<protocol VERSION="4">
<blocks>
<block ID="2004723846" blockType="plugins.adufour.hierarchicalkmeans.HierarchicalKMeans" className="plugins.adufour.hierarchicalkmeans.HierarchicalKMeans" collapsed="false" definedName="HK-Means" height="255" keepsResults="true" width="260" xLocation="13" yLocation="11">
<variables>
<input>
<variable ID="Input" name="Input" runtime="false" value="D:/Stephane/Documents/Pasteur/Icy/support/2021/septembre/Jasper/images/Fluo_contact_2D.lsm" visible="true"/>
<variable ID="Gaussian pre-filter" name="Gaussian pre-filter" runtime="false" value="2.0" visible="true"/>
<variable ID="Frame" name="Frame" runtime="false" value="0" visible="true"/>
<variable ID="Number of classes" name="Intensity classes" runtime="false" value="10" visible="true"/>
<variable ID="Min size (px)" name="Min object size (px)" runtime="false" value="2000" visible="true"/>
<variable ID="Max size (px)" name="Max object size (px)" runtime="false" value="5000" visible="true"/>
<variable ID="Final threshold" name="Min object intensity" runtime="false" value="0.0" visible="true"/>
</input>
<output>
<variable ID="binary sequence" name="binary sequence" runtime="false" visible="true"/>
<variable ID="output regions" name="list of ROI" runtime="false" visible="true"/>
</output>
</variables>
</block>
<block ID="582232060" blockType="plugins.adufour.activecontours.ActiveContours" className="plugins.adufour.activecontours.ActiveContours" collapsed="false" definedName="Active Contours" height="591" keepsResults="true" width="278" xLocation="338" yLocation="11">
<variables>
<input>
<variable ID="input sequence" name="Input" runtime="false" visible="true"/>
<variable ID="Input ROI" name="input ROI" runtime="false" visible="true"/>
<variable ID="regularization: weight" name="Contour smoothness" runtime="false" value="0.05" visible="false"/>
<variable ID="edge: weight" name="Edge weight" runtime="false" value="0.0" visible="false"/>
<variable ID="edge: channel" name="Find edges in channel" runtime="false" value="0" visible="false"/>
<variable ID="region: weight" name="Region weight" runtime="false" value="1.0" visible="false"/>
<variable ID="region: sensitivity" name="Region sensitivity" runtime="false" value="1.0" visible="false"/>
<variable ID="region: channel" name="Find regions in channel" runtime="false" value="0" visible="false"/>
<variable ID="balloon: weight" name="Contour inflation" runtime="false" value="0.0" visible="false"/>
<variable ID="contour resolution" name="Contour sampling" runtime="false" value="2.0" visible="true"/>
<variable ID="region bounds" name="Bound field to ROI of" runtime="false" value="No Sequence" visible="true"/>
<variable ID="time step" name="Evolution time step" runtime="false" value="0.1" visible="true"/>
<variable ID="convergence value" name="Convergence criterion" runtime="false" value="0.001" visible="true"/>
<variable ID="max. iterations" name="Max. iterations" runtime="false" value="100000" visible="true"/>
<variable ID="type of ROI output" name="Type of ROI" runtime="false" value="AREA" visible="true"/>
<variable ID="tracking" name="Track objects over time" runtime="false" value="true" visible="true"/>
<variable ID="division sensitivity" name="Division sensitivity" runtime="false" value="0.0" visible="true"/>
<variable ID="axis constraint" name="Axis constraint" runtime="false" value="0.0" visible="true"/>
<variable ID="Volume weight" name="Volume weight" runtime="false" value="0.01" visible="true"/>
<variable ID="watch entering objects" name="Watch entering objects" runtime="false" value="false" visible="true"/>
</input>
<output>
<variable ID="Regions of interest" name="Regions of interest" runtime="false" visible="true"/>
<variable ID="Tracks" name="Tracks" runtime="false" visible="true"/>
<variable ID="Labels" name="Labels" runtime="false" visible="true"/>
</output>
</variables>
</block>
<block ID="351402236" blockType="plugins.tprovoost.sequenceblocks.infos.GetFileName" className="plugins.tprovoost.sequenceblocks.SequenceBlocks" collapsed="false" definedName="Get file name" height="131" keepsResults="true" width="201" xLocation="46" yLocation="282">
<variables>
<input>
<variable ID="sequence" name="Sequence" runtime="false" visible="true"/>
<variable ID="folder" name="Folder" runtime="false" value="true" visible="true"/>
<variable ID="extension" name="Extension" runtime="false" value="false" visible="true"/>
</input>
<output>
<variable ID="name" name="Filename" runtime="false" visible="true"/>
</output>
</variables>
</block>
<block ID="1449630325" blockType="plugins.adufour.blocks.tools.io.AppendFilePath" className="plugins.adufour.blocks.tools.io.AppendFilePath" collapsed="false" definedName="Append file path" height="132" keepsResults="true" width="218" xLocation="672" yLocation="44">
<variables>
<input>
<variable ID="input file" name="Current file" runtime="false" type="java.lang.String" visible="true"/>
<variable ID="remove ext." name="Remove extension" runtime="false" value="false" visible="true"/>
<variable ID="suffix" name="Add suffix" runtime="false" value="_tracks-motion.xls" visible="true"/>
</input>
<output>
<variable ID="output file" name="New file" runtime="false" visible="true"/>
</output>
</variables>
</block>
<block ID="253614270" blockType="plugins.adufour.trackprocessors.speed.MotionProfiler" className="plugins.adufour.trackprocessors.speed.SpeedProfiler" collapsed="false" definedName="Motion profiler" height="129" keepsResults="true" width="290" xLocation="672" yLocation="196">
<variables>
<input>
<variable ID="trackgroup" name="Track group" runtime="false" visible="true"/>
<variable ID="sequence" name="Sequence (for units info.)" runtime="false" visible="true"/>
<variable ID="displaySpeed" name="Get speed instead of disp." runtime="false" value="false" visible="true"/>
<variable ID="output" name="Output file" runtime="false" type="java.io.File" visible="true"/>
</input>
<output/>
</variables>
</block>
<block ID="1488530171" blockType="plugins.adufour.blocks.tools.io.AppendFilePath" className="plugins.adufour.blocks.tools.io.AppendFilePath" collapsed="false" definedName="Append file path" height="132" keepsResults="true" width="195" xLocation="674" yLocation="341">
<variables>
<input>
<variable ID="input file" name="Current file" runtime="false" type="java.lang.String" visible="true"/>
<variable ID="remove ext." name="Remove extension" runtime="false" value="false" visible="true"/>
<variable ID="suffix" name="Add suffix" runtime="false" value="_tracks-raw.xls" visible="true"/>
</input>
<output>
<variable ID="output file" name="New file" runtime="false" visible="true"/>
</output>
</variables>
</block>
<block ID="1011379103" blockType="plugins.fab.trackmanager.processors.TrackXLSExport" className="plugins.fab.trackmanager.processors.TrackProcessorExportTrackToXLS" collapsed="false" definedName="Track XLS export" height="83" keepsResults="true" width="197" xLocation="688" yLocation="500">
<variables>
<input>
<variable ID="tracks" name="TrackGroup" runtime="false" visible="true"/>
<variable ID="file" name="Output file" runtime="false" type="java.io.File" visible="true"/>
</input>
<output/>
</variables>
</block>
</blocks>
<links>
<link dstBlockID="582232060" dstVarID="Input ROI" srcBlockID="2004723846" srcVarID="output regions"/>
<link dstBlockID="582232060" dstVarID="input sequence" srcBlockID="2004723846" srcVarID="Input"/>
<link dstBlockID="253614270" dstVarID="trackgroup" srcBlockID="582232060" srcVarID="Tracks"/>
<link dstBlockID="1011379103" dstVarID="tracks" srcBlockID="582232060" srcVarID="Tracks"/>
<link dstBlockID="253614270" dstVarID="sequence" srcBlockID="582232060" srcVarID="input sequence"/>
<link dstBlockID="1449630325" dstVarID="input file" srcBlockID="351402236" srcVarID="name"/>
<link dstBlockID="253614270" dstVarID="output" srcBlockID="1449630325" srcVarID="output file"/>
<link dstBlockID="351402236" dstVarID="sequence" srcBlockID="2004723846" srcVarID="Input"/>
<link dstBlockID="1488530171" dstVarID="input file" srcBlockID="351402236" srcVarID="name"/>
<link dstBlockID="1011379103" dstVarID="file" srcBlockID="1488530171" srcVarID="output file"/>
</links>
</protocol>
