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MIA_foci_demo.mia
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MIA_foci_demo.mia
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<?xml version="1.0" encoding="UTF-8"?><ROOT MIA_VERSION="1.2.7"><MODULES><MODULE CLASSNAME="io.github.mianalysis.mia.module.core.InputControl" DISABLEABLE="false" ENABLED="true" ID="1687385105051" NAME="Input control" NICKNAME="Input control" NOTES="" SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false"><PARAMETERS><PARAMETER NAME="Input path" NICKNAME="Input path" VALUE="C:\Users\anast\OneDrive\Documents\Kota-NEUBIAS_Tools\Exemplar images\MIA" VISIBLE="true"/><PARAMETER NAME="Series mode" NICKNAME="Series mode" VALUE="All series" VISIBLE="false"/><PARAMETER NAME="Series list" NICKNAME="Series list" VALUE="1" VISIBLE="false"/><PARAMETER NAME="Only load first file per folder" NICKNAME="Only load first file per folder" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Only load first matching group" NICKNAME="Only load first matching group" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Pattern" NICKNAME="Pattern" VALUE="" VISIBLE="false"/><PARAMETER NAME="Spatial unit" NICKNAME="Spatial unit" VALUE="Micrometres" VISIBLE="false"/><PARAMETER NAME="Temporal unit" NICKNAME="Temporal unit" VALUE="Milliseconds" VISIBLE="false"/><PARAMETER NAME="Ignore case" NICKNAME="Ignore case" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Add filter" NICKNAME="Add filter" VALUE="" VISIBLE="false"><COLLECTION><PARAMS><PARAM NAME="Filter source" NICKNAME="Filter source" VALUE="Filename" VISIBLE="true"/><PARAM NAME="Filter value" NICKNAME="Filter value" VALUE="_over" VISIBLE="true"/><PARAM NAME="Filter type" NICKNAME="Filter type" VALUE="Matches partially (exclude)" VISIBLE="true"/></PARAMS><PARAMS><PARAM NAME="Filter source" NICKNAME="Filter source" VALUE="Extension" VISIBLE="true"/><PARAM NAME="Filter value" NICKNAME="Filter value" VALUE="xls" VISIBLE="true"/><PARAM NAME="Filter type" NICKNAME="Filter type" VALUE="Matches partially (exclude)" VISIBLE="true"/></PARAMS></COLLECTION></PARAMETER><PARAMETER NAME="Simultaneous jobs" NICKNAME="Simultaneous jobs" VALUE="1" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA><METADATUM EXPORT_GLOBAL="true" EXPORT_INDIVIDUAL="true" NAME="Extension" NICKNAME="Extension"/><METADATUM EXPORT_GLOBAL="true" EXPORT_INDIVIDUAL="true" NAME="File" NICKNAME="File"/><METADATUM EXPORT_GLOBAL="true" EXPORT_INDIVIDUAL="true" NAME="Filename" NICKNAME="Filename"/><METADATUM EXPORT_GLOBAL="true" EXPORT_INDIVIDUAL="true" NAME="Filepath" NICKNAME="Filepath"/><METADATUM EXPORT_GLOBAL="true" EXPORT_INDIVIDUAL="true" NAME="Series name" NICKNAME="Series name"/><METADATUM EXPORT_GLOBAL="true" EXPORT_INDIVIDUAL="true" NAME="Series number" NICKNAME="Series number"/></METADATA></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.core.OutputControl" DISABLEABLE="false" ENABLED="true" ID="1687385105058" NAME="Output control" NICKNAME="Output control" NOTES="" SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false"><PARAMETERS><PARAMETER NAME="Add variable" NICKNAME="Add variable" VALUE="" VISIBLE="false"><COLLECTION/></PARAMETER><PARAMETER NAME="Run macro" NICKNAME="Run macro" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Macro mode" NICKNAME="Macro mode" VALUE="Macro text" VISIBLE="false"/><PARAMETER NAME="Macro text" NICKNAME="Macro text" VALUE="run("Enable MIA Extensions"); // Get a list of Workspace IDs with Ext.MIA_GetListOfWorkspaceIDs() and set active workspace with Ext.MIA_SetActiveWorkspace(ID)." VISIBLE="false"/><PARAMETER NAME="Macro file" NICKNAME="Macro file" VALUE="" VISIBLE="false"/><PARAMETER NAME="Export mode" NICKNAME="Export mode" VALUE="All together" VISIBLE="false"/><PARAMETER NAME="Individual save location" NICKNAME="Individual save location" VALUE="Save with input file" VISIBLE="false"/><PARAMETER NAME="Group save location" NICKNAME="Group save location" VALUE="Save with input file" VISIBLE="false"/><PARAMETER NAME="File path" NICKNAME="File path" VALUE="" VISIBLE="false"/><PARAMETER NAME="Mirrored directory root" NICKNAME="Mirrored directory root" VALUE="" VISIBLE="false"/><PARAMETER NAME="Save name mode" NICKNAME="Save name mode" VALUE="Match input file/folder name" VISIBLE="false"/><PARAMETER NAME="File name" NICKNAME="File name" VALUE="" VISIBLE="false"/><PARAMETER NAME="Metadata item for grouping" NICKNAME="Metadata item for grouping" VALUE="" VISIBLE="false"/><PARAMETER NAME="Continuous data export" NICKNAME="Continuous data export" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Save every n files" NICKNAME="Save every n files" VALUE="10" VISIBLE="false"/><PARAMETER NAME="Append date/time mode" NICKNAME="Append date/time mode" VALUE="Never" VISIBLE="false"/><PARAMETER NAME="Export summary" NICKNAME="Export summary" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Summary mode" NICKNAME="Summary mode" VALUE="Per input file" VISIBLE="false"/><PARAMETER NAME="Metadata item for summary" NICKNAME="Metadata item for summary" VALUE="" VISIBLE="false"/><PARAMETER NAME="Show object counts" NICKNAME="Show object counts" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Export individual objects" NICKNAME="Export individual objects" VALUE="true" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA/></MODULE></MODULES><MODULES><MODULE CLASSNAME="io.github.mianalysis.mia.module.system.GUISeparator" DISABLEABLE="false" ENABLED="true" ID="1687468449281" NAME="GUI separator" NICKNAME="Nuclei" NOTES="" SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false"><PARAMETERS><PARAMETER NAME="Show in processing view" NICKNAME="Show in processing view" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Expanded in processing view" NICKNAME="Expanded in processing view" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Expanded in editing view" NICKNAME="Expanded in editing view" VALUE="false" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.inputoutput.ImageLoader" DISABLEABLE="false" ENABLED="true" ID="1687385105549" NAME="Load image" NICKNAME="Load image" NOTES="" SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false"><PARAMETERS><PARAMETER NAME="Output image" NICKNAME="Output image" VALUE="DAPI" VISIBLE="false"/><PARAMETER NAME="Import mode" NICKNAME="Import mode" VALUE="Current file" VISIBLE="false"/><PARAMETER NAME="Reader" NICKNAME="Reader" VALUE="Bio-Formats" VISIBLE="false"/><PARAMETER NAME="Sequence root name" NICKNAME="Sequence root name" VALUE="" VISIBLE="false"/><PARAMETER NAME="Name format" NICKNAME="Name format" VALUE="Generic (from metadata)" VISIBLE="false"/><PARAMETER NAME="Comment" NICKNAME="Comment" VALUE="" VISIBLE="false"/><PARAMETER NAME="Extension" NICKNAME="Extension" VALUE="" VISIBLE="false"/><PARAMETER NAME="Generic format" NICKNAME="Generic format" VALUE="" VISIBLE="false"/><PARAMETER NAME="Include series number" NICKNAME="Include series number" VALUE="true" VISIBLE="false"/><PARAMETER NAME="File path" NICKNAME="File path" VALUE="" VISIBLE="false"/><PARAMETER NAME="Series mode" NICKNAME="Series mode" VALUE="Current series" VISIBLE="false"/><PARAMETER NAME="Series number" NICKNAME="Series number" VALUE="1" VISIBLE="false"/><PARAMETER NAME="Channels" NICKNAME="Channels" VALUE="3" VISIBLE="false"/><PARAMETER NAME="Slices" NICKNAME="Slices" VALUE="1-end" VISIBLE="false"/><PARAMETER NAME="Frames" NICKNAME="Frames" VALUE="1-end" VISIBLE="false"/><PARAMETER NAME="Channel" NICKNAME="Channel" VALUE="1" VISIBLE="false"/><PARAMETER NAME="Crop mode" NICKNAME="Crop mode" VALUE="None" VISIBLE="false"/><PARAMETER NAME="Reference image" NICKNAME="Reference image" VALUE="" VISIBLE="false"/><PARAMETER NAME="Left coordinate" NICKNAME="Left coordinate" VALUE="0" VISIBLE="false"/><PARAMETER NAME="Top coordinate" NICKNAME="Top coordinate" VALUE="0" VISIBLE="false"/><PARAMETER NAME="Width" NICKNAME="Width" VALUE="512" VISIBLE="false"/><PARAMETER NAME="Height" NICKNAME="Height" VALUE="512" VISIBLE="false"/><PARAMETER NAME="Objects for limits" NICKNAME="Objects for limits" VALUE="" VISIBLE="false"/><PARAMETER NAME="Scale mode" NICKNAME="Scale mode" VALUE="No scaling" VISIBLE="false"/><PARAMETER NAME="X scale factor" NICKNAME="X scale factor" VALUE="1.0" VISIBLE="false"/><PARAMETER NAME="Y scale factor" NICKNAME="Y scale factor" VALUE="1.0" VISIBLE="false"/><PARAMETER NAME="Dimension mismatch mode" NICKNAME="Dimension mismatch mode" VALUE="Disallow (fail upon mismatch)" VISIBLE="false"/><PARAMETER NAME="Pad intensity mode" NICKNAME="Pad intensity mode" VALUE="Black (0)" VISIBLE="false"/><PARAMETER NAME="Set manual spatial calibration" NICKNAME="Set manual spatial calibration" VALUE="false" VISIBLE="false"/><PARAMETER NAME="XY calibration (dist/px)" NICKNAME="XY calibration (dist/px)" VALUE="1.0" VISIBLE="false"/><PARAMETER NAME="Z calibration (dist/px)" NICKNAME="Z calibration (dist/px)" VALUE="1.0" VISIBLE="false"/><PARAMETER NAME="Set manual temporal calibration" NICKNAME="Set manual temporal calibration" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Frame interval (time/frame)" NICKNAME="Frame interval (time/frame)" VALUE="1.0" VISIBLE="false"/><PARAMETER NAME="Force bit depth" NICKNAME="Force bit depth" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Output bit depth" NICKNAME="Output bit depth" VALUE="8" VISIBLE="false"/><PARAMETER NAME="Minimum input intensity" NICKNAME="Minimum input intensity" VALUE="0.0" VISIBLE="false"/><PARAMETER NAME="Maximum input intensity" NICKNAME="Maximum input intensity" VALUE="1.0" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.images.process.FilterImage" DISABLEABLE="false" ENABLED="true" ID="1687385155017" NAME="Filter image" NICKNAME="Filter image" NOTES="" SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false"><PARAMETERS><PARAMETER NAME="Input image" NICKNAME="Input image" VALUE="DAPI" VISIBLE="false"/><PARAMETER NAME="Apply to input image" NICKNAME="Apply to input image" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Output image" NICKNAME="Output image" VALUE="Filtered" VISIBLE="false"/><PARAMETER NAME="Filter mode" NICKNAME="Filter mode" VALUE="Median 2D" VISIBLE="false"/><PARAMETER NAME="Filter radius" NICKNAME="Filter radius" VALUE="5" VISIBLE="false"/><PARAMETER NAME="Calibrated units" NICKNAME="Calibrated units" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Rolling filter method" NICKNAME="Rolling filter method" VALUE="Average" VISIBLE="false"/><PARAMETER NAME="Window indices" NICKNAME="Window indices" VALUE="-1-1" VISIBLE="false"/><PARAMETER NAME="Contour contrast" NICKNAME="Contour contrast" VALUE="Dark line" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.images.process.threshold.GlobalAutoThreshold" DISABLEABLE="false" ENABLED="true" ID="1687385226636" NAME="Global auto-threshold" NICKNAME="Global auto-threshold" NOTES="" SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false"><PARAMETERS><PARAMETER NAME="Input image" NICKNAME="Input image" VALUE="Filtered" VISIBLE="false"/><PARAMETER NAME="Output mode" NICKNAME="Output mode" VALUE="Calculate and apply" VISIBLE="false"/><PARAMETER NAME="Apply to input image" NICKNAME="Apply to input image" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Output image" NICKNAME="Output image" VALUE="DAPI_binary" VISIBLE="false"/><PARAMETER NAME="Algorithm" NICKNAME="Algorithm" VALUE="Huang" VISIBLE="true"/><PARAMETER NAME="Threshold multiplier" NICKNAME="Threshold multiplier" VALUE="1.2" VISIBLE="true"/><PARAMETER NAME="Use lower threshold limit" NICKNAME="Use lower threshold limit" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Lower threshold limit" NICKNAME="Lower threshold limit" VALUE="0.0" VISIBLE="false"/><PARAMETER NAME="Binary logic" NICKNAME="Binary logic" VALUE="Black (0) background" VISIBLE="false"/><PARAMETER NAME="Measure on objects" NICKNAME="Measure on objects" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Input objects" NICKNAME="Input objects" VALUE="" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS><MEASUREMENT EXPORT_GLOBAL="true" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" IMAGE_NAME="DAPI_binary" NAME="THRESHOLD // GLOBAL Huang" NICKNAME="THRESHOLD // GLOBAL Huang"/></IMAGE_MEASUREMENTS><OBJECT_MEASUREMENTS/><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.objects.detect.IdentifyObjects" DISABLEABLE="false" ENABLED="true" ID="1687385261668" NAME="Identify objects" NICKNAME="Identify objects" NOTES="" SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false"><PARAMETERS><PARAMETER NAME="Input image" NICKNAME="Input image" VALUE="DAPI_binary" VISIBLE="false"/><PARAMETER NAME="Output objects" NICKNAME="Output objects" VALUE="Nuclei" VISIBLE="false"/><PARAMETER NAME="Binary logic" NICKNAME="Binary logic" VALUE="Black (0) background" VISIBLE="false"/><PARAMETER NAME="Detection mode" NICKNAME="Detection mode" VALUE="3D" VISIBLE="false"/><PARAMETER NAME="Identify as single object" NICKNAME="Identify as single object" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Connectivity" NICKNAME="Connectivity" VALUE="26" VISIBLE="false"/><PARAMETER NAME="Volume type" NICKNAME="Volume type" VALUE="Quadtree" VISIBLE="false"/><PARAMETER NAME="Enable multithreading" NICKNAME="Enable multithreading" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Minimum strip width (px)" NICKNAME="Minimum strip width (px)" VALUE="60" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.objects.transform.FillHolesInObjects" DISABLEABLE="false" ENABLED="true" ID="1687474450946" NAME="Fill holes in objects" NICKNAME="Fill holes in objects" NOTES="" SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false"><PARAMETERS><PARAMETER NAME="Input objects" NICKNAME="Input objects" VALUE="Nuclei" VISIBLE="false"/><PARAMETER NAME="Update input objects" NICKNAME="Update input objects" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Output objects" NICKNAME="Output objects" VALUE="" VISIBLE="false"/><PARAMETER NAME="Method" NICKNAME="Method" VALUE="Fill holes 2D" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.objects.filter.FilterOnImageEdge" DISABLEABLE="false" ENABLED="true" ID="1687385280351" NAME="Remove on image edge" NICKNAME="Remove on image edge" NOTES="" SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false"><PARAMETERS><PARAMETER NAME="Input objects" NICKNAME="Input objects" VALUE="Nuclei" VISIBLE="false"/><PARAMETER NAME="Filter mode" NICKNAME="Filter mode" VALUE="Remove filtered objects" VISIBLE="false"/><PARAMETER NAME="Output (filtered) objects" NICKNAME="Output (filtered) objects" VALUE="" VISIBLE="false"/><PARAMETER NAME="Maximum permitted contact" NICKNAME="Maximum permitted contact" VALUE="0" VISIBLE="false"/><PARAMETER NAME="Remove on top" NICKNAME="Remove on top" VALUE="true" VISIBLE="true"/><PARAMETER NAME="Remove on left" NICKNAME="Remove on left" VALUE="true" VISIBLE="true"/><PARAMETER NAME="Remove on bottom" NICKNAME="Remove on bottom" VALUE="true" VISIBLE="true"/><PARAMETER NAME="Remove on right" NICKNAME="Remove on right" VALUE="true" VISIBLE="true"/><PARAMETER NAME="Include Z-position" NICKNAME="Include Z-position" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Store filter results" NICKNAME="Store filter results" VALUE="false" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.system.GUISeparator" DISABLEABLE="false" ENABLED="true" ID="1687468490239" NAME="GUI separator" NICKNAME="Foci" NOTES="" SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false"><PARAMETERS><PARAMETER NAME="Show in processing view" NICKNAME="Show in processing view" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Expanded in processing view" NICKNAME="Expanded in processing view" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Expanded in editing view" NICKNAME="Expanded in editing view" VALUE="false" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.inputoutput.ImageLoader" DISABLEABLE="false" ENABLED="true" ID="1687385347364" NAME="Load image" NICKNAME="Load image" NOTES="" SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false"><PARAMETERS><PARAMETER NAME="Output image" NICKNAME="Output image" VALUE="gamma_h2ax" VISIBLE="false"/><PARAMETER NAME="Import mode" NICKNAME="Import mode" VALUE="Current file" VISIBLE="false"/><PARAMETER NAME="Reader" NICKNAME="Reader" VALUE="Bio-Formats" VISIBLE="false"/><PARAMETER NAME="Sequence root name" NICKNAME="Sequence root name" VALUE="" VISIBLE="false"/><PARAMETER NAME="Name format" NICKNAME="Name format" VALUE="Generic (from metadata)" VISIBLE="false"/><PARAMETER NAME="Comment" NICKNAME="Comment" VALUE="" VISIBLE="false"/><PARAMETER NAME="Extension" NICKNAME="Extension" VALUE="" VISIBLE="false"/><PARAMETER NAME="Generic format" NICKNAME="Generic format" VALUE="" VISIBLE="false"/><PARAMETER NAME="Include series number" NICKNAME="Include series number" VALUE="true" VISIBLE="false"/><PARAMETER NAME="File path" NICKNAME="File path" VALUE="" VISIBLE="false"/><PARAMETER NAME="Series mode" NICKNAME="Series mode" VALUE="Current series" VISIBLE="false"/><PARAMETER NAME="Series number" NICKNAME="Series number" VALUE="1" VISIBLE="false"/><PARAMETER NAME="Channels" NICKNAME="Channels" VALUE="2" VISIBLE="false"/><PARAMETER NAME="Slices" NICKNAME="Slices" VALUE="1-end" VISIBLE="false"/><PARAMETER NAME="Frames" NICKNAME="Frames" VALUE="1-end" VISIBLE="false"/><PARAMETER NAME="Channel" NICKNAME="Channel" VALUE="1" VISIBLE="false"/><PARAMETER NAME="Crop mode" NICKNAME="Crop mode" VALUE="None" VISIBLE="false"/><PARAMETER NAME="Reference image" NICKNAME="Reference image" VALUE="" VISIBLE="false"/><PARAMETER NAME="Left coordinate" NICKNAME="Left coordinate" VALUE="0" VISIBLE="false"/><PARAMETER NAME="Top coordinate" NICKNAME="Top coordinate" VALUE="0" VISIBLE="false"/><PARAMETER NAME="Width" NICKNAME="Width" VALUE="512" VISIBLE="false"/><PARAMETER NAME="Height" NICKNAME="Height" VALUE="512" VISIBLE="false"/><PARAMETER NAME="Objects for limits" NICKNAME="Objects for limits" VALUE="" VISIBLE="false"/><PARAMETER NAME="Scale mode" NICKNAME="Scale mode" VALUE="No scaling" VISIBLE="false"/><PARAMETER NAME="X scale factor" NICKNAME="X scale factor" VALUE="1.0" VISIBLE="false"/><PARAMETER NAME="Y scale factor" NICKNAME="Y scale factor" VALUE="1.0" VISIBLE="false"/><PARAMETER NAME="Dimension mismatch mode" NICKNAME="Dimension mismatch mode" VALUE="Disallow (fail upon mismatch)" VISIBLE="false"/><PARAMETER NAME="Pad intensity mode" NICKNAME="Pad intensity mode" VALUE="Black (0)" VISIBLE="false"/><PARAMETER NAME="Set manual spatial calibration" NICKNAME="Set manual spatial calibration" VALUE="false" VISIBLE="false"/><PARAMETER NAME="XY calibration (dist/px)" NICKNAME="XY calibration (dist/px)" VALUE="1.0" VISIBLE="false"/><PARAMETER NAME="Z calibration (dist/px)" NICKNAME="Z calibration (dist/px)" VALUE="1.0" VISIBLE="false"/><PARAMETER NAME="Set manual temporal calibration" NICKNAME="Set manual temporal calibration" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Frame interval (time/frame)" NICKNAME="Frame interval (time/frame)" VALUE="1.0" VISIBLE="false"/><PARAMETER NAME="Force bit depth" NICKNAME="Force bit depth" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Output bit depth" NICKNAME="Output bit depth" VALUE="8" VISIBLE="false"/><PARAMETER NAME="Minimum input intensity" NICKNAME="Minimum input intensity" VALUE="0.0" VISIBLE="false"/><PARAMETER NAME="Maximum input intensity" NICKNAME="Maximum input intensity" VALUE="1.0" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.images.process.FilterImage" DISABLEABLE="false" ENABLED="true" ID="1687385390962" NAME="Filter image" NICKNAME="Filter image" NOTES="" SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false"><PARAMETERS><PARAMETER NAME="Input image" NICKNAME="Input image" VALUE="gamma_h2ax" VISIBLE="false"/><PARAMETER NAME="Apply to input image" NICKNAME="Apply to input image" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Output image" NICKNAME="Output image" VALUE="Filter_gamma" VISIBLE="false"/><PARAMETER NAME="Filter mode" NICKNAME="Filter mode" VALUE="Median 2D" VISIBLE="false"/><PARAMETER NAME="Filter radius" NICKNAME="Filter radius" VALUE="2.0" VISIBLE="false"/><PARAMETER NAME="Calibrated units" NICKNAME="Calibrated units" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Rolling filter method" NICKNAME="Rolling filter method" VALUE="Average" VISIBLE="false"/><PARAMETER NAME="Window indices" NICKNAME="Window indices" VALUE="-1-1" VISIBLE="false"/><PARAMETER NAME="Contour contrast" NICKNAME="Contour contrast" VALUE="Dark line" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.images.process.binary.ExtendedMinima" DISABLEABLE="false" ENABLED="true" ID="1687466737481" NAME="Extended minima/maxima" NICKNAME="Extended minima/maxima" NOTES="" SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false"><PARAMETERS><PARAMETER NAME="Input image" NICKNAME="Input image" VALUE="Filter_gamma" VISIBLE="false"/><PARAMETER NAME="Apply to input image" NICKNAME="Apply to input image" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Output image" NICKNAME="Output image" VALUE="Max_gamma_h2ax" VISIBLE="false"/><PARAMETER NAME="Minima/maxima" NICKNAME="Minima/maxima" VALUE="Maxima" VISIBLE="false"/><PARAMETER NAME="Dynamic" NICKNAME="Dynamic" VALUE="20" VISIBLE="true"/><PARAMETER NAME="Connectivity" NICKNAME="Connectivity" VALUE="26" VISIBLE="false"/><PARAMETER NAME="Binary logic" NICKNAME="Binary logic" VALUE="Black (0) background" VISIBLE="false"/><PARAMETER NAME="Enable multithreading" NICKNAME="Enable multithreading" VALUE="true" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.objects.detect.IdentifyObjects" DISABLEABLE="false" ENABLED="true" ID="1687386734127" NAME="Identify objects" NICKNAME="Identify objects" NOTES="" SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false"><PARAMETERS><PARAMETER NAME="Input image" NICKNAME="Input image" VALUE="Max_gamma_h2ax" VISIBLE="false"/><PARAMETER NAME="Output objects" NICKNAME="Output objects" VALUE="Foci" VISIBLE="false"/><PARAMETER NAME="Binary logic" NICKNAME="Binary logic" VALUE="Black (0) background" VISIBLE="false"/><PARAMETER NAME="Detection mode" NICKNAME="Detection mode" VALUE="3D" VISIBLE="false"/><PARAMETER NAME="Identify as single object" NICKNAME="Identify as single object" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Connectivity" NICKNAME="Connectivity" VALUE="26" VISIBLE="false"/><PARAMETER NAME="Volume type" NICKNAME="Volume type" VALUE="Quadtree" VISIBLE="false"/><PARAMETER NAME="Enable multithreading" NICKNAME="Enable multithreading" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Minimum strip width (px)" NICKNAME="Minimum strip width (px)" VALUE="60" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.objects.relate.RelateManyToOne" DISABLEABLE="false" ENABLED="true" ID="1687386797953" NAME="Relate many-to-one" NICKNAME="Relate many-to-one" NOTES="" SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false"><PARAMETERS><PARAMETER NAME="Parent (larger) objects" NICKNAME="Parent (larger) objects" VALUE="Nuclei" VISIBLE="false"/><PARAMETER NAME="Child (smaller) objects" NICKNAME="Child (smaller) objects" VALUE="Foci" VISIBLE="false"/><PARAMETER NAME="Method to relate objects" NICKNAME="Method to relate objects" VALUE="Spatial overlap" VISIBLE="true"/><PARAMETER NAME="Reference mode" NICKNAME="Reference mode" VALUE="Centroid" VISIBLE="false"/><PARAMETER NAME="Limit linking by distance" NICKNAME="Limit linking by distance" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Maximum linking distance (px)" NICKNAME="Maximum linking distance (px)" VALUE="1.0" VISIBLE="false"/><PARAMETER NAME="Inside/outside mode" NICKNAME="Inside/outside mode" VALUE="Inside and outside (all distances)" VISIBLE="false"/><PARAMETER NAME="Minimum overlap (%)" NICKNAME="Minimum overlap (%)" VALUE="80" VISIBLE="true"/><PARAMETER NAME="Require centroid overlap" NICKNAME="Require centroid overlap" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Only link objects in same frame" NICKNAME="Only link objects in same frame" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Calculate fractional distance" NICKNAME="Calculate fractional distance" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Enable multithreading" NICKNAME="Enable multithreading" VALUE="true" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS><MEASUREMENT EXPORT_GLOBAL="true" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="RELATE_MANY_TO_ONE // OVERLAP_WITH_Nuclei_PERCENTAGE" NICKNAME="RELATE_MANY_TO_ONE // OVERLAP_WITH_Nuclei_PERCENTAGE" OBJECT_NAME="Foci"/><MEASUREMENT EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="RELATE_MANY_TO_ONE // WAS_LINKED_Foci" NICKNAME="RELATE_MANY_TO_ONE // WAS_LINKED_Foci" OBJECT_NAME="Nuclei"/><MEASUREMENT EXPORT_GLOBAL="true" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="RELATE_MANY_TO_ONE // WAS_LINKED_Nuclei" NICKNAME="RELATE_MANY_TO_ONE // WAS_LINKED_Nuclei" OBJECT_NAME="Foci"/></OBJECT_MEASUREMENTS><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.system.GUISeparator" DISABLEABLE="false" ENABLED="true" ID="1687468516249" NAME="GUI separator" NICKNAME="Measurements" NOTES="" SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false"><PARAMETERS><PARAMETER NAME="Show in processing view" NICKNAME="Show in processing view" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Expanded in processing view" NICKNAME="Expanded in processing view" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Expanded in editing view" NICKNAME="Expanded in editing view" VALUE="false" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.objects.filter.FilterWithWithoutParent" DISABLEABLE="false" ENABLED="true" ID="1687473267598" NAME="With / without parent" NICKNAME="With / without parent" NOTES="" SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false"><PARAMETERS><PARAMETER NAME="Input objects" NICKNAME="Input objects" VALUE="Foci" VISIBLE="false"/><PARAMETER NAME="Filter mode" NICKNAME="Filter mode" VALUE="Remove filtered objects" VISIBLE="false"/><PARAMETER NAME="Output (filtered) objects" NICKNAME="Output (filtered) objects" VALUE="" VISIBLE="false"/><PARAMETER NAME="Method for filtering" NICKNAME="Method for filtering" VALUE="Remove objects without parent" VISIBLE="false"/><PARAMETER NAME="Parent object" NICKNAME="Parent object" VALUE="Nuclei" VISIBLE="false"/><PARAMETER NAME="Store filter results" NICKNAME="Store filter results" VALUE="false" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.objects.measure.intensity.MeasureObjectIntensity" DISABLEABLE="false" ENABLED="true" ID="1687467783640" NAME="Measure object intensity" NICKNAME="Measure object intensity" NOTES="" SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false"><PARAMETERS><PARAMETER NAME="Input objects" NICKNAME="Input objects" VALUE="Foci" VISIBLE="false"/><PARAMETER NAME="Input image" NICKNAME="Input image" VALUE="gamma_h2ax" VISIBLE="false"/><PARAMETER NAME="Measure weighted centre" NICKNAME="Measure weighted centre" VALUE="false" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS><MEASUREMENT EXPORT_GLOBAL="true" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="INTENSITY // gamma_h2ax_MAX" NICKNAME="INTENSITY // gamma_h2ax_MAX" OBJECT_NAME="Foci"/><MEASUREMENT EXPORT_GLOBAL="true" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="INTENSITY // gamma_h2ax_MEAN" NICKNAME="INTENSITY // gamma_h2ax_MEAN" OBJECT_NAME="Foci"/><MEASUREMENT EXPORT_GLOBAL="true" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="INTENSITY // gamma_h2ax_MIN" NICKNAME="INTENSITY // gamma_h2ax_MIN" OBJECT_NAME="Foci"/><MEASUREMENT EXPORT_GLOBAL="true" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="INTENSITY // gamma_h2ax_STDEV" NICKNAME="INTENSITY // gamma_h2ax_STDEV" OBJECT_NAME="Foci"/><MEASUREMENT EXPORT_GLOBAL="true" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="INTENSITY // gamma_h2ax_SUM" NICKNAME="INTENSITY // gamma_h2ax_SUM" OBJECT_NAME="Foci"/></OBJECT_MEASUREMENTS><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.objects.measure.miscellaneous.ChildObjectCount" DISABLEABLE="false" ENABLED="true" ID="1687468011294" NAME="Child object count" NICKNAME="Child object count" NOTES="" SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false"><PARAMETERS><PARAMETER NAME="Input objects" NICKNAME="Input objects" VALUE="Nuclei" VISIBLE="false"/><PARAMETER NAME="Child objects" NICKNAME="Child objects" VALUE="Foci" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS><MEASUREMENT EXPORT_GLOBAL="true" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="COUNT // Foci" NICKNAME="COUNT // Foci" OBJECT_NAME="Nuclei"/></OBJECT_MEASUREMENTS><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.system.GUISeparator" DISABLEABLE="false" ENABLED="true" ID="1687468574718" NAME="GUI separator" NICKNAME="Image Output" NOTES="" SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false"><PARAMETERS><PARAMETER NAME="Show in processing view" NICKNAME="Show in processing view" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Expanded in processing view" NICKNAME="Expanded in processing view" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Expanded in editing view" NICKNAME="Expanded in editing view" VALUE="false" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.visualise.overlays.AddObjectOutline" DISABLEABLE="false" ENABLED="true" ID="1687472023104" NAME="Add object outline" NICKNAME="Add object outline" NOTES="" SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false"><PARAMETERS><PARAMETER NAME="Colour mode" NICKNAME="Colour mode" VALUE="ID" VISIBLE="false"/><PARAMETER NAME="Colour map" NICKNAME="Colour map" VALUE="Random (vibrant)" VISIBLE="false"/><PARAMETER NAME="Single colour" NICKNAME="Single colour" VALUE="White" VISIBLE="false"/><PARAMETER NAME="Child objects for colour" NICKNAME="Child objects for colour" VALUE="" VISIBLE="false"/><PARAMETER NAME="Measurement for colour" NICKNAME="Measurement for colour" VALUE="" VISIBLE="false"/><PARAMETER NAME="Parent object for colour" NICKNAME="Parent object for colour" VALUE="Nuclei" VISIBLE="false"/><PARAMETER NAME="Partner objects for colour" NICKNAME="Partner objects for colour" VALUE="" VISIBLE="false"/><PARAMETER NAME="Opacity (%)" NICKNAME="Opacity (%)" VALUE="100.0" VISIBLE="false"/><PARAMETER NAME="Range minimum mode" NICKNAME="Range minimum mode" VALUE="Automatic" VISIBLE="false"/><PARAMETER NAME="Minimum value" NICKNAME="Minimum value" VALUE="0.0" VISIBLE="false"/><PARAMETER NAME="Range maximum mode" NICKNAME="Range maximum mode" VALUE="Automatic" VISIBLE="false"/><PARAMETER NAME="Maximum value" NICKNAME="Maximum value" VALUE="1.0" VISIBLE="false"/><PARAMETER NAME="Input image" NICKNAME="Input image" VALUE="gamma_h2ax" VISIBLE="false"/><PARAMETER NAME="Input objects" NICKNAME="Input objects" VALUE="Nuclei" VISIBLE="false"/><PARAMETER NAME="Apply to input image" NICKNAME="Apply to input image" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Add output image to workspace" NICKNAME="Add output image to workspace" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Output image" NICKNAME="Output image" VALUE="Overlay_Nuclei" VISIBLE="false"/><PARAMETER NAME="Reduce line complexity" NICKNAME="Reduce line complexity" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Line interpolation" NICKNAME="Line interpolation" VALUE="1.0" VISIBLE="false"/><PARAMETER NAME="Line width" NICKNAME="Line width" VALUE="3" VISIBLE="false"/><PARAMETER NAME="Render in all frames" NICKNAME="Render in all frames" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Enable multithreading" NICKNAME="Enable multithreading" VALUE="true" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.visualise.overlays.AddObjectOutline" DISABLEABLE="false" ENABLED="true" ID="1687468832422" NAME="Add object outline" NICKNAME="Add object outline" NOTES="" SHOW_BASIC_TITLE="true" SHOW_OUTPUT="true"><PARAMETERS><PARAMETER NAME="Colour mode" NICKNAME="Colour mode" VALUE="Parent ID" VISIBLE="false"/><PARAMETER NAME="Colour map" NICKNAME="Colour map" VALUE="Random (vibrant)" VISIBLE="false"/><PARAMETER NAME="Single colour" NICKNAME="Single colour" VALUE="White" VISIBLE="false"/><PARAMETER NAME="Child objects for colour" NICKNAME="Child objects for colour" VALUE="" VISIBLE="false"/><PARAMETER NAME="Measurement for colour" NICKNAME="Measurement for colour" VALUE="" VISIBLE="false"/><PARAMETER NAME="Parent object for colour" NICKNAME="Parent object for colour" VALUE="Nuclei" VISIBLE="false"/><PARAMETER NAME="Partner objects for colour" NICKNAME="Partner objects for colour" VALUE="" VISIBLE="false"/><PARAMETER NAME="Opacity (%)" NICKNAME="Opacity (%)" VALUE="100.0" VISIBLE="false"/><PARAMETER NAME="Range minimum mode" NICKNAME="Range minimum mode" VALUE="Automatic" VISIBLE="false"/><PARAMETER NAME="Minimum value" NICKNAME="Minimum value" VALUE="0.0" VISIBLE="false"/><PARAMETER NAME="Range maximum mode" NICKNAME="Range maximum mode" VALUE="Automatic" VISIBLE="false"/><PARAMETER NAME="Maximum value" NICKNAME="Maximum value" VALUE="1.0" VISIBLE="false"/><PARAMETER NAME="Input image" NICKNAME="Input image" VALUE="Overlay_Nuclei" VISIBLE="false"/><PARAMETER NAME="Input objects" NICKNAME="Input objects" VALUE="Foci" VISIBLE="false"/><PARAMETER NAME="Apply to input image" NICKNAME="Apply to input image" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Add output image to workspace" NICKNAME="Add output image to workspace" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Output image" NICKNAME="Output image" VALUE="Overlay_Foci" VISIBLE="false"/><PARAMETER NAME="Reduce line complexity" NICKNAME="Reduce line complexity" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Line interpolation" NICKNAME="Line interpolation" VALUE="1.0" VISIBLE="false"/><PARAMETER NAME="Line width" NICKNAME="Line width" VALUE="1" VISIBLE="false"/><PARAMETER NAME="Render in all frames" NICKNAME="Render in all frames" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Enable multithreading" NICKNAME="Enable multithreading" VALUE="true" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.inputoutput.ImageSaver" DISABLEABLE="false" ENABLED="true" ID="1687472706285" NAME="Save image" NICKNAME="Save image" NOTES="" SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false"><PARAMETERS><PARAMETER NAME="Save location" NICKNAME="Save location" VALUE="Save with input file" VISIBLE="false"/><PARAMETER NAME="Mirrored directory root" NICKNAME="Mirrored directory root" VALUE="" VISIBLE="false"/><PARAMETER NAME="File path" NICKNAME="File path" VALUE="" VISIBLE="false"/><PARAMETER NAME="File name (generic)" NICKNAME="File name (generic)" VALUE="" VISIBLE="false"/><PARAMETER NAME="Save name mode" NICKNAME="Save name mode" VALUE="Match input file name" VISIBLE="false"/><PARAMETER NAME="File name" NICKNAME="File name" VALUE="" VISIBLE="false"/><PARAMETER NAME="Append series mode" NICKNAME="Append series mode" VALUE="Series number" VISIBLE="false"/><PARAMETER NAME="Append date/time mode" NICKNAME="Append date/time mode" VALUE="Never" VISIBLE="false"/><PARAMETER NAME="Add filename suffix" NICKNAME="Add filename suffix" VALUE="_overlay" VISIBLE="false"/><PARAMETER NAME="Input image" NICKNAME="Input image" VALUE="Overlay_Foci" VISIBLE="false"/><PARAMETER NAME="File format" NICKNAME="File format" VALUE="TIF" VISIBLE="false"/><PARAMETER NAME="Channel mode" NICKNAME="Channel mode" VALUE="Composite" VISIBLE="false"/><PARAMETER NAME="Save as RGB" NICKNAME="Save as RGB" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Compression mode" NICKNAME="Compression mode" VALUE="None" VISIBLE="false"/><PARAMETER NAME="Quality (0-100)" NICKNAME="Quality (0-100)" VALUE="100" VISIBLE="false"/><PARAMETER NAME="Frame rate (fps)" NICKNAME="Frame rate (fps)" VALUE="25" VISIBLE="false"/><PARAMETER NAME="Flatten overlay" NICKNAME="Flatten overlay" VALUE="false" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA/></MODULE></MODULES></ROOT>