<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<protocol VERSION="4">
<blocks>
<block ID="288679692" blockType="plugins.adufour.blocks.tools.input.Sequence" className="plugins.adufour.blocks.tools.input.Sequence" height="61" width="165" xLocation="0" yLocation="260">
<variables>
<input>
<variable ID="input sequence" name="sequence" runtime="false" visible="false"/>
</input>
<output/>
</variables>
</block>
<block ID="92136104" blockType="plugins.tprovoost.sequenceblocks.extract.ExtractChannel" className="plugins.tprovoost.sequenceblocks.SequenceBlocks" height="108" width="229" xLocation="246" yLocation="148">
<variables>
<input>
<variable ID="sequence" name="sequence" runtime="false" visible="false"/>
<variable ID="channel" name="channel" runtime="false" value="2" visible="false"/>
</input>
<output>
<variable ID="extracted" name="extracted" runtime="false" visible="false"/>
</output>
</variables>
</block>
<block ID="559474620" blockType="plugins.tprovoost.sequenceblocks.extract.ExtractChannel" className="plugins.tprovoost.sequenceblocks.SequenceBlocks" height="108" width="229" xLocation="260" yLocation="365">
<variables>
<input>
<variable ID="sequence" name="sequence" runtime="false" visible="false"/>
<variable ID="channel" name="channel" runtime="false" value="1" visible="false"/>
</input>
<output>
<variable ID="extracted" name="extracted" runtime="false" visible="false"/>
</output>
</variables>
</block>
<block ID="1160712213" blockType="plugins.adufour.hierarchicalkmeans.HierarchicalKMeans" className="plugins.adufour.hierarchicalkmeans.HierarchicalKMeans" height="34" width="166" xLocation="677" yLocation="270">
<variables>
<input>
<variable ID="Input" name="Input" runtime="false" visible="false"/>
<variable ID="Gaussian pre-filter" name="Gaussian pre-filter" runtime="false" value="1.3877787807814457E-16" visible="false"/>
<variable ID="Min size (px)" name="Min size (px)" runtime="false" value="1000" visible="false"/>
<variable ID="Max size (px)" name="Max size (px)" runtime="false" value="1000000" visible="false"/>
<variable ID="Number of classes" name="Number of classes" runtime="false" value="36" visible="false"/>
<variable ID="Final threshold" name="Final threshold" runtime="false" value="0.0" visible="false"/>
</input>
<output>
<variable ID="binary sequence" name="binary sequence" runtime="false" visible="false"/>
<variable ID="output objects" name="objects" runtime="false" visible="false"/>
<variable ID="output regions" name="list of ROI" runtime="false" visible="false"/>
</output>
</variables>
</block>
<block ID="874329857" blockType="plugins.adufour.morphology.FillHolesInROI" className="plugins.adufour.morphology.FillHolesInROI" height="34" width="199" xLocation="584" yLocation="300">
<variables>
<input>
<variable ID="List of ROI" name="List of ROI" runtime="false" visible="false"/>
</input>
<output>
<variable ID="List of hole-filled ROI" name="List of hole-filled ROI" runtime="false" visible="false"/>
</output>
</variables>
</block>
<block ID="1065832243" blockType="plugins.adufour.blocks.tools.roi.DilateROI" className="plugins.adufour.blocks.tools.roi.DilateROI" height="34" width="163" xLocation="596" yLocation="336">
<variables>
<input>
<variable ID="input ROI" name="List of ROI" runtime="false" visible="false"/>
<variable ID="X radius" name="X radius (px)" runtime="false" value="1" visible="false"/>
<variable ID="Y radius" name="Y radius (px)" runtime="false" value="1" visible="false"/>
<variable ID="Z radius" name="Z radius (px)" runtime="false" value="1" visible="false"/>
</input>
<output>
<variable ID="output ROI" name="Dilated ROI" runtime="false" visible="false"/>
</output>
</variables>
</block>
<block ID="2047669516" blockType="plugins.adufour.blocks.tools.roi.AddROIToSequence" className="plugins.adufour.blocks.tools.roi.AddROIToSequence" height="34" width="230" xLocation="625" yLocation="395">
<variables>
<input>
<variable ID="input rois" name="List of ROI" runtime="false" visible="false"/>
<variable ID="target sequence" name="Target sequence" runtime="false" visible="false"/>
<variable ID="replace existing" name="Replace existing ROI" runtime="false" value="true" visible="false"/>
</input>
<output/>
</variables>
</block>
<block ID="1720795077" blockType="plugins.fab.waveletspotdetectorblock.WaveletSpotDetectorBlock" className="plugins.fab.waveletspotdetectorblock.WaveletSpotDetectorBlock" height="34" width="275" xLocation="809" yLocation="456">
<variables>
<input>
<variable ID="input Sequence" name="input Sequence" runtime="false" visible="false"/>
<variable ID="Spot to detect" name="Spot to detect" runtime="false" value="BRIGHT_SPOT" visible="false"/>
<variable ID="input Sequence ROIs" name="input Sequence ROIs" runtime="false" visible="false"/>
<variable ID="Compute WAT considering ROI" name="Compute WAT considering ROI" runtime="false" value="false" visible="false"/>
<variable ID="Scale 1" name="Scale 1" runtime="false" value="false" visible="false"/>
<variable ID="Scale 2" name="Scale 2" runtime="false" value="false" visible="false"/>
<variable ID="Scale 3" name="Scale 3" runtime="false" value="true" visible="false"/>
<variable ID="Scale 4" name="Scale 4" runtime="false" value="false" visible="false"/>
<variable ID="Scale 5" name="Scale 5" runtime="false" value="false" visible="false"/>
<variable ID="Th. scale 1:" name="Th. scale 1:" runtime="false" value="100" visible="false"/>
<variable ID="Th. scale 2:" name="Th. scale 2:" runtime="false" value="100" visible="false"/>
<variable ID="Th. scale 3:" name="Th. scale 3:" runtime="false" value="70" visible="false"/>
<variable ID="Th. scale 4:" name="Th. scale 4:" runtime="false" value="100" visible="false"/>
<variable ID="Th. scale 5:" name="Th. scale 5:" runtime="false" value="100" visible="false"/>
</input>
<output>
<variable ID="binary Spot Sequence" name="binary Spot Sequence" runtime="false" visible="false"/>
</output>
</variables>
</block>
<block ID="946368327" blockType="plugins.adufour.connectedcomponents.ConnectedComponents" className="plugins.adufour.connectedcomponents.ConnectedComponents" height="34" width="250" xLocation="786" yLocation="512">
<variables>
<input>
<variable ID="input" name="Input" runtime="false" visible="false"/>
<variable ID="method" name="Extraction mode" runtime="false" value="VALUE" visible="false"/>
<variable ID="value" name="Value" runtime="false" value="255" visible="false"/>
<variable ID="no edge (X)" name="Remove border objects (X)" runtime="false" value="false" visible="false"/>
<variable ID="no edge (Y)" name="Remove border objects (Y)" runtime="false" value="false" visible="false"/>
<variable ID="no edge (Z)" name="Remove border objects (Z)" runtime="false" value="false" visible="false"/>
<variable ID="size filter" name="Filter objects by size" runtime="false" value="true" visible="false"/>
<variable ID="min. size" name="Min. size" runtime="false" value="30" visible="false"/>
<variable ID="max. size" name="Max. size" runtime="false" value="10170" visible="false"/>
<variable ID="Export to Excel" name="Export to Excel" runtime="false" value="false" visible="false"/>
<variable ID="Excel file" name="Excel file" runtime="false" visible="false"/>
</input>
<output>
<variable ID="labeled sequence" name="output" runtime="false" visible="false"/>
<variable ID="objects" name="components" runtime="false" visible="false"/>
<variable ID="list of extracted ROI" name="list of ROI" runtime="false" visible="false"/>
</output>
</variables>
</block>
<block ID="540950549" blockType="plugins.lagache.DetectionsInRois.DetectionsInRois" className="plugins.lagache.DetectionsInRois.DetectionsInRois" height="127" width="257" xLocation="833" yLocation="292">
<variables>
<input>
<variable ID="input rois" name="Input Rois" runtime="false" visible="false"/>
<variable ID="input detections" name="Input Detections" runtime="false" visible="false"/>
</input>
<output>
<variable ID="Output Rois" name="Output Rois" runtime="false" visible="false"/>
<variable ID="Output detections" name="Output Detections" runtime="false" visible="false"/>
</output>
</variables>
</block>
<block ID="481399148" blockType="plugins.adufour.blocks.tools.Display" className="plugins.adufour.blocks.tools.Display" height="54" width="147" xLocation="1423" yLocation="347">
<variables>
<input>
<variable ID="object" name="object" runtime="false" type="[Licy.roi.ROI;" visible="false"/>
</input>
<output/>
</variables>
</block>
<block ID="2073046922" blockType="plugins.adufour.blocks.tools.roi.AddROIToSequence" className="plugins.adufour.blocks.tools.roi.AddROIToSequence" height="34" width="230" xLocation="1119" yLocation="170">
<variables>
<input>
<variable ID="input rois" name="List of ROI" runtime="false" visible="false"/>
<variable ID="target sequence" name="Target sequence" runtime="false" visible="false"/>
<variable ID="replace existing" name="Replace existing ROI" runtime="false" value="true" visible="false"/>
</input>
<output/>
</variables>
</block>
<block ID="1275377308" blockType="plugins.adufour.blocks.tools.roi.AddROIToSequence" className="plugins.adufour.blocks.tools.roi.AddROIToSequence" height="34" width="230" xLocation="1119" yLocation="485">
<variables>
<input>
<variable ID="input rois" name="List of ROI" runtime="false" visible="false"/>
<variable ID="target sequence" name="Target sequence" runtime="false" visible="false"/>
<variable ID="replace existing" name="Replace existing ROI" runtime="false" value="false" visible="false"/>
</input>
<output/>
</variables>
</block>
<block ID="494685988" blockType="plugins.adufour.blocks.tools.Display" className="plugins.adufour.blocks.tools.Display" height="54" width="147" xLocation="1417" yLocation="407">
<variables>
<input>
<variable ID="object" name="object" runtime="false" type="icy.sequence.Sequence" visible="false"/>
</input>
<output/>
</variables>
</block>
<block ID="663332130" blockType="plugins.adufour.blocks.tools.roi.AddROIToSequence" className="plugins.adufour.blocks.tools.roi.AddROIToSequence" height="108" width="323" xLocation="455" yLocation="556">
<variables>
<input>
<variable ID="input rois" name="List of ROI" runtime="false" visible="false"/>
<variable ID="target sequence" name="Target sequence" runtime="false" visible="false"/>
<variable ID="replace existing" name="Replace existing ROI" runtime="false" value="false" visible="false"/>
</input>
<output/>
</variables>
</block>
<block ID="1203426526" blockType="plugins.adufour.blocks.tools.Display" className="plugins.adufour.blocks.tools.Display" height="54" width="147" xLocation="832" yLocation="587">
<variables>
<input>
<variable ID="object" name="object" runtime="false" type="icy.sequence.Sequence" visible="false"/>
</input>
<output/>
</variables>
</block>
<block ID="757858040" blockType="plugins.adufour.blocks.tools.roi.AddROIToSequence" className="plugins.adufour.blocks.tools.roi.AddROIToSequence" height="108" width="323" xLocation="1080" yLocation="536">
<variables>
<input>
<variable ID="input rois" name="List of ROI" runtime="false" visible="false"/>
<variable ID="target sequence" name="Target sequence" runtime="false" visible="false"/>
<variable ID="replace existing" name="Replace existing ROI" runtime="false" value="true" visible="false"/>
</input>
<output/>
</variables>
</block>
<block ID="1381139353" blockType="plugins.adufour.blocks.tools.roi.AddROIToSequence" className="plugins.adufour.blocks.tools.roi.AddROIToSequence" height="108" width="323" xLocation="1085" yLocation="645">
<variables>
<input>
<variable ID="input rois" name="List of ROI" runtime="false" visible="false"/>
<variable ID="target sequence" name="Target sequence" runtime="false" visible="false"/>
<variable ID="replace existing" name="Replace existing ROI" runtime="false" value="false" visible="false"/>
</input>
<output/>
</variables>
</block>
<block ID="634783659" blockType="plugins.adufour.blocks.tools.Display" className="plugins.adufour.blocks.tools.Display" height="54" width="147" xLocation="1483" yLocation="683">
<variables>
<input>
<variable ID="object" name="object" runtime="false" type="icy.sequence.Sequence" visible="false"/>
</input>
<output/>
</variables>
</block>
</blocks>
<links>
<link dstBlockID="874329857" dstVarID="List of ROI" srcBlockID="1160712213" srcVarID="output regions"/>
<link dstBlockID="1160712213" dstVarID="Input" srcBlockID="92136104" srcVarID="extracted"/>
<link dstBlockID="2047669516" dstVarID="target sequence" srcBlockID="92136104" srcVarID="extracted"/>
<link dstBlockID="1720795077" dstVarID="input Sequence ROIs" srcBlockID="2047669516" srcVarID="target sequence"/>
<link dstBlockID="1065832243" dstVarID="input ROI" srcBlockID="874329857" srcVarID="List of hole-filled ROI"/>
<link dstBlockID="2047669516" dstVarID="input rois" srcBlockID="1065832243" srcVarID="output ROI"/>
<link dstBlockID="1720795077" dstVarID="input Sequence" srcBlockID="559474620" srcVarID="extracted"/>
<link dstBlockID="946368327" dstVarID="input" srcBlockID="1720795077" srcVarID="binary Spot Sequence"/>
<link dstBlockID="540950549" dstVarID="input detections" srcBlockID="946368327" srcVarID="list of extracted ROI"/>
<link dstBlockID="540950549" dstVarID="input rois" srcBlockID="1065832243" srcVarID="output ROI"/>
<link dstBlockID="481399148" dstVarID="object" srcBlockID="540950549" srcVarID="Output Rois"/>
<link dstBlockID="2073046922" dstVarID="input rois" srcBlockID="540950549" srcVarID="Output Rois"/>
<link dstBlockID="2073046922" dstVarID="target sequence" srcBlockID="92136104" srcVarID="extracted"/>
<link dstBlockID="1275377308" dstVarID="target sequence" srcBlockID="92136104" srcVarID="extracted"/>
<link dstBlockID="1275377308" dstVarID="input rois" srcBlockID="540950549" srcVarID="Output detections"/>
<link dstBlockID="494685988" dstVarID="object" srcBlockID="1275377308" srcVarID="target sequence"/>
<link dstBlockID="92136104" dstVarID="sequence" srcBlockID="288679692" srcVarID="input sequence"/>
<link dstBlockID="559474620" dstVarID="sequence" srcBlockID="288679692" srcVarID="input sequence"/>
<link dstBlockID="663332130" dstVarID="input rois" srcBlockID="540950549" srcVarID="Output detections"/>
<link dstBlockID="663332130" dstVarID="target sequence" srcBlockID="559474620" srcVarID="extracted"/>
<link dstBlockID="1203426526" dstVarID="object" srcBlockID="663332130" srcVarID="target sequence"/>
<link dstBlockID="757858040" dstVarID="input rois" srcBlockID="540950549" srcVarID="Output Rois"/>
<link dstBlockID="1381139353" dstVarID="input rois" srcBlockID="540950549" srcVarID="Output detections"/>
<link dstBlockID="634783659" dstVarID="object" srcBlockID="1381139353" srcVarID="target sequence"/>
</links>
</protocol>
