<protocol VERSION="4">
<blocks>
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<variables>
<input>
<variable ID="sequence" name="Sequence" runtime="false" value="No Sequence" visible="false"/>
<variable ID="Type Wanted" name="Type Wanted" runtime="false" value="STACK" visible="false"/>
</input>
<output>
<variable ID="out" name="Out" runtime="false" visible="false"/>
</output>
</variables>
</block>
<block ID="786818186" blockType="plugins.adufour.metrolospim.RescaleSequence" className="plugins.adufour.metrolospim.RescaleSequence" collapsed="false" definedName="Rescale sequence" height="108" keepsResults="true" width="266" xLocation="69" yLocation="152">
<variables>
<input>
<variable ID="input sequence" name="Sequence" runtime="false" visible="false"/>
<variable ID="scale factor" name="Scale factor" runtime="false" value="0.1" visible="false"/>
</input>
<output>
<variable ID="output sequence" name="Rescaled sequence" runtime="false" visible="false"/>
</output>
</variables>
</block>
<block ID="1096159225" blockType="plugins.adufour.filtering.GaussianFilter" className="plugins.adufour.filtering.FilterToolbox" collapsed="false" definedName="Gaussian filter" height="158" keepsResults="true" width="254" xLocation="85" yLocation="281">
<variables>
<input>
<variable ID="input" name="input" runtime="false" visible="false"/>
<variable ID="filterX" name="sigma (x)" runtime="false" value="2.0" visible="false"/>
<variable ID="filterY" name="sigma (y)" runtime="false" value="2.0" visible="false"/>
<variable ID="filterZ" name="sigma (z)" runtime="false" value="6.0" visible="false"/>
</input>
<output>
<variable ID="output" name="output" runtime="false" visible="false"/>
</output>
</variables>
</block>
<block ID="682637361" blockType="plugins.adufour.thresholder.KMeansThresholdBlock" className="plugins.adufour.thresholder.Thresholder" collapsed="false" definedName="K means threshold" height="133" keepsResults="true" width="249" xLocation="84" yLocation="454">
<variables>
<input>
<variable ID="Input" name="Input" runtime="false" visible="false"/>
<variable ID="Channel" name="Channel" runtime="false" value="0" visible="false"/>
<variable ID="Classes" name="Classes" runtime="false" value="3" visible="false"/>
</input>
<output>
<variable ID="thresholds" name="thresholds" runtime="false" visible="false"/>
</output>
</variables>
</block>
<block ID="2025903845" blockType="plugins.adufour.thresholder.Thresholder" className="plugins.adufour.thresholder.Thresholder" collapsed="false" definedName="Thresholder" height="179" keepsResults="true" width="305" xLocation="393" yLocation="454">
<variables>
<input>
<variable ID="Input" name="Input" runtime="false" visible="false"/>
<variable ID="channel" name="channel" runtime="false" value="0" visible="true"/>
<variable ID="Manual thresholds" name="Manual thresholds" runtime="false" visible="false"/>
<variable ID="Treat as percentiles" name="Treat as percentiles" runtime="false" value="false" visible="false"/>
</input>
<output>
<variable ID="output" name="Binary output" runtime="false" visible="false"/>
<variable ID="ROI" name="ROI" runtime="false" visible="false"/>
</output>
</variables>
</block>
<block ID="357719181" blockType="plugins.adufour.connectedcomponents.ConnectedComponents" className="plugins.adufour.connectedcomponents.ConnectedComponents" collapsed="false" definedName="Connected Components" height="366" keepsResults="true" width="345" xLocation="770" yLocation="265">
<variables>
<input>
<variable ID="input" name="Input" runtime="false" visible="false"/>
<variable ID="method" name="Extraction mode" runtime="false" value="BACKGROUND" visible="false"/>
<variable ID="value" name="Value" runtime="false" value="0" 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="10000" visible="false"/>
<variable ID="max. size" name="Max. size" runtime="false" value="2000000" 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" value="" 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="1974696283" blockType="plugins.ylemontag.mathoperationspp.MathOperationPPBlocks$MathExpression1" className="plugins.ylemontag.mathoperationspp.MathOperationPPPlugin" collapsed="false" definedName="Math expression1" height="108" keepsResults="true" width="200" xLocation="439" yLocation="151">
<variables>
<input>
<variable ID="op" name="op" runtime="false" value="1/a" visible="false"/>
<variable ID="a" name="a" runtime="false" type="double" visible="false"/>
</input>
<output>
<variable ID="Out" name="result" runtime="false" type="java.lang.Double" visible="false"/>
</output>
</variables>
</block>
<block ID="2094482017" blockType="plugins.adufour.metrolospim.CreatedScaledRectangleROI" className="plugins.adufour.metrolospim.CreatedScaledRectangleROI" collapsed="false" definedName="Created scaled rectangle ROI" height="108" keepsResults="true" width="264" xLocation="818" yLocation="137">
<variables>
<input>
<variable ID="input ROI" name="list of ROI" runtime="false" visible="false"/>
<variable ID="scale factor" name="scale" runtime="false" visible="false"/>
</input>
<output>
<variable ID="output ROI" name="list of rescaled ROI" runtime="false" visible="false"/>
</output>
</variables>
</block>
<block ID="1735994433" blockType="plugins.adufour.blocks.tools.roi.CropSequenceToROI" className="plugins.adufour.blocks.tools.roi.CropSequenceToROI" collapsed="false" definedName="Crop sequence to ROI" height="105" keepsResults="true" width="297" xLocation="1140" yLocation="54">
<variables>
<input>
<variable ID="sequence to crop" name="Sequence to crop" runtime="false" visible="false"/>
<variable ID="list of ROI" name="List of ROI" runtime="false" visible="false"/>
</input>
<output>
<variable ID="list of crops" name="List of crops" runtime="false" visible="false"/>
</output>
</variables>
</block>
<block ID="853276302" blockType="plugins.adufour.blocks.tools.Indexer" className="plugins.adufour.blocks.tools.Indexer" collapsed="false" definedName="Indexer" height="108" keepsResults="true" width="144" xLocation="1232" yLocation="178">
<variables>
<input>
<variable ID="array" name="array" runtime="false" type="[Licy.sequence.Sequence;" visible="false"/>
<variable ID="index" name="index" runtime="false" value="0" visible="false"/>
</input>
<output>
<variable ID="element" name="element" runtime="false" type="icy.sequence.Sequence" visible="false"/>
</output>
</variables>
</block>
<block ID="1332310955" blockType="plugins.adufour.blocks.tools.sequence.ShowSequence" className="plugins.adufour.blocks.tools.sequence.ShowSequence" collapsed="false" definedName="Show sequence" height="61" keepsResults="true" width="255" xLocation="1171" yLocation="313">
<variables>
<input>
<variable ID="sequence" name="sequence" runtime="false" visible="false"/>
</input>
<output/>
</variables>
</block>
</blocks>
<links>
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<link dstBlockID="1735994433" dstVarID="sequence to crop" srcBlockID="244268099" srcVarID="out"/>
<link dstBlockID="1096159225" dstVarID="input" srcBlockID="786818186" srcVarID="output sequence"/>
<link dstBlockID="1974696283" dstVarID="a" srcBlockID="786818186" srcVarID="scale factor"/>
<link dstBlockID="682637361" dstVarID="Input" srcBlockID="1096159225" srcVarID="output"/>
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<link dstBlockID="2025903845" dstVarID="Manual thresholds" srcBlockID="682637361" srcVarID="thresholds"/>
<link dstBlockID="357719181" dstVarID="input" srcBlockID="2025903845" srcVarID="output"/>
<link dstBlockID="2094482017" dstVarID="input ROI" srcBlockID="357719181" srcVarID="list of extracted ROI"/>
<link dstBlockID="2094482017" dstVarID="scale factor" srcBlockID="1974696283" srcVarID="Out" srcVarType="java.lang.Double"/>
<link dstBlockID="1735994433" dstVarID="list of ROI" srcBlockID="2094482017" srcVarID="output ROI"/>
<link dstBlockID="853276302" dstVarID="array" srcBlockID="1735994433" srcVarID="list of crops"/>
<link dstBlockID="1332310955" dstVarID="sequence" srcBlockID="853276302" srcVarID="element" srcVarType="icy.sequence.Sequence"/>
</links>
</protocol>
