<Protocol name="Exiqon_SingleColor" date="01-Oct-2008 10:12" description="Agilent 1-color Gene Expression Rev 1 - FE 9.5 Default Protocol" derivedFrom="GE1-v1_95_Feb07" protocolType="OneColor" version="9.5" isNotRemovable="False" isPermanent="false"><Step name="GridPlacement" label="Place Grid" description="Place the grid on the image." isEnabled="True" module="FEImageProc"><ChoiceParameterGroup name="ArrayFormat" label="Array Format" description="What is the Array format of the images to be processed " isVisible="True" value="9"><Choice name="SpecialEvaluate" label="Automatically Determine" description="" isVisible="True" value="0"/><Choice name="SingleDensity" label="Single Density" description="11kx2, 22k, 2k 8-Pack" isVisible="True" SpotSpacingVertical="188.148148" SpotSpacingHorizontal="211.666667" value="1"><ChoiceParameter name="placementMode" label="Placement Method" description="Methods for placing the grid on the image: Allow Some Distortion - allows the spot spacing, subgrid spacing, or skew to vary during grid placement; Place and Rotate Only - places and rotates a rigid grid on the image without distorting the grid" isVisible="True" value="0"><Choice name="free" label="Allow Some Distortion" description="" isVisible="True" value="0"/><Choice name="rigid" label="Place And Rotate Only" description="" isVisible="True" value="1"/></ChoiceParameter><ParameterGroup name="customFit" label="Perform Custom Fit?" description="Standard Agilent Arrays (44k, 22k, 11k, 8.4k and a few third party) are found without custom fitting. Custom fitting may be needed when default gridding fails." isVisible="False" value="False"><ChoiceParameter name="gridWithChannel" label="What channel(s) are used for Gridding? " description="Use this option if the background of 1 channel dominates the signal of the other. If single channel tiff this parameter is not used." isVisible="True" value="0"><Choice name="all" label="Sum of All Channels" description="" isVisible="True" value="0"/><Choice name="red" label="Red Channel Only" description="" isVisible="True" value="1"/><Choice name="green" label="Green Channel Only" description="" isVisible="True" value="2"/></ChoiceParameter><Parameter name="ptsPerSide" label="ptsPerSide" description="Number of pixels that should be smaller than the spot radius" isVisible="True" precision="%3.2lf" type="integer" value="5"/><Parameter name="minPeakSpacing" label="minPeakSpacing" description="Absolute minimum distance between spot centers in pixels." isVisible="True" precision="%3.2lf" type="double" value="7.000000"/><Parameter name="blocksizeAllowance" label="blocksizeAllowance" description="" isVisible="False" precision="%9.7f" type="double" value="0.666667"/><Parameter name="initialFilterWidth" label="initialFilterWidth" description="Smoothing factor for initial coarse global grid location in pixels. " isVisible="True" precision="%3.2lf" type="double" value="6.000000"/><Parameter name="coarseFilterWidth" label="coarseFilterWidth" description="Smoothing factor for first coarse spot location in each subgrid in pixels. " isVisible="True" precision="%3.2lf" type="double" value="5.000000"/><Parameter name="fineFilterWidth" label="fineFilterWidth" description="Half the integration window for computing grid and spot spacings in pixels." isVisible="True" precision="%3.2lf" type="double" value="3.000000"/><Parameter name="lineHalfWidth" label="lineHalfWidth" description="Half the window for median filtering in pixels." isVisible="True" precision="%3.2lf" type="integer" value="6"/><Parameter name="halfDepth" label="halfDepth" description="Half the window for median filtering in pixels." isVisible="True" precision="%3.2lf" type="integer" value="2"/><Parameter name="maximumSlope" label="maximumSlope" description="If the computed slope exceed this value it is discarded" isVisible="True" precision="%5.3f" type="double" value="0.015000"/><Parameter name="thinOutCoef" label="Thin Out Coefficient" description="Maximum ratio of found spots over expected (1 dimension)" isVisible="True" precision="%5.3f" low="1.000000" high="2.000000" type="double" value="1.500000"/></ParameterGroup></Choice><Choice name="DoubleDensity" label="Double Density" description="44k" isVisible="True" SpotSpacingVertical="188.148148" SpotSpacingHorizontal="105.8333335" value="2"><ChoiceParameter name="placementMode" label="Placement Method" description="Methods for placing the grid on the image: Allow Some Distortion - allows the spot spacing, subgrid spacing, or skew to vary during grid placement; Place and Rotate Only - places and rotates a rigid grid on the image without distorting the grid" isVisible="True" value="0"><Choice name="free" label="Allow Some Distortion" description="" isVisible="True" value="0"/><Choice name="rigid" label="Place And Rotate Only" description="" isVisible="True" value="1"/></ChoiceParameter><ParameterGroup name="customFit" label="Perform Custom Fit?" description="Standard Agilent Arrays (44k, 22k, 11k, 8.4k and a few third party) are found without custom fitting. Custom fitting may be needed when default gridding fails." isVisible="False" value="False"><ChoiceParameter name="gridWithChannel" label="What channel(s) are used for Gridding? " description="Use this option if the background of 1 channel dominates the signal of the other. If single channel tiff this parameter is not used." isVisible="True" value="0"><Choice name="all" label="Sum of All Channels" description="" isVisible="True" value="0"/><Choice name="red" label="Red Channel Only" description="" isVisible="True" value="1"/><Choice name="green" label="Green Channel Only" description="" isVisible="True" value="2"/></ChoiceParameter><Parameter name="ptsPerSide" label="ptsPerSide" description="Number of pixels that should be smaller than the spot radius" isVisible="True" precision="%3.2lf" type="integer" value="5"/><Parameter name="minPeakSpacing" label="minPeakSpacing" description="Absolute minimum distance between spot centers in pixels." isVisible="True" precision="%3.2lf" type="double" value="7.000000"/><Parameter name="blocksizeAllowance" label="blocksizeAllowance" description="" isVisible="False" precision="%9.7f" type="double" value="0.666667"/><Parameter name="initialFilterWidth" label="initialFilterWidth" description="Smoothing factor for initial coarse global grid location in pixels. " isVisible="True" precision="%3.2lf" type="double" value="6.000000"/><Parameter name="coarseFilterWidth" label="coarseFilterWidth" description="Smoothing factor for first coarse spot location in each subgrid in pixels. " isVisible="True" precision="%3.2lf" type="double" value="5.000000"/><Parameter name="fineFilterWidth" label="fineFilterWidth" description="Half the integration window for computing grid and spot spacings in pixels." isVisible="True" precision="%3.2lf" type="double" value="3.000000"/><Parameter name="lineHalfWidth" label="lineHalfWidth" description="Half the window for median filtering in pixels." isVisible="True" precision="%3.2lf" type="integer" value="6"/><Parameter name="halfDepth" label="halfDepth" description="Half the window for median filtering in pixels." isVisible="True" precision="%3.2lf" type="integer" value="2"/><Parameter name="maximumSlope" label="maximumSlope" description="If the computed slope exceed this value it is discarded" isVisible="True" precision="%5.3f" type="double" value="0.015000"/><Parameter name="thinOutCoef" label="Thin Out Coefficient" description="Maximum ratio of found spots over expected (1 dimension)" isVisible="True" precision="%5.3f" low="1.000000" high="2.000000" type="double" value="1.200000"/></ParameterGroup></Choice><Choice name="95k" label="95k" description="5-swath arrays" isVisible="True" SpotSpacingVertical="117.317575" SpotSpacingHorizontal="101.6" value="3"><ChoiceParameter name="placementMode" label="Placement Method" description="Methods for placing the grid on the image: Allow Some Distortion - allows the spot spacing, subgrid spacing, or skew to vary during grid placement; Place and Rotate Only - places and rotates a rigid grid on the image without distorting the grid" isVisible="True" value="0"><Choice name="free" label="Allow Some Distortion" description="" isVisible="True" value="0"/><Choice name="rigid" label="Place And Rotate Only" description="" isVisible="True" value="1"/></ChoiceParameter><ParameterGroup name="customFit" label="Perform Custom Fit?" description="Standard Agilent Arrays (44k, 22k, 11k, 8.4k and a few third party) are found without custom fitting. Custom fitting may be needed when default gridding fails." isVisible="False" value="False"><ChoiceParameter name="gridWithChannel" label="What channel(s) are used for Gridding? " description="Use this option if the background of 1 channel dominates the signal of the other. If single channel tiff this parameter is not used." isVisible="True" value="0"><Choice name="all" label="Sum of All Channels" description="" isVisible="True" value="0"/><Choice name="red" label="Red Channel Only" description="" isVisible="True" value="1"/><Choice name="green" label="Green Channel Only" description="" isVisible="True" value="2"/></ChoiceParameter><Parameter name="ptsPerSide" label="ptsPerSide" description="Number of pixels that should be smaller than the spot radius" isVisible="True" precision="%3.2lf" type="integer" value="5"/><Parameter name="minPeakSpacing" label="minPeakSpacing" description="Absolute minimum distance between spot centers in pixels." isVisible="True" precision="%3.2lf" type="double" value="7.000000"/><Parameter name="blocksizeAllowance" label="blocksizeAllowance" description="" isVisible="False" precision="%9.7f" type="double" value="0.666667"/><Parameter name="initialFilterWidth" label="initialFilterWidth" description="Smoothing factor for initial coarse global grid location in pixels. " isVisible="True" precision="%3.2lf" type="double" value="6.000000"/><Parameter name="coarseFilterWidth" label="coarseFilterWidth" description="Smoothing factor for first coarse spot location in each subgrid in pixels. " isVisible="True" precision="%3.2lf" type="double" value="5.000000"/><Parameter name="fineFilterWidth" label="fineFilterWidth" description="Half the integration window for computing grid and spot spacings in pixels." isVisible="True" precision="%3.2lf" type="double" value="3.000000"/><Parameter name="lineHalfWidth" label="lineHalfWidth" description="Half the window for median filtering in pixels." isVisible="True" precision="%3.2lf" type="integer" value="6"/><Parameter name="halfDepth" label="halfDepth" description="Half the window for median filtering in pixels." isVisible="True" precision="%3.2lf" type="integer" value="2"/><Parameter name="maximumSlope" label="maximumSlope" description="If the computed slope exceed this value it is discarded" isVisible="True" precision="%5.3f" type="double" value="0.015000"/><Parameter name="thinOutCoef" label="Thin Out Coefficient" description="Maximum ratio of found spots over expected (1 dimension)" isVisible="True" precision="%5.3f" low="1.000000" high="2.000000" type="double" value="1.200000"/></ParameterGroup></Choice><Choice name="185k" label="185k" description="7-swath arrays" isVisible="True" SpotSpacingVertical="83.798268" SpotSpacingHorizontal="72.5714285" MicronsPerPixelX="5.0" value="4"><ChoiceParameter name="placementMode" label="Placement Method" description="Methods for placing the grid on the image: Allow Some Distortion - allows the spot spacing, subgrid spacing, or skew to vary during grid placement; Place and Rotate Only - places and rotates a rigid grid on the image without distorting the grid" isVisible="True" value="0"><Choice name="free" label="Allow Some Distortion" description="" isVisible="True" value="0"/><Choice name="rigid" label="Place And Rotate Only" description="" isVisible="True" value="1"/></ChoiceParameter><ParameterGroup name="customFit" label="Perform Custom Fit?" description="Standard Agilent Arrays (44k, 22k, 11k, 8.4k and a few third party) are found without custom fitting. Custom fitting may be needed when default gridding fails." isVisible="False" value="True"><ChoiceParameter name="gridWithChannel" label="What channel(s) are used for Gridding? " description="Use this option if the background of 1 channel dominates the signal of the other. If single channel tiff this parameter is not used." isVisible="True" value="0"><Choice name="all" label="Sum of All Channels" description="" isVisible="True" value="0"/><Choice name="red" label="Red Channel Only" description="" isVisible="True" value="1"/><Choice name="green" label="Green Channel Only" description="" isVisible="True" value="2"/></ChoiceParameter><Parameter name="ptsPerSide" label="ptsPerSide" description="Number of pixels that should be smaller than the spot radius" isVisible="True" precision="%3.2lf" type="integer" value="5"/><Parameter name="minPeakSpacing" label="minPeakSpacing" description="Absolute minimum distance between spot centers in pixels." isVisible="True" precision="%3.2lf" type="double" value="7.000000"/><Parameter name="blocksizeAllowance" label="blocksizeAllowance" description="" isVisible="False" precision="%9.7f" type="double" value="0.666667"/><Parameter name="initialFilterWidth" label="initialFilterWidth" description="Smoothing factor for initial coarse global grid location in pixels. " isVisible="True" precision="%3.2lf" type="double" value="6.000000"/><Parameter name="coarseFilterWidth" label="coarseFilterWidth" description="Smoothing factor for first coarse spot location in each subgrid in pixels. " isVisible="True" precision="%3.2lf" type="double" value="5.000000"/><Parameter name="fineFilterWidth" label="fineFilterWidth" description="Half the integration window for computing grid and spot spacings in pixels." isVisible="True" precision="%3.2lf" type="double" value="3.000000"/><Parameter name="lineHalfWidth" label="lineHalfWidth" description="Half the window for median filtering in pixels." isVisible="True" precision="%3.2lf" type="integer" value="6"/><Parameter name="halfDepth" label="halfDepth" description="Half the window for median filtering in pixels." isVisible="True" precision="%3.2lf" type="integer" value="2"/><Parameter name="maximumSlope" label="maximumSlope" description="If the computed slope exceed this value it is discarded" isVisible="True" precision="%5.3f" type="double" value="0.015000"/><Parameter name="relativeStartProjectionCol" label="Relative Column Start" description="start of the fraction of columns used in gridding" isVisible="True" precision="%5.3f" type="double" value="0.250000"/><Parameter name="relativeSizeProjectionCol" label="Relative Column Size" description="size of the fraction of columns used in gridding" isVisible="True" precision="%5.3f" type="double" value="0.250000"/><Parameter name="relativeStartProjectionRow" label="Relative Row Start" description="start of the fraction of rows used in gridding" isVisible="True" precision="%5.3f" type="double" value="0.250000"/><Parameter name="relativeSizeProjectionRow" label="Relative Row Size" description="size of the fraction of rows used in gridding" isVisible="True" precision="%5.3f" type="double" value="0.250000"/></ParameterGroup></Choice><Choice name="244k" label="244k" description="8-swath arrays" isVisible="True" SpotSpacingVertical="73.323484" SpotSpacingHorizontal="63.5" MicronsPerPixelX="5.0" value="5"><ChoiceParameter name="placementMode" label="Placement Method" description="Methods for placing the grid on the image: Allow Some Distortion - allows the spot spacing, subgrid spacing, or skew to vary during grid placement; Place and Rotate Only - places and rotates a rigid grid on the image without distorting the grid" isVisible="True" value="0"><Choice name="free" label="Allow Some Distortion" description="" isVisible="True" value="0"/><Choice name="rigid" label="Place And Rotate Only" description="" isVisible="True" value="1"/></ChoiceParameter><ParameterGroup name="customFit" label="Perform Custom Fit?" description="Standard Agilent Arrays (44k, 22k, 11k, 8.4k and a few third party) are found without custom fitting. Custom fitting may be needed when default gridding fails." isVisible="False" value="True"><ChoiceParameter name="gridWithChannel" label="What channel(s) are used for Gridding? " description="Use this option if the background of 1 channel dominates the signal of the other. If single channel tiff this parameter is not used." isVisible="True" value="0"><Choice name="all" label="Sum of All Channels" description="" isVisible="True" value="0"/><Choice name="red" label="Red Channel Only" description="" isVisible="True" value="1"/><Choice name="green" label="Green Channel Only" description="" isVisible="True" value="2"/></ChoiceParameter><Parameter name="ptsPerSide" label="ptsPerSide" description="Number of pixels that should be smaller than the spot radius" isVisible="True" precision="%3.2lf" type="integer" value="5"/><Parameter name="minPeakSpacing" label="minPeakSpacing" description="Absolute minimum distance between spot centers in pixels." isVisible="True" precision="%3.2lf" type="double" value="7.000000"/><Parameter name="blocksizeAllowance" label="blocksizeAllowance" description="" isVisible="False" precision="%9.7f" type="double" value="0.666667"/><Parameter name="initialFilterWidth" label="initialFilterWidth" description="Smoothing factor for initial coarse global grid location in pixels. " isVisible="True" precision="%3.2lf" type="double" value="6.000000"/><Parameter name="coarseFilterWidth" label="coarseFilterWidth" description="Smoothing factor for first coarse spot location in each subgrid in pixels. " isVisible="True" precision="%3.2lf" type="double" value="5.000000"/><Parameter name="fineFilterWidth" label="fineFilterWidth" description="Half the integration window for computing grid and spot spacings in pixels." isVisible="True" precision="%3.2lf" type="double" value="3.000000"/><Parameter name="lineHalfWidth" label="lineHalfWidth" description="Half the window for median filtering in pixels." isVisible="True" precision="%3.2lf" type="integer" value="6"/><Parameter name="halfDepth" label="halfDepth" description="Half the window for median filtering in pixels." isVisible="True" precision="%3.2lf" type="integer" value="3"/><Parameter name="maximumSlope" label="maximumSlope" description="If the computed slope exceed this value it is discarded" isVisible="True" precision="%5.3f" type="double" value="0.015000"/><Parameter name="relativeStartProjectionCol" label="Relative Column Start" description="start of the fraction of columns used in gridding" isVisible="True" precision="%5.3f" type="double" value="0.250000"/><Parameter name="relativeSizeProjectionCol" label="Relative Column Size" description="size of the fraction of columns used in gridding" isVisible="True" precision="%5.3f" type="double" value="0.250000"/><Parameter name="relativeStartProjectionRow" label="Relative Row Start" description="start of the fraction of rows used in gridding" isVisible="True" precision="%5.3f" type="double" value="0.250000"/><Parameter name="relativeSizeProjectionRow" label="Relative Row Size" description="size of the fraction of rows used in gridding" isVisible="True" precision="%5.3f" type="double" value="0.250000"/></ParameterGroup></Choice><Choice name="185k10uM" label="185k 10uM" description="7-swath arrays" isVisible="True" SpotSpacingVertical="83.798268" SpotSpacingHorizontal="72.5714285" MicronsPerPixelX="10.0" value="6"><ChoiceParameter name="placementMode" label="Placement Method" description="Methods for placing the grid on the image: Allow Some Distortion - allows the spot spacing, subgrid spacing, or skew to vary during grid placement; Place and Rotate Only - places and rotates a rigid grid on the image without distorting the grid" isVisible="True" value="0"><Choice name="free" label="Allow Some Distortion" description="" isVisible="True" value="0"/><Choice name="rigid" label="Place And Rotate Only" description="" isVisible="True" value="1"/></ChoiceParameter><ParameterGroup name="customFit" label="Perform Custom Fit?" description="Standard Agilent Arrays (44k, 22k, 11k, 8.4k and a few third party) are found without custom fitting. Custom fitting may be needed when default gridding fails." isVisible="False" value="True"><ChoiceParameter name="gridWithChannel" label="What channel(s) are used for Gridding? " description="Use this option if the background of 1 channel dominates the signal of the other. If single channel tiff this parameter is not used." isVisible="True" value="0"><Choice name="all" label="Sum of All Channels" description="" isVisible="True" value="0"/><Choice name="red" label="Red Channel Only" description="" isVisible="True" value="1"/><Choice name="green" label="Green Channel Only" description="" isVisible="True" value="2"/></ChoiceParameter><Parameter name="ptsPerSide" label="ptsPerSide" description="Number of pixels that should be smaller than the spot radius" isVisible="True" precision="%3.2lf" type="integer" value="4"/><Parameter name="minPeakSpacing" label="minPeakSpacing" description="Absolute minimum distance between spot centers in pixels." isVisible="True" precision="%3.2lf" type="double" value="6.000000"/><Parameter name="blocksizeAllowance" label="blocksizeAllowance" description="" isVisible="False" precision="%9.7f" type="double" value="0.666667"/><Parameter name="initialFilterWidth" label="initialFilterWidth" description="Smoothing factor for initial coarse global grid location in pixels. " isVisible="True" precision="%3.2lf" type="double" value="5.000000"/><Parameter name="coarseFilterWidth" label="coarseFilterWidth" description="Smoothing factor for first coarse spot location in each subgrid in pixels. " isVisible="True" precision="%3.2lf" type="double" value="4.000000"/><Parameter name="fineFilterWidth" label="fineFilterWidth" description="Half the integration window for computing grid and spot spacings in pixels." isVisible="True" precision="%3.2lf" type="double" value="2.000000"/><Parameter name="lineHalfWidth" label="lineHalfWidth" description="Half the window for median filtering in pixels." isVisible="True" precision="%3.2lf" type="integer" value="3"/><Parameter name="halfDepth" label="halfDepth" description="Half the window for median filtering in pixels." isVisible="True" precision="%3.2lf" type="integer" value="2"/><Parameter name="maximumSlope" label="maximumSlope" description="If the computed slope exceed this value it is discarded" isVisible="True" precision="%5.3f" type="double" value="0.015000"/><Parameter name="thinOutCoeff" label="Thin Out Coefficient" description="Maximum ratio of found spots over expected (1 dimension)" isVisible="True" precision="%5.3f" low="1.000000" high="2.000000" type="double" value="1.100000"/><Parameter name="relativeStartProjectionCol" label="Relative Column Start" description="start of the fraction of columns used in gridding" isVisible="True" precision="%5.3f" type="double" value="0.250000"/><Parameter name="relativeSizeProjectionCol" label="Relative Column Size" description="size of the fraction of columns used in gridding" isVisible="True" precision="%5.3f" type="double" value="0.250000"/><Parameter name="relativeStartProjectionRow" label="Relative Row Start" description="start of the fraction of rows used in gridding" isVisible="True" precision="%5.3f" type="double" value="0.250000"/><Parameter name="relativeSizeProjectionRow" label="Relative Row Size" description="size of the fraction of rows used in gridding" isVisible="True" precision="%5.3f" type="double" value="0.250000"/></ParameterGroup></Choice><Choice name="244k10uM" label="244k 10uM" description="8-swath arrays" isVisible="True" SpotSpacingVertical="73.323484" SpotSpacingHorizontal="63.5" MicronsPerPixelX="10.0" value="7"><ChoiceParameter name="placementMode" label="Placement Method" description="Methods for placing the grid on the image: Allow Some Distortion - allows the spot spacing, subgrid spacing, or skew to vary during grid placement; Place and Rotate Only - places and rotates a rigid grid on the image without distorting the grid" isVisible="True" value="0"><Choice name="free" label="Allow Some Distortion" description="" isVisible="True" value="0"/><Choice name="rigid" label="Place And Rotate Only" description="" isVisible="True" value="1"/></ChoiceParameter><ParameterGroup name="customFit" label="Perform Custom Fit?" description="Standard Agilent Arrays (44k, 22k, 11k, 8.4k and a few third party) are found without custom fitting. Custom fitting may be needed when default gridding fails." isVisible="False" value="True"><ChoiceParameter name="gridWithChannel" label="What channel(s) are used for Gridding? " description="Use this option if the background of 1 channel dominates the signal of the other. If single channel tiff this parameter is not used." isVisible="True" value="0"><Choice name="all" label="Sum of All Channels" description="" isVisible="True" value="0"/><Choice name="red" label="Red Channel Only" description="" isVisible="True" value="1"/><Choice name="green" label="Green Channel Only" description="" isVisible="True" value="2"/></ChoiceParameter><Parameter name="ptsPerSide" label="ptsPerSide" description="Number of pixels that should be smaller than the spot radius" isVisible="True" precision="%3.2lf" type="integer" value="4"/><Parameter name="minPeakSpacing" label="minPeakSpacing" description="Absolute minimum distance between spot centers in pixels." isVisible="True" precision="%3.2lf" type="double" value="6.000000"/><Parameter name="blocksizeAllowance" label="blocksizeAllowance" description="" isVisible="False" precision="%9.7f" type="double" value="0.666667"/><Parameter name="initialFilterWidth" label="initialFilterWidth" description="Smoothing factor for initial coarse global grid location in pixels. " isVisible="True" precision="%3.2lf" type="double" value="5.000000"/><Parameter name="coarseFilterWidth" label="coarseFilterWidth" description="Smoothing factor for first coarse spot location in each subgrid in pixels. " isVisible="True" precision="%3.2lf" type="double" value="4.000000"/><Parameter name="fineFilterWidth" label="fineFilterWidth" description="Half the integration window for computing grid and spot spacings in pixels." isVisible="True" precision="%3.2lf" type="double" value="2.000000"/><Parameter name="lineHalfWidth" label="lineHalfWidth" description="Half the window for median filtering in pixels." isVisible="True" precision="%3.2lf" type="integer" value="3"/><Parameter name="halfDepth" label="halfDepth" description="Half the window for median filtering in pixels." isVisible="True" precision="%3.2lf" type="integer" value="2"/><Parameter name="maximumSlope" label="maximumSlope" description="If the computed slope exceed this value it is discarded" isVisible="True" precision="%5.3f" type="double" value="0.015000"/><Parameter name="thinOutCoeff" label="Thin Out Coefficient" description="Maximum ratio of found spots over expected (1 dimension)" isVisible="True" precision="%5.3f" low="1.000000" high="2.000000" type="double" value="1.100000"/><Parameter name="relativeStartProjectionCol" label="Relative Column Start" description="start of the fraction of columns used in gridding" isVisible="True" precision="%5.3f" type="double" value="0.250000"/><Parameter name="relativeSizeProjectionCol" label="Relative Column Size" description="size of the fraction of columns used in gridding" isVisible="True" precision="%5.3f" type="double" value="0.250000"/><Parameter name="relativeStartProjectionRow" label="Relative Row Start" description="start of the fraction of rows used in gridding" isVisible="True" precision="%5.3f" type="double" value="0.250000"/><Parameter name="relativeSizeProjectionRow" label="Relative Row Size" description="size of the fraction of rows used in gridding" isVisible="True" precision="%5.3f" type="double" value="0.250000"/></ParameterGroup></Choice><Choice name="25k" label="25k" description="25k" isVisible="True" SpotSpacingVertical="188.214002" SpotSpacingHorizontal="211.683591" value="8"><ChoiceParameter name="placementMode" label="Placement Method" description="Methods for placing the grid on the image: Allow Some Distortion - allows the spot spacing, subgrid spacing, or skew to vary during grid placement; Place and Rotate Only - places and rotates a rigid grid on the image without distorting the grid" isVisible="True" value="0"><Choice name="free" label="Allow Some Distortion" description="" isVisible="True" value="0"/><Choice name="rigid" label="Place And Rotate Only" description="" isVisible="True" value="1"/></ChoiceParameter><ParameterGroup name="customFit" label="Perform Custom Fit?" description="Standard Agilent Arrays (44k, 22k, 11k, 8.4k and a few third party) are found without custom fitting. Custom fitting may be needed when default gridding fails." isVisible="False" value="False"><ChoiceParameter name="gridWithChannel" label="What channel(s) are used for Gridding? " description="Use this option if the background of 1 channel dominates the signal of the other. If single channel tiff this parameter is not used." isVisible="True" value="0"><Choice name="all" label="Sum of All Channels" description="" isVisible="True" value="0"/><Choice name="red" label="Red Channel Only" description="" isVisible="True" value="1"/><Choice name="green" label="Green Channel Only" description="" isVisible="True" value="2"/></ChoiceParameter><Parameter name="ptsPerSide" label="ptsPerSide" description="Number of pixels that should be smaller than the spot radius" isVisible="True" precision="%3.2lf" type="integer" value="5"/><Parameter name="minPeakSpacing" label="minPeakSpacing" description="Absolute minimum distance between spot centers in pixels." isVisible="True" precision="%3.2lf" type="double" value="7.000000"/><Parameter name="blocksizeAllowance" label="blocksizeAllowance" description="" isVisible="False" precision="%9.7f" type="double" value="0.666667"/><Parameter name="initialFilterWidth" label="initialFilterWidth" description="Smoothing factor for initial coarse global grid location in pixels. " isVisible="True" precision="%3.2lf" type="double" value="6.000000"/><Parameter name="coarseFilterWidth" label="coarseFilterWidth" description="Smoothing factor for first coarse spot location in each subgrid in pixels. " isVisible="True" precision="%3.2lf" type="double" value="5.000000"/><Parameter name="fineFilterWidth" label="fineFilterWidth" description="Half the integration window for computing grid and spot spacings in pixels." isVisible="True" precision="%3.2lf" type="double" value="3.000000"/><Parameter name="lineHalfWidth" label="lineHalfWidth" description="Half the window for median filtering in pixels." isVisible="True" precision="%3.2lf" type="integer" value="6"/><Parameter name="halfDepth" label="halfDepth" description="Half the window for median filtering in pixels." isVisible="True" precision="%3.2lf" type="integer" value="2"/><Parameter name="maximumSlope" label="maximumSlope" description="If the computed slope exceed this value it is discarded" isVisible="True" precision="%5.3f" type="double" value="0.015000"/><Parameter name="thinOutCoef" label="Thin Out Coefficient" description="Maximum ratio of found spots over expected (1 dimension)" isVisible="True" precision="%5.3f" low="1.000000" high="2.000000" type="double" value="1.500000"/></ParameterGroup></Choice><Choice name="Third Party" label="ThirdParty" description="Third Party Arrays" isVisible="True" value="9"><ChoiceParameter name="placementMode" label="Placement Method" description="Methods for placing the grid on the image: Allow Some Distortion - allows the spot spacing, subgrid spacing, or skew to vary during grid placement; Place and Rotate Only - places and rotates a rigid grid on the image without distorting the grid" isVisible="True" value="0"><Choice name="free" label="Allow Some Distortion" description="" isVisible="True" value="0"/><Choice name="rigid" label="Place And Rotate Only" description="" isVisible="True" value="1"/></ChoiceParameter><ParameterGroup name="customFit" label="Perform Custom Fit?" description="Standard Agilent Arrays (44k, 22k, 11k, 8.4k and a few third party) are found without custom fitting. Custom fitting may be needed when default gridding fails." isVisible="False" value="True"><ChoiceParameter name="gridWithChannel" label="What channel(s) are used for Gridding? " description="Use this option if the background of 1 channel dominates the signal of the other. If single channel tiff this parameter is not used." isVisible="True" value="0"><Choice name="all" label="Sum of All Channels" description="" isVisible="True" value="0"/><Choice name="red" label="Red Channel Only" description="" isVisible="True" value="1"/><Choice name="green" label="Green Channel Only" description="" isVisible="True" value="2"/></ChoiceParameter><Parameter name="ptsPerSide" label="ptsPerSide" description="Number of pixels that should be smaller than the spot radius" isVisible="True" precision="%3.2lf" type="integer" value="5"/><Parameter name="minPeakSpacing" label="minPeakSpacing" description="Absolute minimum distance between spot centers in pixels." isVisible="True" precision="%3.2lf" type="double" value="9.000000"/><Parameter name="blocksizeAllowance" label="blocksizeAllowance" description="" isVisible="False" precision="%9.7f" type="double" value="0.666667"/><Parameter name="initialFilterWidth" label="initialFilterWidth" description="Smoothing factor for initial coarse global grid location in pixels. " isVisible="True" precision="%3.2lf" type="double" value="6.000000"/><Parameter name="coarseFilterWidth" label="coarseFilterWidth" description="Smoothing factor for first coarse spot location in each subgrid in pixels. " isVisible="True" precision="%3.2lf" type="double" value="5.000000"/><Parameter name="fineFilterWidth" label="fineFilterWidth" description="Half the integration window for computing grid and spot spacings in pixels." isVisible="True" precision="%3.2lf" type="double" value="4.000000"/><Parameter name="lineHalfWidth" label="lineHalfWidth" description="Half the window for median filtering in pixels." isVisible="True" precision="%3.2lf" type="integer" value="6"/><Parameter name="halfDepth" label="halfDepth" description="Half the window for median filtering in pixels." isVisible="True" precision="%3.2lf" type="integer" value="2"/><Parameter name="maximumSlope" label="maximumSlope" description="If the computed slope exceed this value it is discarded" isVisible="True" precision="%5.3f" type="double" value="0.015000"/><Parameter name="thinOutCoef" label="Thin Out Coefficient" description="Maximum ratio of found spots over expected (1 dimension)" isVisible="True" precision="%5.3f" low="1.000000" high="2.000000" type="double" value="1.500000"/></ParameterGroup></Choice></ChoiceParameterGroup></Step><Step name="SpotAnalysis" label="Find Spots" description="Find spots on the image based upon the grid found above." isEnabled="True" module="FEImageProc"><ChoiceParameterGroup name="SpotFormat" label="Spot Format" description="What is the Array format of the images to be processed " isVisible="True" value="9"><Choice name="SpecialEvaluate" label="Automatically Determine" description="" isVisible="True" value="0"/><Choice name="SingleDensity" label="Single Density" description="11kx2, 22k, 2k 8-Pack" isVisible="True" SpotSpacingVertical="188.148148" SpotSpacingHorizontal="211.666667" value="1"><Parameter name="UseNominalDiameterFromGT" label="Use The Nominal Diameter From GridTemplate" description="Use the nominal spot radius from the grid template rather than the spot radius computed during grid placement as a starting point for final spot radius computation." isVisible="True" precision="%3.2lf" type="boolean" value="True"/><Parameter name="kmeans_cen_reject_factor" label="Spot Deviation Limit" description="The spot deviation limit defines how far the actual spot centroid may move relative to its nominal grid position (in terms of nominal radius)." isVisible="True" precision="%3.2lf" type="double" value="1.500000"/><ParameterGroup name="SpotFind" label="Perform Custom Spot Finding?" description="Custom Parameters For Determining the spot centroids and spot radius." isVisible="False" value="True"><Parameter name="convergence_factor" label="convergence_factor" description="Convergence factor of KMeans algorithm" isVisible="True" precision="%5.3f" type="double" value="0.001000"/><Parameter name="weakthresh" label="weakthresh" description="Minimum difference between the average intensities of feature and background  after Kmeans Initialization" isVisible="True" precision="%3.2lf" type="integer" value="10"/><Parameter name="RegionOfInterestMultiplier" label="Region Of Interest Multiplier" description="Defines how big the Region of Interest(ROI) is in term of nominal spot spacing. For Single density this should be .5 and double should be .75" isVisible="True" precision="%5.3f" low="0.000000" high="1.000000" type="double" value="0.500000"/><Parameter name="max_em_iter" label="max_em_iter" description="Maximum number of iterations of Bayesian Classification" isVisible="True" precision="%3.2lf" type="integer" value="5"/><Parameter name="max_reject_ratio" label="max_reject_ratio" description="" isVisible="False" precision="%3.2lf" type="double" value="0.750000"/><Parameter name="kmeans_rad_reject_factor" label="kmeans_rad_reject_factor" description="Defines by how much individual spotsize may vary relative to the nominal spotsize" isVisible="True" precision="%3.2lf" type="double" value="0.450000"/><Parameter name="kmeans_moi_reject_factor" label="kmeans_moi_reject_factor" description="" isVisible="False" precision="%3.2lf" type="double" value="2.500000"/><Parameter name="isspot_factor" label="isspot_factor" description="Gives an idea from the statistics of the found feature and background, if it is really a spot." isVisible="True" precision="%3.2lf" type="double" value="0.500000"/><Parameter name="isweakspot_factor" label="isweakspot_factor" description="Gives an idea from the statistics of the found feature and background, if it is a weak spot." isVisible="True" precision="%3.2lf" type="double" value="3.000000"/><Parameter name="grid_moved_reject_factor" label="grid_moved_reject_factor" description="" isVisible="False" precision="%3.2lf" type="double" value="1.000000"/><Parameter name="BackgroundThreshold" label="Background Threshold" description="Individual spot background may vary by this factor from the running average of all the background means." isVisible="True" precision="%4.2f" low="1.000000" high="10.000000" type="double" value="10.000000"/></ParameterGroup><ChoiceParameter name="ROIType" label="Type of ROI" description="Should Spotfinder use a rectangular or circular ROI to find the spot?" isVisible="False" value="1"><Choice name="rectangle" label="use rectangle" description="Computes a rectangular ROI to find the spot with" isVisible="True" value="1"/><Choice name="oval" label="use oval" description="Computes a circular ROI to find the spot with" isVisible="True" value="2"/></ChoiceParameter><ChoiceParameterGroup name="SpotStatsMethod" label="Calculation of Spot Statistics Method" description="Different algorithms to calculate spot statistics: CookieCutter and WholeSpot" isVisible="True" value="1"><Choice name="CookieCutter" label="Use Cookie" description="" isVisible="True" value="1"><Parameter name="CookiePercentage" label="Cookie Percentage" description="The fraction of the nominal radius used to draw the cookie around the centroid of each spot" isVisible="True" precision="%5.3f" low="0.000000" high="1.000000" type="double" value="0.650000"/><Parameter name="ExclusionZonePercentage" label="Exclusion Zone Percentage" description="The outer radius of the exclusion zone based on nominal spot size" isVisible="True" precision="%5.3f" low="1.000000" high="2.000000" type="double" value="1.200000"/></Choice><Choice name="WholeSpot" label="Use Whole Spot" description="" isVisible="True" value="2"><Parameter name="ExclusionZonePercentage" label="Exclusion Zone Percentage" description="The outer radius of the exclusion zone based on nominal spot size." isVisible="True" precision="%5.3f" low="1.000000" high="2.000000" type="double" value="1.200000"/></Choice></ChoiceParameterGroup><ChoiceParameterGroup name="EstimateLocalRadius" label="Auto Estimate the Local Radius" description="Use a dynamically determined outer radius for the Local Background (True) or use a protocol supplied value (False)" isVisible="True" value="1"><Choice name="EstimateLocalRadiusTrue" label="True" description="" isVisible="True" value="1"/><Choice name="EstimateLocalRadiusFalse" label="False" description="" isVisible="True" value="0"><Parameter name="LocalBGRadius" label="LocalBGRadius" description="The outer radius of the local background supplied from the protocol if EstimateLocalRadius is not opted." isVisible="True" precision="%4.0f" low="50.000000" high="2100.000000" type="double" value="127.000000"/></Choice></ChoiceParameterGroup><Parameter name="MinimumNumPixels" label="Minimum Number of Pixels" description="Minimum Number of Pixels needed to Calculate Spot Statistics." isVisible="False" precision="%5.0f" low="2.000000" high="2000.000000" type="integer" value="15"/></Choice><Choice name="DoubleDensity" label="Double Density" description="44k" isVisible="True" SpotSpacingVertical="188.148148" SpotSpacingHorizontal="105.8333335" value="2"><Parameter name="UseNominalDiameterFromGT" label="Use The Nominal Diameter From GridTemplate" description="Use the nominal spot radius from the grid template rather than the spot radius computed during grid placement as a starting point for final spot radius computation." isVisible="True" precision="%3.2lf" type="boolean" value="True"/><Parameter name="kmeans_cen_reject_factor" label="Spot Deviation Limit" description="The spot deviation limit defines how far the actual spot centroid may move relative to its nominal grid position (in terms of nominal radius)." isVisible="True" precision="%3.2lf" type="double" value="1.500000"/><ParameterGroup name="SpotFind" label="Perform Custom Spot Finding?" description="Custom Parameters For Determining the spot centroids and spot radius." isVisible="False" value="True"><Parameter name="convergence_factor" label="convergence_factor" description="Convergence factor of KMeans algorithm" isVisible="True" precision="%5.3f" type="double" value="0.001000"/><Parameter name="weakthresh" label="weakthresh" description="Minimum difference between the average intensities of feature and background  after Kmeans Initialization" isVisible="True" precision="%3.2lf" type="integer" value="10"/><Parameter name="RegionOfInterestMultiplier" label="Region Of Interest Multiplier" description="Defines how big the Region of Interest(ROI) is in term of nominal spot spacing. For Single density this should be .5 and double should be .6" isVisible="True" precision="%5.3f" low="0.000000" high="1.000000" type="double" value="0.600000"/><Parameter name="max_em_iter" label="max_em_iter" description="Maximum number of iterations of Bayesian Classification" isVisible="True" precision="%3.2lf" type="integer" value="5"/><Parameter name="max_reject_ratio" label="max_reject_ratio" description="" isVisible="False" precision="%3.2lf" type="double" value="0.750000"/><Parameter name="kmeans_rad_reject_factor" label="kmeans_rad_reject_factor" description="Defines by how much individual spotsize may vary relative to the nominal spotsize" isVisible="True" precision="%3.2lf" type="double" value="0.450000"/><Parameter name="kmeans_moi_reject_factor" label="kmeans_moi_reject_factor" description="" isVisible="False" precision="%3.2lf" type="double" value="2.500000"/><Parameter name="isspot_factor" label="isspot_factor" description="Gives an idea from the statistics of the found feature and background, if it is really a spot." isVisible="True" precision="%3.2lf" type="double" value="0.500000"/><Parameter name="isweakspot_factor" label="isweakspot_factor" description="Gives an idea from the statistics of the found feature and background, if it is a weak spot." isVisible="True" precision="%3.2lf" type="double" value="3.000000"/><Parameter name="grid_moved_reject_factor" label="grid_moved_reject_factor" description="" isVisible="False" precision="%3.2lf" type="double" value="1.000000"/><Parameter name="BackgroundThreshold" label="Background Threshold" description="Individual spot background may vary by this factor from the running average of all the background means." isVisible="True" precision="%4.2f" low="1.000000" high="10.000000" type="double" value="10.000000"/></ParameterGroup><ChoiceParameter name="ROIType" label="Type of ROI" description="Should Spotfinder use a rectangular or circular ROI to find the spot?" isVisible="False" value="1"><Choice name="rectangle" label="use rectangle" description="Computes a rectangular ROI to find the spot with" isVisible="True" value="1"/><Choice name="oval" label="use oval" description="Computes a circular ROI to find the spot with" isVisible="True" value="2"/></ChoiceParameter><ChoiceParameterGroup name="SpotStatsMethod" label="Calculation of Spot Statistics Method" description="Different algorithms to calculate spot statistics: CookieCutter and WholeSpot" isVisible="True" value="1"><Choice name="CookieCutter" label="Use Cookie" description="" isVisible="True" value="1"><Parameter name="CookiePercentage" label="Cookie Percentage" description="The fraction of the nominal radius used to draw the cookie around the centroid of each spot" isVisible="True" precision="%5.3f" low="0.000000" high="1.000000" type="double" value="0.561000"/><Parameter name="ExclusionZonePercentage" label="Exclusion Zone Percentage" description="The outer radius of the exclusion zone based on nominal spot size" isVisible="True" precision="%5.3f" low="1.000000" high="2.000000" type="double" value="1.200000"/></Choice><Choice name="WholeSpot" label="Use Whole Spot" description="" isVisible="True" value="2"><Parameter name="ExclusionZonePercentage" label="Exclusion Zone Percentage" description="The outer radius of the exclusion zone based on nominal spot size." isVisible="True" precision="%5.3f" low="1.000000" high="2.000000" type="double" value="1.200000"/></Choice></ChoiceParameterGroup><ChoiceParameterGroup name="EstimateLocalRadius" label="Auto Estimate the Local Radius" description="Use a dynamically determined outer radius for the Local Background (True) or use a protocol supplied value (False)" isVisible="True" value="1"><Choice name="EstimateLocalRadiusTrue" label="True" description="" isVisible="True" value="1"/><Choice name="EstimateLocalRadiusFalse" label="False" description="" isVisible="True" value="0"><Parameter name="LocalBGRadius" label="LocalBGRadius" description="The outer radius of the local background supplied from the protocol if EstimateLocalRadius is not opted." isVisible="True" precision="%4.0f" low="50.000000" high="2100.000000" type="double" value="127.000000"/></Choice></ChoiceParameterGroup><Parameter name="MinimumNumPixels" label="Minimum Number of Pixels" description="Minimum Number of Pixels needed to Calculate Spot Statistics." isVisible="False" precision="%5.0f" low="2.000000" high="2000.000000" type="integer" value="15"/></Choice><Choice name="95k" label="95k" description="5-swath arrays" isVisible="True" SpotSpacingVertical="117.317575" SpotSpacingHorizontal="101.6" value="3"><Parameter name="UseNominalDiameterFromGT" label="Use The Nominal Diameter From GridTemplate" description="Use the nominal spot radius from the grid template rather than the spot radius computed during grid placement as a starting point for final spot radius computation." isVisible="True" precision="%3.2lf" type="boolean" value="True"/><Parameter name="kmeans_cen_reject_factor" label="Spot Deviation Limit" description="The spot deviation limit defines how far the actual spot centroid may move relative to its nominal grid position (in terms of nominal radius)." isVisible="True" precision="%3.2lf" type="double" value="1.500000"/><ParameterGroup name="SpotFind" label="Perform Custom Spot Finding?" description="Custom Parameters For Determining the spot centroids and spot radius." isVisible="False" value="True"><Parameter name="convergence_factor" label="convergence_factor" description="Convergence factor of KMeans algorithm" isVisible="True" precision="%5.3f" type="double" value="0.001000"/><Parameter name="weakthresh" label="weakthresh" description="Minimum difference between the average intensities of feature and background  after Kmeans Initialization" isVisible="True" precision="%3.2lf" type="integer" value="10"/><Parameter name="RegionOfInterestMultiplier" label="Region Of Interest Multiplier" description="Defines how big the Region of Interest(ROI) is in term of nominal spot spacing. For Single density this should be .5 and double should be .6" isVisible="True" precision="%5.3f" low="0.000000" high="1.000000" type="double" value="0.600000"/><Parameter name="max_em_iter" label="max_em_iter" description="Maximum number of iterations of Bayesian Classification" isVisible="True" precision="%3.2lf" type="integer" value="5"/><Parameter name="max_reject_ratio" label="max_reject_ratio" description="" isVisible="False" precision="%3.2lf" type="double" value="0.750000"/><Parameter name="kmeans_rad_reject_factor" label="kmeans_rad_reject_factor" description="Defines by how much individual spotsize may vary relative to the nominal spotsize" isVisible="True" precision="%3.2lf" type="double" value="0.450000"/><Parameter name="kmeans_moi_reject_factor" label="kmeans_moi_reject_factor" description="" isVisible="False" precision="%3.2lf" type="double" value="2.500000"/><Parameter name="isspot_factor" label="isspot_factor" description="Gives an idea from the statistics of the found feature and background, if it is really a spot." isVisible="True" precision="%3.2lf" type="double" value="0.500000"/><Parameter name="isweakspot_factor" label="isweakspot_factor" description="Gives an idea from the statistics of the found feature and background, if it is a weak spot." isVisible="True" precision="%3.2lf" type="double" value="3.000000"/><Parameter name="grid_moved_reject_factor" label="grid_moved_reject_factor" description="" isVisible="False" precision="%3.2lf" type="double" value="1.000000"/><Parameter name="BackgroundThreshold" label="Background Threshold" description="Individual spot background may vary by this factor from the running average of all the background means." isVisible="True" precision="%4.2f" low="1.000000" high="10.000000" type="double" value="10.000000"/></ParameterGroup><ChoiceParameter name="ROIType" label="Type of ROI" description="Should Spotfinder use a rectangular or circular ROI to find the spot?" isVisible="False" value="1"><Choice name="rectangle" label="use rectangle" description="Computes a rectangular ROI to find the spot with" isVisible="True" value="1"/><Choice name="oval" label="use oval" description="Computes a circular ROI to find the spot with" isVisible="True" value="2"/></ChoiceParameter><ChoiceParameterGroup name="SpotStatsMethod" label="Calculation of Spot Statistics Method" description="Different algorithms to calculate spot statistics: CookieCutter and WholeSpot" isVisible="True" value="1"><Choice name="CookieCutter" label="Use Cookie" description="" isVisible="True" value="1"><Parameter name="CookiePercentage" label="Cookie Percentage" description="The fraction of the nominal radius used to draw the cookie around the centroid of each spot" isVisible="True" precision="%5.3f" low="0.000000" high="1.000000" type="double" value="0.561000"/><Parameter name="ExclusionZonePercentage" label="Exclusion Zone Percentage" description="The outer radius of the exclusion zone based on nominal spot size" isVisible="True" precision="%5.3f" low="1.000000" high="2.000000" type="double" value="1.200000"/></Choice><Choice name="WholeSpot" label="Use Whole Spot" description="" isVisible="True" value="2"><Parameter name="ExclusionZonePercentage" label="Exclusion Zone Percentage" description="The outer radius of the exclusion zone based on nominal spot size." isVisible="True" precision="%5.3f" low="1.000000" high="2.000000" type="double" value="1.200000"/></Choice></ChoiceParameterGroup><ChoiceParameterGroup name="EstimateLocalRadius" label="Auto Estimate the Local Radius" description="Use a dynamically determined outer radius for the Local Background (True) or use a protocol supplied value (False)" isVisible="True" value="1"><Choice name="EstimateLocalRadiusTrue" label="True" description="" isVisible="True" value="1"/><Choice name="EstimateLocalRadiusFalse" label="False" description="" isVisible="True" value="0"><Parameter name="LocalBGRadius" label="LocalBGRadius" description="The outer radius of the local background supplied from the protocol if EstimateLocalRadius is not opted." isVisible="True" precision="%4.0f" low="50.000000" high="2100.000000" type="double" value="127.000000"/></Choice></ChoiceParameterGroup><Parameter name="MinimumNumPixels" label="Minimum Number of Pixels" description="Minimum Number of Pixels needed to Calculate Spot Statistics." isVisible="False" precision="%5.0f" low="2.000000" high="2000.000000" type="integer" value="15"/></Choice><Choice name="185k" label="185k" description="7-swath arrays" isVisible="True" SpotSpacingVertical="83.798268" SpotSpacingHorizontal="72.5714285" MicronsPerPixelX="5.0" value="4"><Parameter name="UseNominalDiameterFromGT" label="Use The Nominal Diameter From GridTemplate" description="Use the nominal spot radius from the grid template rather than the spot radius computed during grid placement as a starting point for final spot radius computation." isVisible="True" precision="%3.2lf" type="boolean" value="True"/><Parameter name="kmeans_cen_reject_factor" label="Spot Deviation Limit" description="The spot deviation limit defines how far the actual spot centroid may move relative to its nominal grid position (in terms of nominal radius)." isVisible="True" precision="%3.2lf" type="double" value="1.500000"/><ParameterGroup name="SpotFind" label="Perform Custom Spot Finding?" description="Custom Parameters For Determining the spot centroids and spot radius." isVisible="False" value="True"><Parameter name="convergence_factor" label="convergence_factor" description="Convergence factor of KMeans algorithm" isVisible="True" precision="%5.3f" type="double" value="0.001000"/><Parameter name="weakthresh" label="weakthresh" description="Minimum difference between the average intensities of feature and background  after Kmeans Initialization" isVisible="True" precision="%3.2lf" type="integer" value="10"/><Parameter name="RegionOfInterestMultiplier" label="Region Of Interest Multiplier" description="Defines how big the Region of Interest(ROI) is in term of nominal spot spacing. For Single density this should be .5 and double should be .6" isVisible="True" precision="%5.3f" low="0.000000" high="1.000000" type="double" value="0.600000"/><Parameter name="max_em_iter" label="max_em_iter" description="Maximum number of iterations of Bayesian Classification" isVisible="True" precision="%3.2lf" type="integer" value="5"/><Parameter name="max_reject_ratio" label="max_reject_ratio" description="" isVisible="False" precision="%3.2lf" type="double" value="0.750000"/><Parameter name="kmeans_rad_reject_factor" label="kmeans_rad_reject_factor" description="Defines by how much individual spotsize may vary relative to the nominal spotsize" isVisible="True" precision="%3.2lf" type="double" value="0.450000"/><Parameter name="kmeans_moi_reject_factor" label="kmeans_moi_reject_factor" description="" isVisible="False" precision="%3.2lf" type="double" value="2.500000"/><Parameter name="isspot_factor" label="isspot_factor" description="Gives an idea from the statistics of the found feature and background, if it is really a spot." isVisible="True" precision="%3.2lf" type="double" value="0.500000"/><Parameter name="isweakspot_factor" label="isweakspot_factor" description="Gives an idea from the statistics of the found feature and background, if it is a weak spot." isVisible="True" precision="%3.2lf" type="double" value="3.000000"/><Parameter name="grid_moved_reject_factor" label="grid_moved_reject_factor" description="" isVisible="False" precision="%3.2lf" type="double" value="1.000000"/><Parameter name="BackgroundThreshold" label="Background Threshold" description="Individual spot background may vary by this factor from the running average of all the background means." isVisible="True" precision="%4.2f" low="1.000000" high="10.000000" type="double" value="10.000000"/></ParameterGroup><ChoiceParameter name="ROIType" label="Type of ROI" description="Should Spotfinder use a rectangular or circular ROI to find the spot?" isVisible="False" value="1"><Choice name="rectangle" label="use rectangle" description="Computes a rectangular ROI to find the spot with" isVisible="True" value="1"/><Choice name="oval" label="use oval" description="Computes a circular ROI to find the spot with" isVisible="True" value="2"/></ChoiceParameter><ChoiceParameterGroup name="SpotStatsMethod" label="Calculation of Spot Statistics Method" description="Different algorithms to calculate spot statistics: CookieCutter and WholeSpot" isVisible="True" value="1"><Choice name="CookieCutter" label="Use Cookie" description="" isVisible="True" value="1"><Parameter name="CookiePercentage" label="Cookie Percentage" description="The fraction of the nominal radius used to draw the cookie around the centroid of each spot" isVisible="True" precision="%5.3f" low="0.000000" high="1.000000" type="double" value="0.700000"/><Parameter name="ExclusionZonePercentage" label="Exclusion Zone Percentage" description="The outer radius of the exclusion zone based on nominal spot size" isVisible="True" precision="%5.3f" low="1.000000" high="2.000000" type="double" value="1.200000"/></Choice><Choice name="WholeSpot" label="Use Whole Spot" description="" isVisible="True" value="2"><Parameter name="ExclusionZonePercentage" label="Exclusion Zone Percentage" description="The outer radius of the exclusion zone based on nominal spot size." isVisible="True" precision="%5.3f" low="1.000000" high="2.000000" type="double" value="1.200000"/></Choice></ChoiceParameterGroup><ChoiceParameterGroup name="EstimateLocalRadius" label="Auto Estimate the Local Radius" description="Use a dynamically determined outer radius for the Local Background (True) or use a protocol supplied value (False)" isVisible="True" value="0"><Choice name="EstimateLocalRadiusTrue" label="True" description="" isVisible="True" value="1"/><Choice name="EstimateLocalRadiusFalse" label="False" description="" isVisible="True" value="0"><Parameter name="LocalBGRadius" label="LocalBGRadius" description="The outer radius of the local background supplied from the protocol if EstimateLocalRadius is not opted." isVisible="True" precision="%4.0f" low="50.000000" high="2100.000000" type="double" value="100.000000"/></Choice></ChoiceParameterGroup><Parameter name="MinimumNumPixels" label="Minimum Number of Pixels" description="Minimum Number of Pixels needed to Calculate Spot Statistics." isVisible="False" precision="%5.0f" low="2.000000" high="2000.000000" type="integer" value="15"/></Choice><Choice name="244k" label="244k" description="8-swath arrays" isVisible="True" SpotSpacingVertical="73.323484" SpotSpacingHorizontal="63.5" MicronsPerPixelX="5.0" value="5"><Parameter name="UseNominalDiameterFromGT" label="Use The Nominal Diameter From GridTemplate" description="Use the nominal spot radius from the grid template rather than the spot radius computed during grid placement as a starting point for final spot radius computation." isVisible="True" precision="%3.2lf" type="boolean" value="True"/><Parameter name="kmeans_cen_reject_factor" label="Spot Deviation Limit" description="The spot deviation limit defines how far the actual spot centroid may move relative to its nominal grid position (in terms of nominal radius)." isVisible="True" precision="%3.2lf" type="double" value="1.500000"/><ParameterGroup name="SpotFind" label="Perform Custom Spot Finding?" description="Custom Parameters For Determining the spot centroids and spot radius." isVisible="False" value="True"><Parameter name="convergence_factor" label="convergence_factor" description="Convergence factor of KMeans algorithm" isVisible="True" precision="%5.3f" type="double" value="0.001000"/><Parameter name="weakthresh" label="weakthresh" description="Minimum difference between the average intensities of feature and background  after Kmeans Initialization" isVisible="True" precision="%3.2lf" type="integer" value="10"/><Parameter name="RegionOfInterestMultiplier" label="Region Of Interest Multiplier" description="Defines how big the Region of Interest(ROI) is in term of nominal spot spacing. For Single density this should be .5 and double should be .6" isVisible="True" precision="%5.3f" low="0.000000" high="1.000000" type="double" value="0.600000"/><Parameter name="max_em_iter" label="max_em_iter" description="Maximum number of iterations of Bayesian Classification" isVisible="True" precision="%3.2lf" type="integer" value="5"/><Parameter name="max_reject_ratio" label="max_reject_ratio" description="" isVisible="False" precision="%3.2lf" type="double" value="0.750000"/><Parameter name="kmeans_rad_reject_factor" label="kmeans_rad_reject_factor" description="Defines by how much individual spotsize may vary relative to the nominal spotsize" isVisible="True" precision="%3.2lf" type="double" value="0.450000"/><Parameter name="kmeans_moi_reject_factor" label="kmeans_moi_reject_factor" description="" isVisible="False" precision="%3.2lf" type="double" value="2.500000"/><Parameter name="isspot_factor" label="isspot_factor" description="Gives an idea from the statistics of the found feature and background, if it is really a spot." isVisible="True" precision="%3.2lf" type="double" value="0.500000"/><Parameter name="isweakspot_factor" label="isweakspot_factor" description="Gives an idea from the statistics of the found feature and background, if it is a weak spot." isVisible="True" precision="%3.2lf" type="double" value="3.000000"/><Parameter name="grid_moved_reject_factor" label="grid_moved_reject_factor" description="" isVisible="False" precision="%3.2lf" type="double" value="1.000000"/><Parameter name="BackgroundThreshold" label="Background Threshold" description="Individual spot background may vary by this factor from the running average of all the background means." isVisible="True" precision="%4.2f" low="1.000000" high="10.000000" type="double" value="10.000000"/></ParameterGroup><ChoiceParameter name="ROIType" label="Type of ROI" description="Should Spotfinder use a rectangular or circular ROI to find the spot?" isVisible="False" value="1"><Choice name="rectangle" label="use rectangle" description="Computes a rectangular ROI to find the spot with" isVisible="True" value="1"/><Choice name="oval" label="use oval" description="Computes a circular ROI to find the spot with" isVisible="True" value="2"/></ChoiceParameter><ChoiceParameterGroup name="SpotStatsMethod" label="Calculation of Spot Statistics Method" description="Different algorithms to calculate spot statistics: CookieCutter and WholeSpot" isVisible="True" value="1"><Choice name="CookieCutter" label="Use Cookie" description="" isVisible="True" value="1"><Parameter name="CookiePercentage" label="Cookie Percentage" description="The fraction of the nominal radius used to draw the cookie around the centroid of each spot" isVisible="True" precision="%5.3f" low="0.000000" high="1.000000" type="double" value="0.700000"/><Parameter name="ExclusionZonePercentage" label="Exclusion Zone Percentage" description="The outer radius of the exclusion zone based on nominal spot size" isVisible="True" precision="%5.3f" low="1.000000" high="2.000000" type="double" value="1.200000"/></Choice><Choice name="WholeSpot" label="Use Whole Spot" description="" isVisible="True" value="2"><Parameter name="ExclusionZonePercentage" label="Exclusion Zone Percentage" description="The outer radius of the exclusion zone based on nominal spot size." isVisible="True" precision="%5.3f" low="1.000000" high="2.000000" type="double" value="1.200000"/></Choice></ChoiceParameterGroup><ChoiceParameterGroup name="EstimateLocalRadius" label="Auto Estimate the Local Radius" description="Use a dynamically determined outer radius for the Local Background (True) or use a protocol supplied value (False)" isVisible="True" value="0"><Choice name="EstimateLocalRadiusTrue" label="True" description="" isVisible="True" value="1"/><Choice name="EstimateLocalRadiusFalse" label="False" description="" isVisible="True" value="0"><Parameter name="LocalBGRadius" label="LocalBGRadius" description="The outer radius of the local background supplied from the protocol if EstimateLocalRadius is not opted." isVisible="True" precision="%4.0f" low="50.000000" high="2100.000000" type="double" value="100.000000"/></Choice></ChoiceParameterGroup><Parameter name="MinimumNumPixels" label="Minimum Number of Pixels" description="Minimum Number of Pixels needed to Calculate Spot Statistics." isVisible="False" precision="%5.0f" low="2.000000" high="2000.000000" type="integer" value="15"/></Choice><Choice name="185k10uM" label="185k 10uM" description="7-swath arrays" isVisible="True" SpotSpacingVertical="83.798268" SpotSpacingHorizontal="72.5714285" MicronsPerPixelX="10.0" value="6"><Parameter name="UseNominalDiameterFromGT" label="Use The Nominal Diameter From GridTemplate" description="Use the nominal spot radius from the grid template rather than the spot radius computed during grid placement as a starting point for final spot radius computation." isVisible="True" precision="%3.2lf" type="boolean" value="True"/><Parameter name="kmeans_cen_reject_factor" label="Spot Deviation Limit" description="The spot deviation limit defines how far the actual spot centroid may move relative to its nominal grid position (in terms of nominal radius)." isVisible="True" precision="%3.2lf" type="double" value="1.500000"/><ParameterGroup name="SpotFind" label="Perform Custom Spot Finding?" description="Custom Parameters For Determining the spot centroids and spot radius." isVisible="False" value="True"><Parameter name="convergence_factor" label="convergence_factor" description="Convergence factor of KMeans algorithm" isVisible="True" precision="%5.3f" type="double" value="0.001000"/><Parameter name="weakthresh" label="weakthresh" description="Minimum difference between the average intensities of feature and background  after Kmeans Initialization" isVisible="True" precision="%3.2lf" type="integer" value="10"/><Parameter name="RegionOfInterestMultiplier" label="Region Of Interest Multiplier" description="Defines how big the Region of Interest(ROI) is in term of nominal spot spacing. For Single density this should be .5 and double should be .6" isVisible="True" precision="%5.3f" low="0.000000" high="1.000000" type="double" value="0.600000"/><Parameter name="max_em_iter" label="max_em_iter" description="Maximum number of iterations of Bayesian Classification" isVisible="True" precision="%3.2lf" type="integer" value="5"/><Parameter name="max_reject_ratio" label="max_reject_ratio" description="" isVisible="False" precision="%3.2lf" type="double" value="0.750000"/><Parameter name="kmeans_rad_reject_factor" label="kmeans_rad_reject_factor" description="Defines by how much individual spotsize may vary relative to the nominal spotsize" isVisible="True" precision="%3.2lf" type="double" value="0.450000"/><Parameter name="kmeans_moi_reject_factor" label="kmeans_moi_reject_factor" description="" isVisible="False" precision="%3.2lf" type="double" value="2.500000"/><Parameter name="isspot_factor" label="isspot_factor" description="Gives an idea from the statistics of the found feature and background, if it is really a spot." isVisible="True" precision="%3.2lf" type="double" value="0.500000"/><Parameter name="isweakspot_factor" label="isweakspot_factor" description="Gives an idea from the statistics of the found feature and background, if it is a weak spot." isVisible="True" precision="%3.2lf" type="double" value="3.000000"/><Parameter name="grid_moved_reject_factor" label="grid_moved_reject_factor" description="" isVisible="False" precision="%3.2lf" type="double" value="1.000000"/><Parameter name="BackgroundThreshold" label="Background Threshold" description="Individual spot background may vary by this factor from the running average of all the background means." isVisible="True" precision="%4.2f" low="1.000000" high="10.000000" type="double" value="10.000000"/></ParameterGroup><ChoiceParameter name="ROIType" label="Type of ROI" description="Should Spotfinder use a rectangular or circular ROI to find the spot?" isVisible="False" value="1"><Choice name="rectangle" label="use rectangle" description="Computes a rectangular ROI to find the spot with" isVisible="True" value="1"/><Choice name="oval" label="use oval" description="Computes a circular ROI to find the spot with" isVisible="True" value="2"/></ChoiceParameter><ChoiceParameterGroup name="SpotStatsMethod" label="Calculation of Spot Statistics Method" description="Different algorithms to calculate spot statistics: CookieCutter and WholeSpot" isVisible="True" value="1"><Choice name="CookieCutter" label="Use Cookie" description="" isVisible="True" value="1"><Parameter name="CookiePercentage" label="Cookie Percentage" description="The fraction of the nominal radius used to draw the cookie around the centroid of each spot" isVisible="True" precision="%5.3f" low="0.000000" high="1.000000" type="double" value="0.700000"/><Parameter name="ExclusionZonePercentage" label="Exclusion Zone Percentage" description="The outer radius of the exclusion zone based on nominal spot size" isVisible="True" precision="%5.3f" low="1.000000" high="2.000000" type="double" value="1.200000"/></Choice><Choice name="WholeSpot" label="Use Whole Spot" description="" isVisible="True" value="2"><Parameter name="ExclusionZonePercentage" label="Exclusion Zone Percentage" description="The outer radius of the exclusion zone based on nominal spot size." isVisible="True" precision="%5.3f" low="1.000000" high="2.000000" type="double" value="1.200000"/></Choice></ChoiceParameterGroup><ChoiceParameterGroup name="EstimateLocalRadius" label="Auto Estimate the Local Radius" description="Use a dynamically determined outer radius for the Local Background (True) or use a protocol supplied value (False)" isVisible="True" value="0"><Choice name="EstimateLocalRadiusTrue" label="True" description="" isVisible="True" value="1"/><Choice name="EstimateLocalRadiusFalse" label="False" description="" isVisible="True" value="0"><Parameter name="LocalBGRadius" label="LocalBGRadius" description="The outer radius of the local background supplied from the protocol if EstimateLocalRadius is not opted." isVisible="True" precision="%4.0f" low="50.000000" high="2100.000000" type="double" value="100.000000"/></Choice></ChoiceParameterGroup><Parameter name="MinimumNumPixels" label="Minimum Number of Pixels" description="Minimum Number of Pixels needed to Calculate Spot Statistics." isVisible="False" precision="%5.0f" low="2.000000" high="2000.000000" type="integer" value="5"/></Choice><Choice name="244k10uM" label="244k 10uM" description="8-swath arrays" isVisible="True" SpotSpacingVertical="73.323484" SpotSpacingHorizontal="63.5" MicronsPerPixelX="10.0" value="7"><Parameter name="UseNominalDiameterFromGT" label="Use The Nominal Diameter From GridTemplate" description="Use the nominal spot radius from the grid template rather than the spot radius computed during grid placement as a starting point for final spot radius computation." isVisible="True" precision="%3.2lf" type="boolean" value="True"/><Parameter name="kmeans_cen_reject_factor" label="Spot Deviation Limit" description="The spot deviation limit defines how far the actual spot centroid may move relative to its nominal grid position (in terms of nominal radius)." isVisible="True" precision="%3.2lf" type="double" value="1.500000"/><ParameterGroup name="SpotFind" label="Perform Custom Spot Finding?" description="Custom Parameters For Determining the spot centroids and spot radius." isVisible="False" value="True"><Parameter name="convergence_factor" label="convergence_factor" description="Convergence factor of KMeans algorithm" isVisible="True" precision="%5.3f" type="double" value="0.001000"/><Parameter name="weakthresh" label="weakthresh" description="Minimum difference between the average intensities of feature and background  after Kmeans Initialization" isVisible="True" precision="%3.2lf" type="integer" value="10"/><Parameter name="RegionOfInterestMultiplier" label="Region Of Interest Multiplier" description="Defines how big the Region of Interest(ROI) is in term of nominal spot spacing. For Single density this should be .5 and double should be .6" isVisible="True" precision="%5.3f" low="0.000000" high="1.000000" type="double" value="0.600000"/><Parameter name="max_em_iter" label="max_em_iter" description="Maximum number of iterations of Bayesian Classification" isVisible="True" precision="%3.2lf" type="integer" value="5"/><Parameter name="max_reject_ratio" label="max_reject_ratio" description="" isVisible="False" precision="%3.2lf" type="double" value="0.750000"/><Parameter name="kmeans_rad_reject_factor" label="kmeans_rad_reject_factor" description="Defines by how much individual spotsize may vary relative to the nominal spotsize" isVisible="True" precision="%3.2lf" type="double" value="0.450000"/><Parameter name="kmeans_moi_reject_factor" label="kmeans_moi_reject_factor" description="" isVisible="False" precision="%3.2lf" type="double" value="2.500000"/><Parameter name="isspot_factor" label="isspot_factor" description="Gives an idea from the statistics of the found feature and background, if it is really a spot." isVisible="True" precision="%3.2lf" type="double" value="0.500000"/><Parameter name="isweakspot_factor" label="isweakspot_factor" description="Gives an idea from the statistics of the found feature and background, if it is a weak spot." isVisible="True" precision="%3.2lf" type="double" value="3.000000"/><Parameter name="grid_moved_reject_factor" label="grid_moved_reject_factor" description="" isVisible="False" precision="%3.2lf" type="double" value="1.000000"/><Parameter name="BackgroundThreshold" label="Background Threshold" description="Individual spot background may vary by this factor from the running average of all the background means." isVisible="True" precision="%4.2f" low="1.000000" high="10.000000" type="double" value="10.000000"/></ParameterGroup><ChoiceParameter name="ROIType" label="Type of ROI" description="Should Spotfinder use a rectangular or circular ROI to find the spot?" isVisible="False" value="1"><Choice name="rectangle" label="use rectangle" description="Computes a rectangular ROI to find the spot with" isVisible="True" value="1"/><Choice name="oval" label="use oval" description="Computes a circular ROI to find the spot with" isVisible="True" value="2"/></ChoiceParameter><ChoiceParameterGroup name="SpotStatsMethod" label="Calculation of Spot Statistics Method" description="Different algorithms to calculate spot statistics: CookieCutter and WholeSpot" isVisible="True" value="1"><Choice name="CookieCutter" label="Use Cookie" description="" isVisible="True" value="1"><Parameter name="CookiePercentage" label="Cookie Percentage" description="The fraction of the nominal radius used to draw the cookie around the centroid of each spot" isVisible="True" precision="%5.3f" low="0.000000" high="1.000000" type="double" value="0.700000"/><Parameter name="ExclusionZonePercentage" label="Exclusion Zone Percentage" description="The outer radius of the exclusion zone based on nominal spot size" isVisible="True" precision="%5.3f" low="1.000000" high="2.000000" type="double" value="1.200000"/></Choice><Choice name="WholeSpot" label="Use Whole Spot" description="" isVisible="True" value="2"><Parameter name="ExclusionZonePercentage" label="Exclusion Zone Percentage" description="The outer radius of the exclusion zone based on nominal spot size." isVisible="True" precision="%5.3f" low="1.000000" high="2.000000" type="double" value="1.200000"/></Choice></ChoiceParameterGroup><ChoiceParameterGroup name="EstimateLocalRadius" label="Auto Estimate the Local Radius" description="Use a dynamically determined outer radius for the Local Background (True) or use a protocol supplied value (False)" isVisible="True" value="0"><Choice name="EstimateLocalRadiusTrue" label="True" description="" isVisible="True" value="1"/><Choice name="EstimateLocalRadiusFalse" label="False" description="" isVisible="True" value="0"><Parameter name="LocalBGRadius" label="LocalBGRadius" description="The outer radius of the local background supplied from the protocol if EstimateLocalRadius is not opted." isVisible="True" precision="%4.0f" low="50.000000" high="2100.000000" type="double" value="100.000000"/></Choice></ChoiceParameterGroup><Parameter name="MinimumNumPixels" label="Minimum Number of Pixels" description="Minimum Number of Pixels needed to Calculate Spot Statistics." isVisible="False" precision="%5.0f" low="2.000000" high="2000.000000" type="integer" value="5"/></Choice><Choice name="25k" label="25k" description="25k" isVisible="True" SpotSpacingVertical="188.214002" SpotSpacingHorizontal="211.683591" value="8"><Parameter name="UseNominalDiameterFromGT" label="Use The Nominal Diameter From GridTemplate" description="Use the nominal spot radius from the grid template rather than the spot radius computed during grid placement as a starting point for final spot radius computation." isVisible="True" precision="%3.2lf" type="boolean" value="True"/><Parameter name="kmeans_cen_reject_factor" label="Spot Deviation Limit" description="The spot deviation limit defines how far the actual spot centroid may move relative to its nominal grid position (in terms of nominal radius)." isVisible="True" precision="%3.2lf" type="double" value="1.500000"/><ParameterGroup name="SpotFind" label="Perform Custom Spot Finding?" description="Custom Parameters For Determining the spot centroids and spot radius." isVisible="False" value="True"><Parameter name="convergence_factor" label="convergence_factor" description="Convergence factor of KMeans algorithm" isVisible="True" precision="%5.3f" type="double" value="0.001000"/><Parameter name="weakthresh" label="weakthresh" description="Minimum difference between the average intensities of feature and background  after Kmeans Initialization" isVisible="True" precision="%3.2lf" type="integer" value="10"/><Parameter name="RegionOfInterestMultiplier" label="Region Of Interest Multiplier" description="Defines how big the Region of Interest(ROI) is in term of nominal spot spacing. For Single density this should be .5 and double should be .75" isVisible="True" precision="%5.3f" low="0.000000" high="1.000000" type="double" value="0.500000"/><Parameter name="max_em_iter" label="max_em_iter" description="Maximum number of iterations of Bayesian Classification" isVisible="True" precision="%3.2lf" type="integer" value="5"/><Parameter name="max_reject_ratio" label="max_reject_ratio" description="" isVisible="False" precision="%3.2lf" type="double" value="0.750000"/><Parameter name="kmeans_rad_reject_factor" label="kmeans_rad_reject_factor" description="Defines by how much individual spotsize may vary relative to the nominal spotsize" isVisible="True" precision="%3.2lf" type="double" value="0.450000"/><Parameter name="kmeans_moi_reject_factor" label="kmeans_moi_reject_factor" description="" isVisible="False" precision="%3.2lf" type="double" value="2.500000"/><Parameter name="isspot_factor" label="isspot_factor" description="Gives an idea from the statistics of the found feature and background, if it is really a spot." isVisible="True" precision="%3.2lf" type="double" value="0.500000"/><Parameter name="isweakspot_factor" label="isweakspot_factor" description="Gives an idea from the statistics of the found feature and background, if it is a weak spot." isVisible="True" precision="%3.2lf" type="double" value="3.000000"/><Parameter name="grid_moved_reject_factor" label="grid_moved_reject_factor" description="" isVisible="False" precision="%3.2lf" type="double" value="1.000000"/><Parameter name="BackgroundThreshold" label="Background Threshold" description="Individual spot background may vary by this factor from the running average of all the background means." isVisible="True" precision="%4.2f" low="1.000000" high="10.000000" type="double" value="10.000000"/></ParameterGroup><ChoiceParameter name="ROIType" label="Type of ROI" description="Should Spotfinder use a rectangular or circular ROI to find the spot?" isVisible="False" value="1"><Choice name="rectangle" label="use rectangle" description="Computes a rectangular ROI to find the spot with" isVisible="True" value="1"/><Choice name="oval" label="use oval" description="Computes a circular ROI to find the spot with" isVisible="True" value="2"/></ChoiceParameter><ChoiceParameterGroup name="SpotStatsMethod" label="Calculation of Spot Statistics Method" description="Different algorithms to calculate spot statistics: CookieCutter and WholeSpot" isVisible="True" value="1"><Choice name="CookieCutter" label="Use Cookie" description="" isVisible="True" value="1"><Parameter name="CookiePercentage" label="Cookie Percentage" description="The fraction of the nominal radius used to draw the cookie around the centroid of each spot" isVisible="True" precision="%5.3f" low="0.000000" high="1.000000" type="double" value="0.650000"/><Parameter name="ExclusionZonePercentage" label="Exclusion Zone Percentage" description="The outer radius of the exclusion zone based on nominal spot size" isVisible="True" precision="%5.3f" low="1.000000" high="2.000000" type="double" value="1.200000"/></Choice><Choice name="WholeSpot" label="Use Whole Spot" description="" isVisible="True" value="2"><Parameter name="ExclusionZonePercentage" label="Exclusion Zone Percentage" description="The outer radius of the exclusion zone based on nominal spot size." isVisible="True" precision="%5.3f" low="1.000000" high="2.000000" type="double" value="1.200000"/></Choice></ChoiceParameterGroup><ChoiceParameterGroup name="EstimateLocalRadius" label="Auto Estimate the Local Radius" description="Use a dynamically determined outer radius for the Local Background (True) or use a protocol supplied value (False)" isVisible="True" value="1"><Choice name="EstimateLocalRadiusTrue" label="True" description="" isVisible="True" value="1"/><Choice name="EstimateLocalRadiusFalse" label="False" description="" isVisible="True" value="0"><Parameter name="LocalBGRadius" label="LocalBGRadius" description="The outer radius of the local background supplied from the protocol if EstimateLocalRadius is not opted." isVisible="True" precision="%4.0f" low="50.000000" high="2100.000000" type="double" value="127.000000"/></Choice></ChoiceParameterGroup><Parameter name="MinimumNumPixels" label="Minimum Number of Pixels" description="Minimum Number of Pixels needed to Calculate Spot Statistics." isVisible="False" precision="%5.0f" low="2.000000" high="2000.000000" type="integer" value="15"/></Choice><Choice name="Third Party" label="ThirdParty" description="Third Party Arrays" isVisible="True" value="9"><Parameter name="UseNominalDiameterFromGT" label="Use The Nominal Diameter From GridTemplate?" description="Use the nominal spot radius from the Grid Template rather than the spot radius computed during Grid Placement as a starting point for final spot radius computation." isVisible="True" precision="%3.2lf" type="boolean" value="True"/><Parameter name="kmeans_cen_reject_factor" label="Spot Deviation Limit" description="Defines how far the actual centroid may move relative to its nominal grid position (in terms of nominal radius)" isVisible="True" precision="%3.2lf" type="double" value="1.100000"/><ParameterGroup name="SpotFind" label="Perform Custom Spot Finding?" description="Custom Parameters For Determining the spot centroids and spot radius." isVisible="False" value="True"><Parameter name="convergence_factor" label="convergence_factor" description="Convergence factor of KMeans algorithm" isVisible="True" precision="%5.3f" type="double" value="0.001000"/><Parameter name="weakthresh" label="weakthresh" description="Minimum difference between the average intensities of feature and background  after Kmeans Initialization" isVisible="True" precision="%3.2lf" type="integer" value="10"/><Parameter name="RegionOfInterestMultiplier" label="Region Of Interest Multiplier" description="Defines how big the Region of Interest(ROI) is in term of nominal spot spacing. For Single density this should be .5 and double should be .75" isVisible="True" precision="%5.3f" low="0.000000" high="1.000000" type="double" value="0.500000"/><Parameter name="max_em_iter" label="max_em_iter" description="Maximum number of iterations of Bayesian Classification" isVisible="True" precision="%3.2lf" type="integer" value="5"/><Parameter name="max_reject_ratio" label="max_reject_ratio" description="" isVisible="False" precision="%3.2lf" type="double" value="0.750000"/><Parameter name="kmeans_rad_reject_factor" label="kmeans_rad_reject_factor" description="Defines by how much individual spotsize may vary relative to the nominal spotsize" isVisible="True" precision="%3.2lf" type="double" value="0.600000"/><Parameter name="kmeans_moi_reject_factor" label="kmeans_moi_reject_factor" description="" isVisible="False" precision="%3.2lf" type="double" value="2.500000"/><Parameter name="isspot_factor" label="isspot_factor" description="Gives an idea from the statistics of the found feature and background, if it is really a spot." isVisible="True" precision="%3.2lf" type="double" value="0.500000"/><Parameter name="isweakspot_factor" label="isweakspot_factor" description="Gives an idea from the statistics of the found feature and background, if it is a weak spot." isVisible="True" precision="%3.2lf" type="double" value="3.000000"/><Parameter name="grid_moved_reject_factor" label="grid_moved_reject_factor" description="" isVisible="False" precision="%3.2lf" type="double" value="1.000000"/><Parameter name="BackgroundThreshold" label="Background Threshold" description="Individual spot background may vary by this factor from the running average of all the background means." isVisible="True" precision="%4.2f" low="1.000000" high="15.000000" type="double" value="10.000000"/></ParameterGroup><ChoiceParameter name="ROIType" label="Type of ROI" description="Should Spotfinder use a rectangular or circular ROI to find the spot?" isVisible="False" value="1"><Choice name="rectangle" label="use rectangle" description="Computes a rectangular ROI to find the spot with" isVisible="True" value="1"/><Choice name="oval" label="use oval" description="Computes a circular ROI to find the spot with" isVisible="True" value="2"/></ChoiceParameter><ChoiceParameterGroup name="SpotStatsMethod" label="Calculation of Spot Statistics Method" description="Different algorithms to calculate spot statistics: CookieCutter and WholeSpot" isVisible="True" value="1"><Choice name="CookieCutter" label="Use Cookie" description="" isVisible="True" value="1"><Parameter name="CookiePercentage" label="Cookie Percentage" description="The fraction of the nominal radius used to draw the cookie around the centroid of each spot" isVisible="True" precision="%5.3f" low="0.000000" high="1.000000" type="double" value="0.650000"/><Parameter name="ExclusionZonePercentage" label="Exclusion Zone Percentage" description="The outer radius of the exclusion zone based on nominal spot size" isVisible="True" precision="%5.3f" low="1.000000" high="2.000000" type="double" value="1.200000"/></Choice><Choice name="WholeSpot" label="Use Whole Spot" description="" isVisible="True" value="2"><Parameter name="ExclusionZonePercentage" label="Exclusion Zone Percentage" description="The outer radius of the exclusion zone based on nominal spot size." isVisible="True" precision="%5.3f" low="1.000000" high="2.000000" type="double" value="1.200000"/></Choice></ChoiceParameterGroup><ChoiceParameterGroup name="EstimateLocalRadius" label="Auto Estimate the Local Radius" description="Use a dynamically determined outer radius for the Local Background (True) or use a protocol supplied value (False)" isVisible="True" value="1"><Choice name="EstimateLocalRadiusTrue" label="True" description="" isVisible="True" value="1"/><Choice name="EstimateLocalRadiusFalse" label="False" description="" isVisible="True" value="0"><Parameter name="LocalBGRadius" label="LocalBGRadius" description="The outer radius of the local background supplied from the protocol if EstimateLocalRadius is not opted." isVisible="True" precision="%4.0f" low="50.000000" high="2100.000000" type="double" value="127.000000"/></Choice></ChoiceParameterGroup><Parameter name="MinimumNumPixels" label="Minimum Number of Pixels" description="Minimum Number of Pixels needed to Calculate Spot Statistics." isVisible="False" precision="%5.0f" low="2.000000" high="2000.000000" type="integer" value="15"/></Choice></ChoiceParameterGroup><ChoiceParameterGroup name="RejectMethod" label="Pixel Outlier Rejection Method" description="Methods for rejecting pixels from feature and local background mean signal calculations: IQR and SD" isVisible="True" value="3"><Choice name="SD" label="Standard Deviation" description="Rejects pixels outside a certain number of standard deviations from the mean of all pixels in the Feature or Local Background." isVisible="True" value="2"><Parameter name="StatBoundFeat" label="Feature SD" description="Standard deviation limit used to reject feature pixels" isVisible="True" precision="%3.1f" low="1.000000" high="3.000000" type="double" value="2.000000"/><Parameter name="StatBoundBG" label="Background SD" description="Standard deviation limit used to reject local background pixels" isVisible="True" precision="%3.1f" low="1.000000" high="3.000000" type="double" value="2.000000"/></Choice><Choice name="IQR" label="Inter Quartile Region" description="Rejects pixels in the Feature or Local Background based on the Inter-Quartile Range." isVisible="True" value="3"><Parameter name="StatBoundFeat" label="RejectIQRFeat" description="Rejects feature pixels if the signal is outside the boundary of this IQR factor multiplied by IQR (25th and 75th percentile) distribution" isVisible="True" precision="%4.2f" low="1.000000" high="2.000000" type="double" value="1.420000"/><Parameter name="StatBoundBG" label="RejectIQRBG" description="Rejects local background pixels if the signal is outside the boundary of this IQR factor multiplied by IQR (25th and 75th percentile) distribution" isVisible="True" precision="%4.2f" low="1.000000" high="2.000000" type="double" value="1.420000"/></Choice><Choice name="none" label="none" description="" isVisible="True" value="0"/></ChoiceParameterGroup><ChoiceParameterGroup name="SignalMethod" label="Statistical Method for Spot Value from Pixels" description="Use unbiased estimators (mean/standard dev.) or robust statistics (median / IQR)" isVisible="True" value="1"><Choice name="MeanStddev" label="Use Mean / Standard Deviation" description="" isVisible="True" value="1"/><Choice name="MedianNormIQR" label="Use Median / Normalized Inter Quartile Range" description="" isVisible="True" value="2"/></ChoiceParameterGroup></Step><Step name="PolyOutlierFlagger" label="Flag Outliers" description="" isEnabled="True" module="FEAnalysisProc"><ParameterGroup name="PopnOLOn" label="Compute Population Outliers" description="Flag features and local backgrounds as population outliers if the minimum number of replicates is met and the mean signal varies significantly from the distribution" isVisible="True" value="True"><Parameter name="MinPopulation" label="Minimum Population" description="Minimum number of relicates in a population needed to compute Population Outliers" isVisible="True" precision="%3.2lf" low="5.000000" high="200.000000" type="integer" value="5"/><Parameter name="IQRatio" label="IQRatio" description="Flag feature population outliers if the signal is outside the boundary of this IQR factor multiplied by IQR (25th and 75th percentile) distribution" isVisible="True" precision="%4.2f" low="1.000000" high="2.000000" type="double" value="1.420000"/><Parameter name="BackgroundIQRatio" label="Background IQRatio" description="Flag background population outliers if the signal is outside the boundary of this IQR factor multiplied by IQR (25th and 75th percentile) distribution" isVisible="True" precision="%4.2f" low="1.000000" high="10.000000" type="double" value="1.420000"/><Parameter name="UseQtest" label="Use Qtest for Small Populations?" description="Use the Qtest for small populations Greater than 3 but less than Minimum Population" isVisible="True" precision="%3.2lf" type="boolean" value="False"/></ParameterGroup><ParameterGroup name="NonUnifOLOn" label="Compute NonUniform Outliers" description="Flag features or local backgrounds as NonUniform if the pixel distribution is outside the boundary defined by the three-parameter noise model" isVisible="True" value="True"><ChoiceParameterGroup name="Scanner" label="Scanner" description="What is the Scanner used to process images" isVisible="True" value="1"><Choice name="SpecialEvaluate" label="Automatically Determine" description="" isVisible="True" value="0"/><Choice name="Agilent" label="Agilent Scanner" description="Agilent scanner" isVisible="True" ScannerMake="Agilent" value="1"><ChoiceParameterGroup name="OLAutoComputeABC" label="Automatically Compute OL Polynomial Terms" description="Enables estimation of the B and C terms of the polynomiaal outlier rejection equation from 25th percentile of signal and background mean and SD" isVisible="True" value="0"><Choice name="ComputeOLAutoABC" label="True" description="" isVisible="True" value="1"><Group name="Feature" label="Feature" description="Parameters used in the noise model for Feature nonuniformity flagging" isVisible="True"><Parameter name="FeatATerm" label="(%CV)^2 Term" description="Noise proportional to the signal" isVisible="True" precision="%7.5f" low="0.000000" high="3.000000" type="double" value="0.016900"/><Parameter name="FeatBCoeff" label="Green Poissonian Noise Term Multiplier" description="Mutiplicative factor for the green mean signal 25th percentile" isVisible="True" precision="%6.0f" low="0.000000" high="1000.000000" type="double" value="40.000000"/><Parameter name="FeatCCoeff" label="Green Signal Constant Term Multiplier" description="Mutiplicative factor for the red signal SD 25th percentile" isVisible="True" precision="%6.0f" low="0.000000" high="1000.000000" type="double" value="1.000000"/><Parameter name="FeatBCoeff2" label="unused for 1 color Poissonian Noise Term Multiplier" description="Mutiplicative factor for the green mean signal 25th percentile" isVisible="False" precision="%6.0f" low="0.000000" high="1000.000000" type="double" value="40.000000"/><Parameter name="FeatCCoeff2" label="unused for 1 color Signal Constant Term Multiplier" description="Mutiplicative factor for the green signal SD 25th percentile" isVisible="False" precision="%6.0f" low="0.000000" high="1000.000000" type="double" value="1.000000"/></Group><Group name="Background" label="Background" description="Parameters used in the noise model for Local Background nonuniformity flagging" isVisible="True"><Parameter name="BGATerm" label="(%CV)^2 Term" description="Noise proportional to the signal" isVisible="True" precision="%7.5f" low="0.000000" high="3.000000" type="double" value="0.090000"/><Parameter name="BGBCoeff" label="Green Poissonian Noise Term" description="Mutiplicative factor for the green mean background 25th percentile" isVisible="True" precision="%6.0f" low="0.000000" high="1000.000000" type="double" value="3.000000"/><Parameter name="BGCCoeff" label="Green Background Constant Term Multiplier" description="Mutiplicative factor for the red constant noise term" isVisible="True" precision="%6.0f" low="0.000000" high="1000.000000" type="double" value="1.000000"/><Parameter name="BGBCoeff2" label="unused for 1 color Poissonian Noise Term" description="Mutiplicative factor for the green mean background 25th percentile" isVisible="False" precision="%6.0f" low="0.000000" high="1000.000000" type="double" value="3.000000"/><Parameter name="BGCCoeff2" label="unused for 1 color Background Constant Term Multiplier" description="Mutiplicative factor for the green constant noise term" isVisible="False" precision="%6.0f" low="0.000000" high="1000.000000" type="double" value="1.000000"/></Group></Choice><Choice name="DoNotComputeOLAutoABC" label="False" description="" isVisible="True" value="0"><Group name="Feature" label="Feature" description="Parameters used in the noise model for feature nonuniformity flagging" isVisible="True"><Parameter name="FeatATerm" label="(%CV)^2 Term" description="Noise proportional to the signal" isVisible="True" precision="%7.5f" low="0.000000" high="3.000000" type="double" value="0.008100"/><Parameter name="FeatBTerm" label="Poissonian Noise Term" description="Noise proportional to the square root of the signal" isVisible="True" precision="%6.0f" low="0.000000" high="1000.000000" type="double" value="320.000000"/><Parameter name="FeatCTerm" label="Background Term" description="Constant noise term" isVisible="True" precision="%6.0f" low="0.000000" high="1000.000000" type="double" value="600.000000"/></Group><Group name="Background" label="Background" description="Parameters used in the noise model for local background nonuniformity flagging" isVisible="True"><Parameter name="BGATerm" label="(%CV)^2 Term" description="Noise proportional to the signal" isVisible="True" precision="%7.5f" low="0.000000" high="3.000000" type="double" value="0.022500"/><Parameter name="BGBTerm" label="Poissonian Noise Term" description="Noise proportional to the square root of the signal" isVisible="True" precision="%6.0f" low="0.000000" high="1000.000000" type="double" value="320.000000"/><Parameter name="BGCTerm" label="Background Term" description="Constant noise term" isVisible="True" precision="%6.0f" low="0.000000" high="1000.000000" type="double" value="600.000000"/></Group></Choice></ChoiceParameterGroup></Choice><Choice name="Axon" label="Axon Scanner" description="Axon scanner" isVisible="True" ScannerMake="Axon" value="2"><ChoiceParameterGroup name="OLAutoComputeABC" label="Automatically Compute OL Polynomial Terms" description="Enables estimation of the B and C terms of the polynomiaal outlier rejection equation from 25th percentile of signal and background mean and SD" isVisible="True" value="1"><Choice name="ComputeOLAutoABC" label="True" description="" isVisible="True" value="1"><Group name="Feature" label="Feature" description="Parameters used in the noise model for Feature nonuniformity flagging" isVisible="True"><Parameter name="FeatATerm" label="(%CV)^2 Term" description="Noise proportional to the signal" isVisible="True" precision="%7.5f" low="0.000000" high="3.000000" type="double" value="0.014400"/><Parameter name="FeatBCoeff" label="Green Poissonian Noise Term Multiplier" description="Mutiplicative factor for the green mean signal 25th percentile" isVisible="True" precision="%6.0f" low="0.000000" high="1000.000000" type="double" value="20.000000"/><Parameter name="FeatCCoeff" label="Green Signal Constant Term Multiplier" description="Mutiplicative factor for the red signal SD 25th percentile" isVisible="True" precision="%6.0f" low="0.000000" high="1000.000000" type="double" value="1.000000"/><Parameter name="FeatBCoeff2" label="unused for 1 color Poissonian Noise Term Multiplier" description="Mutiplicative factor for the green mean signal 25th percentile" isVisible="False" precision="%6.0f" low="0.000000" high="1000.000000" type="double" value="20.000000"/><Parameter name="FeatCCoeff2" label="unused for 1 color Signal Constant Term Multiplier" description="Mutiplicative factor for the green signal SD 25th percentile" isVisible="False" precision="%6.0f" low="0.000000" high="1000.000000" type="double" value="1.000000"/></Group><Group name="Background" label="Background" description="Parameters used in the noise model for Local Background nonuniformity flagging" isVisible="True"><Parameter name="BGATerm" label="(%CV)^2 Term" description="Noise proportional to the signal" isVisible="True" precision="%7.5f" low="0.000000" high="3.000000" type="double" value="0.090000"/><Parameter name="BGBCoeff" label="Green Poissonian Noise Term" description="Mutiplicative factor for the green mean background 25th percentile" isVisible="True" precision="%6.0f" low="0.000000" high="1000.000000" type="double" value="1.000000"/><Parameter name="BGCCoeff" label="Green Background Constant Term Multiplier" description="Mutiplicative factor for the red constant noise term" isVisible="True" precision="%6.0f" low="0.000000" high="1000.000000" type="double" value="1.000000"/><Parameter name="BGBCoeff2" label="unused for 1 color Poissonian Noise Term" description="Mutiplicative factor for the green mean background 25th percentile" isVisible="False" precision="%6.0f" low="0.000000" high="1000.000000" type="double" value="1.000000"/><Parameter name="BGCCoeff2" label="unused for 1 color Background Constant Term Multiplier" description="Mutiplicative factor for the green constant noise term" isVisible="False" precision="%6.0f" low="0.000000" high="1000.000000" type="double" value="1.000000"/></Group></Choice><Choice name="DoNotComputeOLAutoABC" label="False" description="" isVisible="True" value="0"><Group name="Feature" label="Feature" description="Parameters used in the noise model for feature nonuniformity flagging" isVisible="True"><Parameter name="FeatATerm" label="(%CV)^2 Term" description="Noise proportional to the signal" isVisible="True" precision="%7.5f" low="0.000000" high="3.000000" type="double" value="0.010000"/><Parameter name="FeatBTerm" label="Poissonian Noise Term" description="Noise proportional to the square root of the signal" isVisible="True" precision="%6.0f" low="0.000000" high="1000.000000" type="double" value="320.000000"/><Parameter name="FeatCTerm" label="Background Term" description="Constant noise term" isVisible="True" precision="%6.0f" low="0.000000" high="1000.000000" type="double" value="600.000000"/></Group><Group name="Background" label="Background" description="Parameters used in the noise model for local background nonuniformity flagging" isVisible="True"><Parameter name="BGATerm" label="(%CV)^2 Term" description="Noise proportional to the signal" isVisible="True" precision="%7.5f" low="0.000000" high="3.000000" type="double" value="0.022500"/><Parameter name="BGBTerm" label="Poissonian Noise Term" description="Noise proportional to the square root of the signal" isVisible="True" precision="%6.0f" low="0.000000" high="1000.000000" type="double" value="320.000000"/><Parameter name="BGCTerm" label="Background Term" description="Constant noise term" isVisible="True" precision="%6.0f" low="0.000000" high="1000.000000" type="double" value="600.000000"/></Group></Choice></ChoiceParameterGroup></Choice></ChoiceParameterGroup></ParameterGroup></Step><Step name="BGSub" label="Compute Bkgd, Bias and Error" description="" isEnabled="True" module="FEAnalysisProc"><ChoiceParameter name="BGSubMethod" label="Background Subtraction Method" description="Method used to subtract background from the feature signal" isVisible="True" value="6"><Choice name="NoBackgroundSubtraction" label="No Background Subtraction" description="No subtraction is done." isVisible="True" value="7"/><Choice name="LocalBackground" label="Local Background" description="Subtract from each Feature its Local Background" isVisible="True" value="5"/><Choice name="AverageOfAllBackgrounds" label="Average Of All Background Areas" description="Subtract from all Features the average level of all inlier Local Backgrounds" isVisible="True" value="2"/><Choice name="NegativeControls" label="Average Of All Negative Control Features" description="Subtract from all Features the average of all inlier negative Control Features" isVisible="True" value="3"/><Choice name="MinimumSignalFeatOrBG" label="Minimum Signal (Feature Or Background) on Array" description="Subtract from all Features the minimum Feature or Local Background signal on the array." isVisible="True" value="1"/><Choice name="MinimumSignalFeat" label="Minimum Signal (Feature) on Array" description="Subtract from all Features the minimum Feature signal on the array." isVisible="True" value="6"/></ChoiceParameter><ChoiceParameterGroup name="ErrModelSignificance" label="Significance (for IsPosAndSignif and IsWellAboveBG)" description="Base Significance test on the Error Model and not the Pixel Standard Deviations" isVisible="True" value="0"><Choice name="PixelSignificance" label="Use Pixel Statistics for Significance" description="Use Pixel Statistics to calculate IsPosANdSignif and IsWellAbove Background -- Use Error model only in the Ratio Tab" isVisible="True" value="0"><Parameter name="MaxPVal" label="2-sided t-test of feature vs. background maximum p-value" description="The p-value at which a feature is determined to be statistically significant above background" isVisible="True" precision="%7.5f" low="0.000000" high="1.000000" type="double" value="0.010000"/><Parameter name="WellAboveMulti" label="WellAboveMulti" description="The number of standard deviations above background at which the feature is flagged as well above background" isVisible="True" precision="%3.1f" low="0.000000" high="5.000000" type="double" value="2.600000"/></Choice><Choice name="ErrorModelSignificance" label="Use Error Model for Significance" description="Use the Error Model to calculate IsPosANdSignif and IsWellAbove Background -- Apply error model to features after background subtraction and before ratio" isVisible="True" value="1"><Parameter name="MaxPVal" label="2-sided t-test of feature vs. background maximum p-value" description="The p-value at which a feature is determined to be statistically significant above background" isVisible="True" precision="%7.5f" low="0.000000" high="1.000000" type="double" value="0.010000"/><Parameter name="WellAboveMulti" label="WellAboveMulti" description="The number of standard deviations above background at which the feature is flagged as well above background" isVisible="True" precision="%3.1f" low="0.000000" high="5.000000" type="double" value="2.600000"/></Choice></ChoiceParameterGroup><Group name="SignalCorrection" label="Signal Correction" description="Signal correction after first pass background subtraction" isVisible="True"><ParameterGroup name="CalculateSurfaceMetricsOn" label="Calculate Surface Fit (required for Spatial Detrend)" description="Fit a surface to a subset of features that represent the low signals" isVisible="True" value="False"><ChoiceParameter name="AdditiveDetrendFeatureSet" label="Feature Set For Surface Fit" description="Features to use for spatial detrending" isVisible="True" value="2"><Choice name="AllFeatures" label="AllFeatureTypes" description="All Features" isVisible="True" value="0"/><Choice name="OnlyNegativeControlFeatures" label="OnlyNegativeControlFeatures" description="Only Negative Control Features [control type -1]." isVisible="True" value="1"/><Choice name="FeaturesInNegativeControlRange" label="FeaturesInNegativeControlRange" description="Features which have a signal within 3 neg sontrol stddev of close neg controls." isVisible="True" value="2"/></ChoiceParameter><Parameter name="NegCtrlSpreadRobustOn" label="NegCtrlSpread Outlier Rejection On" description="Filter Outlier before computimg Negaitve Control Sperad" isVisible="False" precision="%3.2lf" type="boolean" value="True"/><Parameter name="NegCtrlSpreadCoeff" label="NegCtrlSpreadCoeff" description="Glenda Special Green" isVisible="False" precision="%5.3f" low="0.010000" high="10.000000" type="double" value="3.000000"/><ParameterGroup name="DetrendLowPassFilter" label="Perform Filtering For Surface Fit" description="Uses low 1-2% of spatially picked feature signals If AllFeaturesTypes is selected above; If FeaturesInNegativeControlRange is selected then uses a spatially randomly selected set of feature signals with percentages specified;  Select False if using OnlyNegativeControlFeatures" isVisible="True" value="True"><Parameter name="DetrendLowPassPercentage" label="Detrend Low Pass Percentage" description="Specifies percentage of features based on the lowest intensity probes in each window that will be used to fit the surface." isVisible="False" precision="%3.2lf" low="1.000000" high="99.000000" type="integer" value="1"/><Parameter name="DetrendLowPassWindow" label="Detrend Low Pass Window" description="Specifies size of the square window by the number of rows and columns.  The specified percentage of low intensity features is chosen from this window size." isVisible="False" precision="%3.2lf" low="1.000000" high="1000.000000" type="integer" value="10"/><Parameter name="DetrendLowPassIncrement" label="Detrend Low Pass Increment" description="The increment in number of features that the above window will be shifted horizontally and vertically on the microarray." isVisible="False" precision="%3.2lf" low="1.000000" high="1000.000000" type="integer" value="10"/></ParameterGroup><Parameter name="DetrendNeighborhoodSize" label="DetrendNeighborhoodSize" description="Specifies the fraction of the data points in the fitting set that are used for the linear regression for surface fitting at any given point." isVisible="False" precision="%3.1f" low="0.000000" high="1.000000" type="double" value="0.200000"/><Parameter name="SpatialDetrendOn" label="Perform Spatial Detrending" description="Subtract any systematic trend from the data found from the surface metrics" isVisible="True" precision="%3.2lf" type="boolean" value="False"/></ParameterGroup><ParameterGroup name="BackgroundCorrectionOn" label="Adjust Background Globally" description="Adjust signal level globally by a value determined from a set of very dim feature signals" isVisible="True" value="True"><Parameter name="BgCorrectionOffset" label="Adjust Background Globally to:" description="A value to adjust the very dim features to" isVisible="True" precision="%3.2lf" low="0.000000" high="65535.000000" type="integer" value="0"/></ParameterGroup><ParameterGroup name="MultiplicativeDetrendOn" label="Perform Multiplicative Detrending" description="Perform Multiplicate Detrending on the Adjusted Signals and Add columns that calculate the detrend values" isVisible="True" value="False"><Parameter name="TestMultDetrendOnCVs" label="TestMultDetrendOnCVs" description="Glenda Special Green #2 -- Come On -- Get on the list of Glendas" isVisible="False" precision="%3.2lf" type="boolean" value="True"/><Parameter name="MultDetrendOnReplicates" label="Detrend on Replicates Only" description="Perform the detrending using Positive control and experimental replicates only." isVisible="True" precision="%3.2lf" type="boolean" value="False"/><ParameterGroup name="MultHighPassFilter" label="Filter Low signal probes from Fit?" description="If true this will filter out the low signal probes from the fit" isVisible="True" value="True"><Parameter name="NegCtrlThresholdMultDetrendFactor" label="Neg. Ctrl. Threshold Mult. Detrend Factor" description="multiplies the neg. control spread to form the threshold for filtering out low intensity signals" isVisible="True" precision="%4.0f" low="0.000001" high="10000.000000" type="double" value="3.000000"/></ParameterGroup><ChoiceParameter name="MultDetrendWinFilter" label="Perform Filtering for Fit" description="" isVisible="True" value="1"><Choice name="NoFiltering" label="Use All Features" description="Use All Features to fit surface" isVisible="True" value="0"/><Choice name="AverageFiltering" label="Use Window Average" description="Use Window Average to fit surface" isVisible="True" value="1"/><Choice name="MedianFiltering" label="Use Window Median" description="Use Window Median value to fit surface" isVisible="True" value="2"/></ChoiceParameter><Group name="Multitrend Window Parameters" label="Multiplicative Detrend Filter Window Parameters" description="How to parameterize filtering for Multiplicative Detrending" isVisible="False"><Parameter name="MultDetrendIncrement" label="Detrend Increment" description="" isVisible="True" precision="%4.0f" type="integer" value="2"/><Parameter name="MultDetrendWindow" label="Detrend Window" description="" isVisible="True" precision="%4.0f" type="integer" value="3"/></Group><Parameter name="MultDetrendNeighborhoodSize" label="NieghborhoodSize" description="" isVisible="False" precision="%6.4f" type="double" value="0.200000"/><ParameterGroup name="PolynomialMultiplicativeDetrend" label="Use Polynomial data fit instead of LOESS?" description="" isVisible="True" value="True"><Parameter name="PolynomialMultiplicativeDetrendDegree" label="Polynomial Multiplicative DetrendDegree" description="" isVisible="True" precision="%4.0f" low="-1.000000" high="5.000000" type="integer" value="2"/></ParameterGroup></ParameterGroup></Group><Parameter name="RobustNCStats" label="Robust Neg Ctrl Stats?" description="Does a Outlier Rejection on the Neg Ctrls as a population before Calculating the stats for the Background Subtracted signal (CGHAnalytics request)." isVisible="True" precision="%6.2f" type="boolean" value="False"/><Parameter name="RobustNCOutlierFactor" label="Robust NC Stats Reject Factor" description="What Rejection Factor should be used 99.99% Population Outlier Rejection on the Neg Ctrls as a population before Calculating the stats for the Background Subtracted signal (CGHAnalytics request)." isVisible="False" precision="%5.2f" low="0.000000" high="50.000000" type="double" value="5.000000"/><ChoiceParameterGroup name="ErrorModel" label="Choose universal error, or the most conservative (of propagated and universal)" description="Choice of error model used to determine p-values for Log Ratio data" isVisible="True" value="0"><Choice name="UniversalError" label="Use Universal Error Model" description="" isVisible="True" value="2"><Parameter name="MultErrorGreen" label="MultErrorGreen" description="Multiplicative error term for Green in Universal Error Model" isVisible="True" precision="%6.4f" low="0.000000" high="1.000000" type="double" value="0.100000"/><ChoiceParameterGroup name="AutoEstimateAddErrorGreen" label="Auto Estimate Add Error Green" description="Dynamically compute for each array the additive error term (i.e. noise of the features with zero signal)" isVisible="True" value="1"><Choice name="AutoEstimateGreenTrue" label="True" description="" isVisible="True" value="1"/><Choice name="AutoEstimateGreenFalse" label="False" description="" isVisible="True" value="0"><Parameter name="AddErrorGreen" label="Additive Error Value Green" description="" isVisible="True" precision="%4.0f" low="0.000000" high="500.000000" type="double" value="25.000000"/></Choice></ChoiceParameterGroup><Parameter name="MultNcAutoEstimate" label="Negative Control Multiplier" description="Factor to multiply the standard deviation of the inlier negative control features for the additive error computation" isVisible="False" precision="%3.0f" low="0.000000" high="10.000000" type="double" value="0.000000"/><Parameter name="MultRMSAutoEstimate" label="Surface Fit RMS Multiplier" description="Factor to multiply the rms of the surface fit for the additive error computation. This is a surrogate for sequence dependent noise in the feature foreground that may be missed on arrays with a single negative Control sequence." isVisible="False" precision="%3.0f" low="0.000000" high="10.000000" type="double" value="0.000000"/><Parameter name="MultResidualsRMSAutoEstimate" label="Surface Fit Residual RMS Multiplier" description="Factor to multiply the rms of the surface fit for the additive error computation.  This is a surrogate for sequence dependent noise in the Feature foreground that may be missed on arrays with a single Negative Control sequence." isVisible="False" precision="%3.0f" low="0.000000" high="10.000000" type="double" value="1.000000"/></Choice><Choice name="MostConservative" label="Most Conservative" description="" isVisible="True" value="0"><Parameter name="MultErrorGreen" label="MultErrorGreen" description="Multiplicative error term for Green in Universal Error Model." isVisible="True" precision="%6.4f" low="0.000000" high="1.000000" type="double" value="0.100000"/><ChoiceParameterGroup name="AutoEstimateAddErrorGreen" label="Auto Estimate Add Error Green" description="Dynamically compute for each array the additive error term (i.e. noise of the features with zero signal)." isVisible="True" value="1"><Choice name="AutoEstimateGreenTrue" label="True" description="" isVisible="True" value="1"/><Choice name="AutoEstimateGreenFalse" label="False" description="" isVisible="True" value="0"><Parameter name="AddErrorGreen" label="Additive Error Value Green" description="" isVisible="True" precision="%4.0f" low="0.000000" high="500.000000" type="double" value="25.000000"/></Choice></ChoiceParameterGroup><Parameter name="MultNcAutoEstimate" label="Negative Control Multiplier" description="Factor to multiply the standard deviation of the inlier Negative control Features for the additive error computation." isVisible="False" precision="%3.0f" low="0.000000" high="10.000000" type="double" value="0.000000"/><Parameter name="MultRMSAutoEstimate" label="Surface Fit RMS Multiplier" description="Factor to multiply the rms of the surface fit for the additive error computation.  This is a surrogate for sequence dependent noise in the Feature foreground that may be missed on arrays with a single Negative Control sequence." isVisible="False" precision="%3.0f" low="0.000000" high="10.000000" type="double" value="0.000000"/><Parameter name="MultResidualsRMSAutoEstimate" label="Surface Fit Residual RMS Multiplier" description="Factor to multiply the rms of the surface fit for the additive error computation.  This is a surrogate for sequence dependent noise in the Feature foreground that may be missed on arrays with a single Negative Control sequence." isVisible="False" precision="%3.0f" low="0.000000" high="10.000000" type="double" value="1.000000"/></Choice></ChoiceParameterGroup><Parameter name="UseSurrogates" label="Use Surrogates" description="Use surrogate signals for features whose signal is not statistically significantly different from the background." isVisible="True" precision="%3.2lf" type="boolean" value="False"/></Step><Step name="QCMetrics" label="Calculate Metrics" description="Generate metrics to be used during QC." isEnabled="True" module="FEAnalysisProc"><Parameter name="UseSpikeIns" label="Spikein Target Used" description="Metrics for Agilent QC Spike Ins will be calculated on the QC Report, if labeled Spike Ins were present during hybridization and this field is set to True." isVisible="True" precision="%3.2lf" type="boolean" value="False"/><Parameter name="minReplicatePopulation" label="Min Population for Replicate Stats?" description="The minimum number of probe replicates for calculating population statistics on the QC report" isVisible="True" precision="%3.0f" low="2.000000" high="5000.000000" type="integer" value="5"/><Parameter name="MaxEdgeDefectThreshold" label="Maximum fraction of NonUnif Features on the Edges" description="Threshold fraction of either NonUniform Features on any edge row or column for Grid Goodness of Fit warning." isVisible="False" precision="%3.2f" low="0.000000" high="1.000000" type="double" value="0.100000"/><Parameter name="MaxEdgeNotFoundThreshold" label="Maximum fraction of NotFound Features on the Edges" description="Threshold fraction of either NotFound Features on any edge row or column for Grid Goodness of Fit warning." isVisible="False" precision="%3.2f" low="0.000000" high="1.000000" type="double" value="0.720000"/><Parameter name="MaxLocalBGNonUnifThreshold" label="Maximum percentage of Local Background NonUnif Features" description="Percentage of Local Background NonUniform Features Tolerated before Grid Goodness of Fit warning is generated." isVisible="False" precision="%3.2f" low="0.000000" high="100.000000" type="double" value="0.020000"/><Parameter name="MinNegCtrlSDev" label="Maximum Neg Ctrl SDev" description="Maximum Negative Ctrl SDev" isVisible="False" precision="%3.2f" low="0.000000" high="1000.000000" type="double" value="100.000000"/><Parameter name="MinReproducibility" label="Maximum Med %CV" description="Maximum Median %CV" isVisible="False" precision="%3.2f" low="0.000000" high="1000.000000" type="double" value="50.000000"/><Parameter name="MaxCentroidDiffThreshold" label="Maximum difference between Grid and Spot Centroid" description="Maximum difference averaged across the array between Nominal Grid Positions and Spot Centroids for Grid Goodness of Fit warning in microns." isVisible="False" precision="%4.2f" low="0.000000" high="1000.000000" type="double" value="10.000000"/><Parameter name="differentialExpressionPValue" label="PValue for Differential Expression" description="P-value cutoff for features marked as significantly up-regulated and down-regulated on the QC report" isVisible="True" precision="%1.6f" low="0.000000" high="1.000000" type="double" value="0.010000"/><Parameter name="PercentileValueForSignal" label="Percentile Value" description="Returns the Percentile Value of all NonCtrl probes for ProcessSignals, Background Subtracted Signals and Net Signals. Percentile value used in normalizing datasets (mostly for 1-color)" isVisible="True" precision="%6.2f" low="0.000000" high="100.000000" type="double" value="75.000000"/></Step><Step name="FEOutput" label="Generate Results" description="Options for output generation." isEnabled="True" module="FEAnalysisProc"><ChoiceParameter name="ColorMode" label="Color Mode Output" description="Should we output assuming 1 color data or 2 color data?" isVisible="False" value="0"><Choice name="OneColorGreen" label="OneColor (Green only)" description="" isVisible="True" value="0"/><Choice name="BothChannels" label="TwoColor" description="" isVisible="True" value="1"/></ChoiceParameter><ChoiceParameter name="QCReportType" label="Type of QC Report" description="What Type of QC report should we generate?" isVisible="False" value="0"><Choice name="GeneExpression" label="Gene Expression" description="" isVisible="True" value="0"/><Choice name="CGH" label="CGH" description="" isVisible="True" value="1"/><Choice name="MiRNA" label="miRNA" description="" isVisible="True" value="2"/><Choice name="LocationAnalysis" label="Location Analysis" description="" isVisible="True" value="3"/></ChoiceParameter><Parameter name="SingleTextFileOutput" label="Generate Single Text File" description="Save the tables (Params, Stats and Features) same text file" isVisible="True" precision="%3.2lf" type="boolean" value="True"/><Parameter name="JPEGDownSampleFactor" label="JPEG Down Sample Factor" description="Scale the image down by this factor in both directions and convert to JPEG" isVisible="True" precision="%3.0f" low="1.000000" high="64.000000" type="integer" value="4"/><Parameter name="OutputQCReportGraphText" label="Output QC Report Graphs as Tables" description="Outputs QC report Graphs as tables for Validation purposes" isVisible="False" precision="%3.2lf" type="boolean" value="False"/></Step></Protocol>
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