{"channelImages":{"list":[{"importKeyword":"_REF","name":"RFP"},{"importKeyword":"","name":"YFP"}]},"template":{"trimFrames":[0.0,0.0],"transformations":{"list":[{"pluginName":"RemoveHotPixels","params":[{"Local Threshold":20.0},{"Frame Radius":4}],"inputChannel":[1]},{"pluginName":"RemoveHotPixels","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":{"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":{"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"},{"Angle range search":[-10.0,10.0]},{"Angular Precision of first search":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 Length":350},{"Crop Margin":45},{"Object Size Filter":200},{"Threshold":{"pluginName":"BackgroundThresholder","params":[{"Sigma factor":3.0},{"Final Sigma factor":6.0},{"Iteration number":3},{"Starting value":{"pluginName":"no selection"}}]}},{"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}]}}]}]},"frameDuration":120.0,"useImageScale":"Custom Calibration","scaleXY":0.0646,"scaleZ":1},"note":"","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"}}]}}]}}],"channelImagesDuplicated":{"list":[]},"structures":{"list":[{"name":"Microchannels","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 Length":320},{"Microchannel Width":60},{"y-Start Shift":20},{"Threshold":{"pluginName":"BackgroundFit","params":[{"Sigma factor":10.0}]}},{"Microchannel filling proportion":0.3},{"Min. Object Size":200}]}},{"Maximal Distance for Frame-to-Frame Tracking":10},{"Maximal Distance for Gap-Closing procedure":40},{"Maximum Frame Gap":10},{"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":"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":"BacteriaFluo","params":[{"Variation coefficient threshold":0.085},{"Edge Map":{"list":[{"pluginName":"ImageFeature","params":[{"Feature":{"action":"Gaussian Smooth","params":[{"Scale":{"scaleXY":1.5,"scaleZ":1.0,"useImageCalibration":"true"}}]}}]},{"pluginName":"StandardDeviation","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":0.8},{"Background Removal":{"action":"BORDER_CONTACT"}}]}},{"Hessian scale":4},{"Split Threshold":0.3},{"Smooth scale":2},{"Contour adjustment":{"action":"LOCAL_THLD_IQR","params":[{"Local Threshold Factor":1.25}]}}]}},{"Feature used for Size":"Size"},{"Size Ratio":[0.8,1.5]},{"Correction: operation cost limit":0.25},{"Correction: cumulative cost limit":1.25},{"End of channel contact Threshold":0.9}]}},{"Post-Filters":{"list":[{"pluginName":"FeatureFilter","params":[{"Feature":{"pluginName":"Size","params":[{"Scaled":"Pixel"}]}},{"Threshold":50.0},{"Keep over threshold":"true"},{"Strict comparison with threshold":"true"}]}]}},{"Track Post-Filters":{"list":[{"pluginName":"PostFilter","params":[{"Filter":{"pluginName":"RemoveEndofChannelBacteria","params":[{"Do not remove if only one object":"true"},{"Contact Proportion":0.005},{"Minimum Size":100},{"Contact with Sides Proportion":0}]}},{"Delete method":"Prune Track"},{"Merge Policy":"MERGE_TRACKS_BACT_SIZE_COND"}]},{"pluginName":"RemoveTrackByFeature","params":[{"Feature":{"pluginName":"Size","params":[{"Scaled":"Pixel"}]}},{"Statistics":{"action":"Quantile","params":[{"Quantile":0.25}]}},{"Threshold":150.0},{"Keep over threshold":"true"},{"Merge Policy":"MERGE_TRACKS_BACT_SIZE_COND"}]}]}}]}},{"name":"Spots","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":[{"Band-pass range":[0.0,7.0]},{"Remove Stripes":{"action":"None","params":[]}}]}]}},{"Track Pre-Filters":{"list":[]}},{"Tracker":{"pluginName":"NestedSpotTracker","params":[{"Segmentation algorithm":{"pluginName":"SpotDetector","params":[{"Radial Symmetry Threshold":0.15},{"Seed Threshold":1.2},{"Intensity normalization":"PER_CELL"},{"Radial Symmetry Radii":{"list":[1.0,2.0,3.0,4.0]}},{"Smooth globalScale":1.5},{"Max local radius":{"scaleXY":1.5,"scaleZ":1.5,"useImageCalibration":"false"}},{"Typical sigma":2},{"Sigma Filter":4}]}},{"Bacteria Object Class":[1]},{"Bacteria Growth Mode":"PROPORTIONAL"},{"Correct Rotation":"true"},{"Maximum Linking Distance (FTF)":0.4},{"Maximum Linking Distance":0.75},{"Maximum Frame Gap":0},{"Gap Distance Penalty":0.15},{"Spot Quality Threshold":0.7},{"Allow splitting":"false"},{"Allow merging":"false"}]}},{"Post-Filters":{"list":[{"pluginName":"FeatureFilter","params":[{"Feature":{"pluginName":"Quality"}},{"Threshold":0.5},{"Keep over threshold":"true"},{"Strict comparison with threshold":"true"}]}]}},{"Track Post-Filters":{"list":[]}}]}}]},"importMethod":{"action":"One File Per Channel And Position","params":[{"Swap T & Z dimension":"false"}]},"positions":{"list":[]},"measurements":{"list":[{"pluginName":"BacteriaLineageMeasurements","params":[{"Object Class":[1]},{"Lineage Index Name":"BacteriaLineage"}]},{"pluginName":"SimpleTrackMeasurements","params":[{"Objects":[1]}]},{"pluginName":"ObjectFeatures","params":[{"Object class":[1]},{"Pre-Filters":{"list":[]}},{"Features":{"list":[{"pluginName":"Mean","addParams":[{"Name":"MeanIntensity"}],"params":[{"Intensity":[1]}]}]}}]},{"pluginName":"ObjectFeatures","params":[{"Object class":[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":[{"Name":"MeanIntensityBorderGrad"}],"params":[{"Intensity":[1]}]}]}}],"activated":false},{"pluginName":"ObjectFeatures","params":[{"Object class":[1]},{"Pre-Filters":{"list":[]}},{"Features":{"list":[{"pluginName":"SNR","addParams":[{"Name":"SpotSignalSNR"}],"params":[{"Intensity":[2]},{"Background Object Class":[0]},{"Formula":"(F-B)\/std(B)"},{"Foreground":"mean"},{"Dilatation radius for foreground object":3.0},{"Radius for background mask erosion":0.0}]}]}}],"activated":false},{"pluginName":"ContainerObject","params":[{"Objects":[2]},{"Container Object":[1]},{"Key Name: ":"Bacteria"},{"Attribute of container to return":[0,1]}]},{"pluginName":"SimpleTrackMeasurements","params":[{"Objects":[2]}]},{"pluginName":"SimpleTrackMeasurements","params":[{"Objects":[0]}]},{"pluginName":"ObjectFeatures","params":[{"Object class":[2]},{"Pre-Filters":{"list":[]}},{"Features":{"list":[{"pluginName":"Mean","addParams":[{"Name":"MeanIntensity"}],"params":[{"Intensity":[2]}]},{"pluginName":"Max","addParams":[{"Name":"Max"}],"params":[{"Intensity":[2]}]},{"pluginName":"Min","addParams":[{"Name":"Min"}],"params":[{"Intensity":[2]}]}]}}]},{"pluginName":"ObjectInclusionCount","params":[{"Containing Objects":[1]},{"Objects to count":[2]},{"Minimum percentage of inclusion":10.0},{"Count Only TrackHeads":"false"},{"Measurement Name":"SpotNumber"}]},{"pluginName":"ObjectFeatures","params":[{"Object class":[2]},{"Pre-Filters":{"list":[]}},{"Features":{"list":[{"pluginName":"Quality","addParams":[{"Name":"Quality"}]}]}}]},{"pluginName":"RelativePosition","params":[{"Objects":[1]},{"Reference Objects":[0]},{"Object Point":"Geometrical Center"},{"Reference Point":"Upper Left Corner"},{"Column Name":"Center"},{"Include Z":"true"}]},{"pluginName":"GrowthRate","params":[{"Object Class":[1]},{"Feature":{"pluginName":"Size","params":[{"Scaled":"Unit"}]}},{"Minimum cell number":3},{"Suffix":"Area"},{"Save Feature":{"action":"true","params":[{"Feature Name":"Size"}]}},{"Save Size at Birth":"true"}]},{"pluginName":"GrowthRate","params":[{"Object Class":[1]},{"Feature":{"pluginName":"FeretMax","params":[{"Scaled":"Unit"}]}},{"Minimum cell number":3},{"Suffix":"Length"},{"Save Feature":{"action":"true","params":[{"Feature Name":"Length"}]}},{"Save Size at Birth":"true"}]}]}}