BacteriaLineageMeasurements","params":[{"Bacteria Structure":[1]},{"Lineage Index Name":"BacteriaLineage"}]},{"pluginName":"ObjectFeatures","params":[{"Structure":[1]},{"Pre-Filters":{"list":[]}},{"Features":{"list":[{"pluginName":"Size","addParams":[{"Key":"Size"}],"params":[{"Scale":"Unit"}]},{"pluginName":"FeretMax","addParams":[{"Key":"Length"}],"params":[{"Scale":"Unit"}]},{"pluginName":"Mean","addParams":[{"Key":"MeanIntensity"}],"params":[{"Intensity":[1]}]}]}}]},{"pluginName":"ObjectFeatures","params":[{"Structure":[1]},{"Pre-Filters":{"list":[{"pluginName":"ImageFeature","params":[{"Feature":{"action":"Gradient","params":[{"Scale":{"scaleXY":2.5,"scaleZ":1.0,"useImageCalibration":"true"}}]}}]}]}},{"Features":{"list":[{"pluginName":"MeanAtBorder","addParams":[{"Key":"MeanIntensityBorder"}],"params":[{"Intensity":[1]}]}]}}]},{"pluginName":"MutationTrackMeasurements","params":[{"Bacteria Structure":[1]},{"Mutation Structure":[2]}]},{"pluginName":"ObjectInclusionCount","params":[{"Containing Structure":[1]},{"Structure to count":[2]},{"Minimum percentage of inclusion":10.0},{"Count Only TrackHeads":"false"},{"Inclusion Key Name":"MutationNumber"}]},{"pluginName":"ObjectFeatures","params":[{"Structure":[2]},{"Pre-Filters":{"list":[]}},{"Features":{"list":[{"pluginName":"Quality","addParams":[{"Key":"Quality"}]}]}}]},{"pluginName":"RelativePosition","params":[{"Structure":[1]},{"Reference Structure":[0]},{"Object Point":"Geometrical Center"},{"Reference Point":"Upper Left Corner"},{"Key Name":"Center"}]},{"pluginName":"GrowthRate","params":[{"Bacteria Structure":[1]},{"Feature":{"pluginName":"Size","params":[{"Scale":"Pixel"}]}},{"Suffix":"Area"},{"Save Feature":{"action":"false"}},{"Save Residuals":"false"},{"Save Intersection":"false"}]},{"pluginName":"GrowthRate","params":[{"Bacteria Structure":[1]},{"Feature":{"pluginName":"FeretMax","params":[{"Scale":"Unit"}]}},{"Suffix":"Length"},{"Save Feature":{"action":"false"}},{"Save Residuals":"false"},{"Save Intersection":"false"}]},{"pluginName":"GrowthRate","params":[{"Bacteria Structure":[1]},{"Feature":{"pluginName":"SpineLength","params":[{"Scale":"Pixel"}]}},{"Suffix":"SpineLength"},{"Save Feature":{"action":"false"}},{"Save Residuals":"false"},{"Save Intersection":"false"}]}]}}