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<meta name=Keywords
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<body bgcolor=white lang=ZH-CN link=blue vlink=purple style='tab-interval:36.0pt'>
<div class=Section1>
<p class=MsoNormal align=center style='text-align:center'><b><u><span
lang=EN-US style='font-size:20.0pt'>PoroMedia Help<o:p></o:p></span></u></b></p>
<p class=MsoNormal align=center style='text-align:center'><span lang=EN-US
style='font-size:20.0pt'><o:p> </o:p></span></p>
<p class=MsoNormal align=center style='text-align:center'><span lang=EN-US
style='font-size:20.0pt'><o:p> </o:p></span></p>
<p class=MsoNormal align=center style='text-align:center'><span lang=EN-US
style='font-size:20.0pt'><o:p> </o:p></span></p>
<p class=MsoNormal><b><span lang=EN-US style='font-size:16.0pt'>TOPICS:<o:p></o:p></span></b></p>
<p class=MsoNormal><span lang=EN-US style='font-size:14.0pt'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:14.0pt'><a
href="#HorizontalPrep">Sample preparation for Porosity SSA, 3D Structure Data,
Tortuosity, and Random Walk.</a><o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:14.0pt'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:14.0pt'><a href="#SSA">Porosity
SSA and 3D Structure Data guide.</a><o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:14.0pt'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:14.0pt'><a
href="#Tortuosity">Tortuosity guide.</a><o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:14.0pt'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:14.0pt'><a
href="#RandomWalk">Random Walk guide.</a><o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:14.0pt'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:14.0pt'><a
href="#VerticalPrep">Sample preparation for Surface Structure Analysis.</a><o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:14.0pt'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:14.0pt'><a
href="#SurfaceStructure">SurfaceStructure guide.</a><o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:14.0pt'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:14.0pt'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:14.0pt'><o:p> </o:p></span></p>
<p class=MsoNormal><!--[if gte vml 1]><v:line id="_x0000_s1060" style='position:absolute;
z-index:3' from="-5.95pt,6.25pt" to="1110.05pt,6.25pt"/><![endif]--><![if !vml]><span
style='mso-ignore:vglayout;position:relative;z-index:3;left:-9px;top:7px;
width:1490px;height:9px'><img width=1490 height=2
src="PoroMedia%20Help_files/image003.png" v:shapes="_x0000_s1060"></span><![endif]><span
lang=EN-US style='font-size:14.0pt'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:14.0pt'><o:p> </o:p></span></p>
<br style='mso-ignore:vglayout' clear=ALL>
<p class=MsoNormal><a name=HorizontalPrep></a><b><span lang=EN-US
style='font-size:16.0pt'>Horizontal Slice preparation (for Porosity SSA, 3D
Structure Data, Tortuosity, Random Walk):<o:p></o:p></span></b></p>
<p class=MsoNormal><span lang=EN-US style='font-size:14.0pt'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:14.0pt'>Below is a sample
of a .bmp image file used in Porosity SSA, 3D Structure Data, Tortuosity and
Random Walk analysis.<span style='mso-spacerun:yes'> </span>This
represents one layer of many required to reconstruct a porous 3D
structure.<span style='mso-spacerun:yes'> </span>From a given sample set
(example:<span style='mso-spacerun:yes'> </span>oak_000 to oak_100), it
is recommended to use as many slices as possible.<span
style='mso-spacerun:yes'> </span>Often, the first few and last layers are
not ideal. Find the subset that represents the largest consistent cube of the
sample (perhaps oak_025 to oak_075).<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:14.0pt'><o:p> </o:p></span></p>
<p class=MsoNormal align=center style='text-align:center'><a
name="Horizontal_Slice"><span lang=EN-US style='font-size:14.0pt'><!--[if gte vml 1]><v:shapetype
id="_x0000_t75" coordsize="21600,21600" o:spt="75" o:preferrelative="t"
path="m@4@5l@4@11@9@11@9@5xe" filled="f" stroked="f">
<v:stroke joinstyle="miter"/>
<v:formulas>
<v:f eqn="if lineDrawn pixelLineWidth 0"/>
<v:f eqn="sum @0 1 0"/>
<v:f eqn="sum 0 0 @1"/>
<v:f eqn="prod @2 1 2"/>
<v:f eqn="prod @3 21600 pixelWidth"/>
<v:f eqn="prod @3 21600 pixelHeight"/>
<v:f eqn="sum @0 0 1"/>
<v:f eqn="prod @6 1 2"/>
<v:f eqn="prod @7 21600 pixelWidth"/>
<v:f eqn="sum @8 21600 0"/>
<v:f eqn="prod @7 21600 pixelHeight"/>
<v:f eqn="sum @10 21600 0"/>
</v:formulas>
<v:path o:extrusionok="f" gradientshapeok="t" o:connecttype="rect"/>
<o:lock v:ext="edit" aspectratio="t"/>
</v:shapetype><v:shape id="_x0000_i1025" type="#_x0000_t75" style='width:580.5pt;
height:449.25pt' o:allowoverlap="f">
<v:imagedata src="PoroMedia%20Help_files/image002.gif" o:title="Top-View"/>
</v:shape><![endif]--><![if !vml]><img border=0 width=774 height=599
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lang=EN-US style='font-size:14.0pt'><o:p></o:p></span></p>
<p class=MsoNormal align=center style='text-align:center'><span lang=EN-US
style='font-size:14.0pt'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:14.0pt'>There are several
required coordinates that need to be extracted from this image as input to the
desired analysis.<span style='mso-spacerun:yes'> </span>This can be done
using any image editing software (such as Microsoft Paint, or Adobe
Photoshop).<span style='mso-spacerun:yes'> </span>Keep in mind that these
coordinates need to be valid for all slices of this sample (it is recommended
to look at the first slice and last slice, and confirm the coordinates are
valid for both).<span style='mso-spacerun:yes'> </span>The black square
outline in the above image represents an area that is valid in all other slices
that are part of this sample.<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:14.0pt'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:14.0pt'>First, find the
coordinates that represent the top-left most valid location of the sample. In
the above image, these coordinates are represented in yellow (100,100).<span
style='mso-spacerun:yes'> </span>These are the X and Y start points.<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:14.0pt'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:14.0pt'>Next, find the
width of the valid area.<span style='mso-spacerun:yes'> </span>The above
image represents this in green (300).<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:14.0pt'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:14.0pt'>Finally, find the
height of the valid area.<span style='mso-spacerun:yes'> </span>Seen
above in blue (200).<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:14.0pt'>(Hint:<span
style='mso-spacerun:yes'> </span>If you use MS Paint, simply drag a
rectangle from the start point to see a (width, height) set).<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:14.0pt'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:14.0pt'>The following is a
more detailed description for each type of analysis.<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:14.0pt'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:14.0pt'><o:p> </o:p></span></p>
<p class=MsoNormal><!--[if gte vml 1]><v:line id="_x0000_s1061" style='position:absolute;
z-index:4' from="-5.95pt,14.2pt" to="1110.05pt,14.2pt"/><![endif]--><![if !vml]><span
style='mso-ignore:vglayout;position:relative;z-index:4;left:-9px;top:18px;
width:1490px;height:20px'><img width=1490 height=2
src="PoroMedia%20Help_files/image009.png" v:shapes="_x0000_s1061"></span><![endif]><span
lang=EN-US style='font-size:14.0pt'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:14.0pt'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:14.0pt'><o:p> </o:p></span></p>
<br style='mso-ignore:vglayout' clear=ALL>
<p class=MsoNormal><a name=SSA></a><b><span lang=EN-US style='font-size:14.0pt'>Porosity
SSA and 3D Structure Data:<o:p></o:p></span></b></p>
<p class=MsoNormal><span lang=EN-US style='font-size:14.0pt'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:14.0pt'>Below is the setup
dialog for Porosity SSA and 3D Structure Data analysis (3D Structure Data becomes
available after Porosity SSA is ran). It is accessed through <i>Analysis</i>
-> <i>Porosity SSA</i> menu.<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:14.0pt'><o:p> </o:p></span></p>
<p class=MsoNormal align=center style='text-align:center'><span lang=EN-US
style='font-size:14.0pt'><!--[if gte vml 1]><v:shape id="_x0000_i1026" type="#_x0000_t75"
style='width:468pt;height:473.25pt'>
<v:imagedata src="PoroMedia%20Help_files/image005.jpg" o:title="SSA"/>
</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=631
src="PoroMedia%20Help_files/image012.jpg" v:shapes="_x0000_i1026"><![endif]><o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:14.0pt'><o:p> </o:p></span></p>
<p class=MsoNormal><a name="Horizontal_Fields"></a><span lang=EN-US
style='font-size:14.0pt'>Labels <span style='color:red'>1</span> through <span
style='color:red'>13</span> are the same for all horizontal slice analysis
(SSA, 3D Structure, Tortuosity, and Random Walk).<span
style='mso-spacerun:yes'> </span>Here is a description of each:<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:14.0pt'><o:p> </o:p></span></p>
<p class=MsoNormal style='margin-left:54.0pt;text-indent:-36.0pt;mso-list:l2 level1 lfo2;
tab-stops:list 54.0pt'><![if !supportLists]><span lang=EN-US style='font-size:
14.0pt;mso-fareast-font-family:"Times New Roman";color:red'><span
style='mso-list:Ignore'>1)<span style='font:7.0pt "Times New Roman"'>
</span></span></span><![endif]><span lang=EN-US style='font-size:14.0pt'>Click
to pick the directory with sample images.<o:p></o:p></span></p>
<p class=MsoNormal style='margin-left:54.0pt;text-indent:-36.0pt;mso-list:l2 level1 lfo2;
tab-stops:list 54.0pt'><![if !supportLists]><span lang=EN-US style='font-size:
14.0pt;mso-fareast-font-family:"Times New Roman";color:red'><span
style='mso-list:Ignore'>2)<span style='font:7.0pt "Times New Roman"'>
</span></span></span><![endif]><span lang=EN-US style='font-size:14.0pt'>Displays
directory, can copy/paste into this field.<o:p></o:p></span></p>
<p class=MsoNormal style='margin-left:54.0pt;text-indent:-36.0pt;mso-list:l2 level1 lfo2;
tab-stops:list 54.0pt'><![if !supportLists]><span lang=EN-US style='font-size:
14.0pt;mso-fareast-font-family:"Times New Roman";color:red'><span
style='mso-list:Ignore'>3)<span style='font:7.0pt "Times New Roman"'>
</span></span></span><![endif]><span lang=EN-US style='font-size:14.0pt'>Enter
the <i>constant</i> part of all image files.<span
style='mso-spacerun:yes'> </span>For example, if a sample set contains
images oak_025.bmp tooak_075.bmp, oak_0 must be entered into this field.<o:p></o:p></span></p>
<p class=MsoNormal style='margin-left:54.0pt;text-indent:-36.0pt;mso-list:l2 level1 lfo2;
tab-stops:list 54.0pt'><![if !supportLists]><span lang=EN-US style='font-size:
14.0pt;mso-fareast-font-family:"Times New Roman";color:red'><span
style='mso-list:Ignore'>4)<span style='font:7.0pt "Times New Roman"'>
</span></span></span><![endif]><span lang=EN-US style='font-size:14.0pt'>Enter
a distinguishable name for this run.<o:p></o:p></span></p>
<p class=MsoNormal><i style='mso-bidi-font-style:normal'><span lang=EN-US
style='font-size:14.0pt'>Sample Size:<o:p></o:p></span></i></p>
<p class=MsoNormal style='margin-left:54.0pt;text-indent:-36.0pt;mso-list:l2 level1 lfo2;
tab-stops:list 54.0pt'><![if !supportLists]><span lang=EN-US style='font-size:
14.0pt;mso-fareast-font-family:"Times New Roman";color:red'><span
style='mso-list:Ignore'>5)<span style='font:7.0pt "Times New Roman"'>
</span></span></span><![endif]><span lang=EN-US style='font-size:14.0pt'>Enter
the first slice number (the number that is attached to the constant part of
image file).<span style='mso-spacerun:yes'> </span>Continuing on the
previous example, 25 would be entered here (from oak_025.bmp).<o:p></o:p></span></p>
<p class=MsoNormal style='margin-left:54.0pt;text-indent:-36.0pt;mso-list:l2 level1 lfo2;
tab-stops:list 54.0pt'><![if !supportLists]><span lang=EN-US style='font-size:
14.0pt;mso-fareast-font-family:"Times New Roman";color:red'><span
style='mso-list:Ignore'>6)<span style='font:7.0pt "Times New Roman"'>
</span></span></span><![endif]><span lang=EN-US style='font-size:14.0pt'>Enter
the last slice number.<span style='mso-spacerun:yes'> </span>Continuing
on the previous example, 75 would be entered here (from oak_075.bmp).<o:p></o:p></span></p>
<p class=MsoNormal style='margin-left:54.0pt;text-indent:-36.0pt;mso-list:l2 level1 lfo2;
tab-stops:list 54.0pt'><![if !supportLists]><span lang=EN-US style='font-size:
14.0pt;mso-fareast-font-family:"Times New Roman";color:red'><span
style='mso-list:Ignore'>7)<span style='font:7.0pt "Times New Roman"'>
</span></span></span><![endif]><span lang=EN-US style='font-size:14.0pt;
color:black'>Enter the start of X-coordinate (<a href="#HorizontalPrep">description</a>).<o:p></o:p></span></p>
<p class=MsoNormal style='margin-left:54.0pt;text-indent:-36.0pt;mso-list:l2 level1 lfo2;
tab-stops:list 54.0pt'><![if !supportLists]><span lang=EN-US style='font-size:
14.0pt;mso-fareast-font-family:"Times New Roman";color:red'><span
style='mso-list:Ignore'>8)<span style='font:7.0pt "Times New Roman"'>
</span></span></span><![endif]><span lang=EN-US style='font-size:14.0pt;
color:black'>Enter the start of Y-coordinate (<a href="#HorizontalPrep">description</a>).<o:p></o:p></span></p>
<p class=MsoNormal style='margin-left:54.0pt;text-indent:-36.0pt;mso-list:l2 level1 lfo2;
tab-stops:list 54.0pt'><![if !supportLists]><span lang=EN-US style='font-size:
14.0pt;mso-fareast-font-family:"Times New Roman";color:red'><span
style='mso-list:Ignore'>9)<span style='font:7.0pt "Times New Roman"'>
</span></span></span><![endif]><span lang=EN-US style='font-size:14.0pt;
color:black'>Enter Width (<a href="#HorizontalPrep">description</a>).<o:p></o:p></span></p>
<p class=MsoNormal style='margin-left:54.0pt;text-indent:-36.0pt;mso-list:l2 level1 lfo2;
tab-stops:list 54.0pt'><![if !supportLists]><span lang=EN-US style='font-size:
14.0pt;mso-fareast-font-family:"Times New Roman";color:red'><span
style='mso-list:Ignore'>10)<span style='font:7.0pt "Times New Roman"'>
</span></span></span><![endif]><span lang=EN-US style='font-size:14.0pt;
color:black'>Enter Height (<a href="#HorizontalPrep">description</a>).<o:p></o:p></span></p>
<p class=MsoNormal><i style='mso-bidi-font-style:normal'><span lang=EN-US
style='font-size:14.0pt;color:black'>Threshold:<o:p></o:p></span></i></p>
<p class=MsoNormal style='margin-left:54.0pt;text-indent:-36.0pt;mso-list:l2 level1 lfo2;
tab-stops:list 54.0pt'><![if !supportLists]><span lang=EN-US style='font-size:
14.0pt;mso-fareast-font-family:"Times New Roman";color:red'><span
style='mso-list:Ignore'>11)<span style='font:7.0pt "Times New Roman"'>
</span></span></span><![endif]><span lang=EN-US style='font-size:14.0pt;
color:black'>Check this box if the image is inverted (pores are white, fiber is
black).<span style='mso-spacerun:yes'> </span><a href="#Horizontal_Slice">This
is an inverted image.</a><o:p></o:p></span></p>
<p class=MsoNormal style='margin-left:54.0pt;text-indent:-36.0pt;mso-list:l2 level1 lfo2;
tab-stops:list 54.0pt'><![if !supportLists]><span lang=EN-US style='font-size:
14.0pt;mso-fareast-font-family:"Times New Roman";color:red'><span
style='mso-list:Ignore'>12)<span style='font:7.0pt "Times New Roman"'>
</span></span></span><![endif]><span lang=EN-US style='font-size:14.0pt;
color:black'>Check this box to enable field </span><span lang=EN-US
style='font-size:14.0pt;color:red'>13</span><span lang=EN-US style='font-size:
14.0pt;color:black'> for entering a desired threshold.<span
style='mso-spacerun:yes'> </span>If this box is not checked, the
threshold is automatically computed as part of the run.<span
style='mso-spacerun:yes'> </span>It may sometimes be necessary to use a
manual threshold for certain samples for desired results.<o:p></o:p></span></p>
<p class=MsoNormal style='margin-left:54.0pt;text-indent:-36.0pt;mso-list:l2 level1 lfo2;
tab-stops:list 54.0pt'><![if !supportLists]><span lang=EN-US style='font-size:
14.0pt;mso-fareast-font-family:"Times New Roman";color:red'><span
style='mso-list:Ignore'>13)<span style='font:7.0pt "Times New Roman"'>
</span></span></span><![endif]><span lang=EN-US style='font-size:14.0pt;
color:black'>Enter a threshold if field </span><span lang=EN-US
style='font-size:14.0pt;color:red'>12</span><span lang=EN-US style='font-size:
14.0pt;color:black'> is checked.<span style='mso-spacerun:yes'>
</span>The threshold determines how the .bmp images are converted to binary
form.<span style='mso-spacerun:yes'> </span>A brief explanation is as
follows.<span style='mso-spacerun:yes'> </span>The .bmp images are
first converted to raw form, with each pixel having intensity between 0 and
255.<span style='mso-spacerun:yes'> </span>Then, any value greater than
the threshold value becomes a binary 1 (fiber), and any value less than the
threshold value becomes a binary 0 (pore).<span
style='mso-spacerun:yes'> </span>If there are problems such as .bmp
images being converted to an all black binary files, the threshold should be
raised to a higher value, and vice versa.<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:14.0pt;color:black'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:14.0pt;color:black'>This
is the only unique field for SSA/3D Structure.<o:p></o:p></span></p>
<p class=MsoNormal style='margin-left:54.0pt;text-indent:-36.0pt;mso-list:l2 level1 lfo2;
tab-stops:list 54.0pt'><![if !supportLists]><span lang=EN-US style='font-size:
14.0pt;mso-fareast-font-family:"Times New Roman";color:red'><span
style='mso-list:Ignore'>14)<span style='font:7.0pt "Times New Roman"'>
</span></span></span><![endif]><span lang=EN-US style='font-size:14.0pt;
color:black'>Enter the pixel size (in micrometers) of the image file.<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:14.0pt;color:black'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:14.0pt;color:black'>Press
OK to start the run, the window will be minimized until the run is
complete.<span style='mso-spacerun:yes'> </span>After it is complete <i>3D
Structure Data</i> becomes available in the <i>Analysis</i> menu.<span
style='mso-spacerun:yes'> </span>Select it to finish the analysis.<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:14.0pt;color:black'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:14.0pt;color:black'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:14.0pt;color:black'><o:p> </o:p></span></p>
<p class=MsoNormal><!--[if gte vml 1]><v:line id="_x0000_s1062" style='position:absolute;
flip:x;z-index:5' from="-14.95pt,7.2pt" to="1110.05pt,7.2pt"/><![endif]--><![if !vml]><span
style='mso-ignore:vglayout;position:relative;z-index:5;left:-21px;top:9px;
width:1502px;height:11px'><img width=1502 height=2
src="PoroMedia%20Help_files/image015.png" v:shapes="_x0000_s1062"></span><![endif]><span
lang=EN-US style='font-size:14.0pt;color:black'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:14.0pt;color:black'><o:p> </o:p></span></p>
<br style='mso-ignore:vglayout' clear=ALL>
<p class=MsoNormal><a name=Tortuosity></a><b><span lang=EN-US style='font-size:
14.0pt'>Tortuosity:<o:p></o:p></span></b></p>
<p class=MsoNormal><span lang=EN-US style='font-size:14.0pt'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:14.0pt'>Below is the setup
dialog for Tortuosity analysis. It is accessed through <i>Analysis</i> -> <i>Tortuosity</i>
menu.<span style='color:black'><o:p></o:p></span></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:14.0pt;color:black'><o:p> </o:p></span></p>
<p class=MsoNormal align=center style='text-align:center'><span lang=EN-US
style='font-size:14.0pt;color:black'><!--[if gte vml 1]><v:shape id="_x0000_i1027"
type="#_x0000_t75" style='width:467.25pt;height:422.25pt'>
<v:imagedata src="PoroMedia%20Help_files/image008.jpg" o:title="Tortuosity"/>
</v:shape><![endif]--><![if !vml]><img border=0 width=623 height=563
src="PoroMedia%20Help_files/image008.jpg" v:shapes="_x0000_i1027"><![endif]><o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:14.0pt;color:black'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:14.0pt;color:black'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:14.0pt;color:black'>Description
of fields </span><span lang=EN-US style='font-size:14.0pt;color:red'>1</span><span
lang=EN-US style='font-size:14.0pt;color:black'> through </span><span
lang=EN-US style='font-size:14.0pt;color:red'>13</span><span lang=EN-US
style='font-size:14.0pt;color:black'> can be found <a href="#Horizontal_Fields">here</a>.<span
style='mso-spacerun:yes'> </span>There are two different directions for
tortuosity analysis.<span style='mso-spacerun:yes'> </span>Transverse
sends a tracer from the top layer to the bottom, while Inplane sends a tracer
from the side of the sample, to a specified distance inside.<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:14.0pt;color:black'><o:p> </o:p></span></p>
<p class=MsoNormal><i style='mso-bidi-font-style:normal'><span lang=EN-US
style='font-size:14.0pt;color:black'>Transverse Tortuosity:<o:p></o:p></span></i></p>
<p class=MsoNormal style='margin-left:54.0pt;text-indent:-36.0pt;mso-list:l0 level1 lfo4;
tab-stops:list 54.0pt'><![if !supportLists]><span lang=EN-US style='font-size:
14.0pt;mso-fareast-font-family:"Times New Roman";color:red'><span
style='mso-list:Ignore'>14)<span style='font:7.0pt "Times New Roman"'>
</span></span></span><![endif]><span lang=EN-US style='font-size:14.0pt;
color:black'>Enter the number of tracers to run through the sample in
transverse direction.<span style='mso-spacerun:yes'> </span>Entering a
higher number results in a linearly longer run time, but higher accuracy.<span
style='mso-spacerun:yes'> </span>1000 runs is a good balance.<o:p></o:p></span></p>
<p class=MsoNormal style='margin-left:54.0pt;text-indent:-36.0pt;mso-list:l0 level1 lfo4;
tab-stops:list 54.0pt'><![if !supportLists]><span lang=EN-US style='font-size:
14.0pt;mso-fareast-font-family:"Times New Roman";color:red'><span
style='mso-list:Ignore'>15)<span style='font:7.0pt "Times New Roman"'>
</span></span></span><![endif]><span lang=EN-US style='font-size:14.0pt;
color:black'>Check this box to run Transverse Tortuosity.<o:p></o:p></span></p>
<p class=MsoNormal><i style='mso-bidi-font-style:normal'><span lang=EN-US
style='font-size:14.0pt;color:black'>Inplane Tortuosity:<o:p></o:p></span></i></p>
<p class=MsoNormal style='margin-left:54.0pt;text-indent:-36.0pt;mso-list:l0 level1 lfo4;
tab-stops:list 54.0pt'><![if !supportLists]><span lang=EN-US style='font-size:
14.0pt;mso-fareast-font-family:"Times New Roman";color:red'><span
style='mso-list:Ignore'>16)<span style='font:7.0pt "Times New Roman"'>
</span></span></span><![endif]><span lang=EN-US style='font-size:14.0pt;
color:black'>This specifies the limit of pixel distance for inplane
tracers.<span style='mso-spacerun:yes'> </span>Setting this value too
high can result in very long run times.<o:p></o:p></span></p>
<p class=MsoNormal style='margin-left:54.0pt;text-indent:-36.0pt;mso-list:l0 level1 lfo4;
tab-stops:list 54.0pt'><![if !supportLists]><span lang=EN-US style='font-size:
14.0pt;mso-fareast-font-family:"Times New Roman";color:red'><span
style='mso-list:Ignore'>17)<span style='font:7.0pt "Times New Roman"'>
</span></span></span><![endif]><span lang=EN-US style='font-size:14.0pt;
color:black'>Similar to </span><span lang=EN-US style='font-size:14.0pt;
color:red'>14</span><span lang=EN-US style='font-size:14.0pt;color:black'>, but
for Inplane Tortuosity only.<o:p></o:p></span></p>
<p class=MsoNormal style='margin-left:54.0pt;text-indent:-36.0pt;mso-list:l0 level1 lfo4;
tab-stops:list 54.0pt'><![if !supportLists]><span lang=EN-US style='font-size:
14.0pt;mso-fareast-font-family:"Times New Roman";color:red'><span
style='mso-list:Ignore'>18)<span style='font:7.0pt "Times New Roman"'>
</span></span></span><![endif]><span lang=EN-US style='font-size:14.0pt;
color:black'>Check this box to run Inplane Tortuosity.<o:p></o:p></span></p>
<p class=MsoNormal><i style='mso-bidi-font-style:normal'><span lang=EN-US
style='font-size:14.0pt;color:black'>Advanced:<o:p></o:p></span></i></p>
<p class=MsoNormal style='margin-left:54.0pt;text-indent:-36.0pt;mso-list:l0 level1 lfo4;
tab-stops:list 54.0pt'><![if !supportLists]><span lang=EN-US style='font-size:
14.0pt;mso-fareast-font-family:"Times New Roman";color:red'><span
style='mso-list:Ignore'>19)<span style='font:7.0pt "Times New Roman"'>
</span></span></span><![endif]><span lang=EN-US style='font-size:14.0pt;
color:black'>This determines how many buckets are in the final tracer
distribution results.<o:p></o:p></span></p>
<p class=MsoNormal style='margin-left:54.0pt;text-indent:-36.0pt;mso-list:l0 level1 lfo4;
tab-stops:list 54.0pt'><![if !supportLists]><span lang=EN-US style='font-size:
14.0pt;mso-fareast-font-family:"Times New Roman";color:red'><span
style='mso-list:Ignore'>20)<span style='font:7.0pt "Times New Roman"'>
</span></span></span><![endif]><span lang=EN-US style='font-size:14.0pt;
color:black'>Saves the converted raw image files for examination/debugging.<o:p></o:p></span></p>
<p class=MsoNormal style='margin-left:54.0pt;text-indent:-36.0pt;mso-list:l0 level1 lfo4;
tab-stops:list 54.0pt'><![if !supportLists]><span lang=EN-US style='font-size:
14.0pt;mso-fareast-font-family:"Times New Roman";color:red'><span
style='mso-list:Ignore'>21)<span style='font:7.0pt "Times New Roman"'>
</span></span></span><![endif]><span lang=EN-US style='font-size:14.0pt;
color:black'>Saves the converted binary image files for examination/debugging.<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:14.0pt;color:black'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:14.0pt;color:black'>Press
OK to start the run, the window will be minimized until the run is complete.<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:14.0pt;color:black'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:14.0pt;color:black'><o:p> </o:p></span></p>
<p class=MsoNormal><!--[if gte vml 1]><v:line id="_x0000_s1057" style='position:absolute;
z-index:1' from="-50.95pt,9.2pt" to="1056.05pt,9.2pt"/><![endif]--><![if !vml]><span
style='mso-ignore:vglayout;position:relative;z-index:1;left:-69px;top:11px;
width:1478px;height:13px'><img width=1478 height=2
src="PoroMedia%20Help_files/image018.png" v:shapes="_x0000_s1057"></span><![endif]><span
lang=EN-US style='font-size:14.0pt;color:black'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:14.0pt;color:black'><o:p> </o:p></span></p>
<br style='mso-ignore:vglayout' clear=ALL>
<p class=MsoNormal><a name=RandomWalk></a><b><span lang=EN-US style='font-size:
14.0pt'>Random Walk:<o:p></o:p></span></b></p>
<p class=MsoNormal><span lang=EN-US style='font-size:14.0pt'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:14.0pt'>Below is the setup
dialog for Random Walk analysis. It is accessed through <i>Analysis</i> -> <i>Random
Walk</i> menu.<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:14.0pt;color:black'><o:p> </o:p></span></p>
<p class=MsoNormal align=center style='text-align:center'><span lang=EN-US
style='font-size:14.0pt;color:black'><!--[if gte vml 1]><v:shape id="_x0000_i1028"
type="#_x0000_t75" style='width:468pt;height:356.25pt'>
<v:imagedata src="PoroMedia%20Help_files/image011.jpg" o:title="RandomWalk"/>
</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=475
src="PoroMedia%20Help_files/image019.jpg" v:shapes="_x0000_i1028"><![endif]><o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:14.0pt;color:black'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:14.0pt;color:black'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:14.0pt;color:black'>Description
of fields </span><span lang=EN-US style='font-size:14.0pt;color:red'>1</span><span
lang=EN-US style='font-size:14.0pt;color:black'> through </span><span
lang=EN-US style='font-size:14.0pt;color:red'>13</span><span lang=EN-US
style='font-size:14.0pt;color:black'> can be found <a href="#Horizontal_Fields">here</a>.<span
style='mso-spacerun:yes'> </span>There are two different directions for
tortuosity analysis.<span style='mso-spacerun:yes'> </span>Transverse
sends a tracer from the top layer to the bottom, while Inplane sends a tracer
from the side of the sample, to a specified distance inside.<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:14.0pt;color:black'><o:p> </o:p></span></p>
<p class=MsoNormal><i style='mso-bidi-font-style:normal'><span lang=EN-US
style='font-size:14.0pt;color:black'>Random Walk Settings:<o:p></o:p></span></i></p>
<p class=MsoNormal style='margin-left:54.0pt;text-indent:-36.0pt;mso-list:l1 level1 lfo6;
tab-stops:list 54.0pt'><![if !supportLists]><span lang=EN-US style='font-size:
14.0pt;mso-fareast-font-family:"Times New Roman";color:red'><span
style='mso-list:Ignore'>14)<span style='font:7.0pt "Times New Roman"'>
</span></span></span><![endif]><span lang=EN-US style='font-size:14.0pt;
color:black'>Enter the number of molecules to diffuse.<o:p></o:p></span></p>
<p class=MsoNormal style='margin-left:54.0pt;text-indent:-36.0pt;mso-list:l1 level1 lfo6;
tab-stops:list 54.0pt'><![if !supportLists]><span lang=EN-US style='font-size:
14.0pt;mso-fareast-font-family:"Times New Roman";color:red'><span
style='mso-list:Ignore'>15)<span style='font:7.0pt "Times New Roman"'>
</span></span></span><![endif]><span lang=EN-US style='font-size:14.0pt;
color:black'>Set the limit for the distance (in pixels) that a particle can
travel.<span style='mso-spacerun:yes'> </span>This prevents an infinite
run if the particle is in a chamber.<o:p></o:p></span></p>
<p class=MsoNormal style='margin-left:54.0pt;text-indent:-36.0pt;mso-list:l1 level1 lfo6;
tab-stops:list 54.0pt'><![if !supportLists]><span lang=EN-US style='font-size:
14.0pt;mso-fareast-font-family:"Times New Roman";color:red'><span
style='mso-list:Ignore'>16)<span style='font:7.0pt "Times New Roman"'>
</span></span></span><![endif]><span lang=EN-US style='font-size:14.0pt;
color:black'>How great of a distance to travel before a data point is recorded.<o:p></o:p></span></p>
<p class=MsoNormal><i style='mso-bidi-font-style:normal'><span lang=EN-US
style='font-size:14.0pt;color:black'>Advanced Settings:<o:p></o:p></span></i></p>
<p class=MsoNormal style='margin-left:54.0pt;text-indent:-36.0pt;mso-list:l1 level1 lfo6;
tab-stops:list 54.0pt'><![if !supportLists]><span lang=EN-US style='font-size:
14.0pt;mso-fareast-font-family:"Times New Roman";color:red'><span
style='mso-list:Ignore'>17)<span style='font:7.0pt "Times New Roman"'>
</span></span></span><![endif]><span lang=EN-US style='font-size:14.0pt;
color:black'>Enter the pixel size in microns.<o:p></o:p></span></p>
<p class=MsoNormal style='margin-left:54.0pt;text-indent:-36.0pt;mso-list:l1 level1 lfo6;
tab-stops:list 54.0pt'><![if !supportLists]><span lang=EN-US style='font-size:
14.0pt;mso-fareast-font-family:"Times New Roman";color:red'><span
style='mso-list:Ignore'>18)<span style='font:7.0pt "Times New Roman"'>
</span></span></span><![endif]><span lang=EN-US style='font-size:14.0pt;
color:black'>Option for saving converted raw image files.<o:p></o:p></span></p>
<p class=MsoNormal style='margin-left:54.0pt;text-indent:-36.0pt;mso-list:l1 level1 lfo6;
tab-stops:list 54.0pt'><![if !supportLists]><span lang=EN-US style='font-size:
14.0pt;mso-fareast-font-family:"Times New Roman";color:red'><span
style='mso-list:Ignore'>19)<span style='font:7.0pt "Times New Roman"'>
</span></span></span><![endif]><span lang=EN-US style='font-size:14.0pt;
color:black'>Option for saving converted Binary image files.<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:14.0pt;color:black'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:14.0pt;color:black'>Press
OK to start the run, the window will be minimized until the run is complete.<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:14.0pt;color:black'><o:p> </o:p></span></p>
<p class=MsoNormal><!--[if gte vml 1]><v:line id="_x0000_s1063" style='position:absolute;
z-index:6' from="-5.95pt,13.2pt" to="1110.05pt,13.2pt"/><![endif]--><![if !vml]><span
style='mso-ignore:vglayout;position:relative;z-index:6;left:-9px;top:17px;
width:1490px;height:19px'><img width=1490 height=2
src="PoroMedia%20Help_files/image009.png" v:shapes="_x0000_s1063"></span><![endif]><span
lang=EN-US style='font-size:14.0pt;color:black'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:14.0pt;color:black'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:14.0pt;color:black'><o:p> </o:p></span></p>
<br style='mso-ignore:vglayout' clear=ALL>
<p class=MsoNormal><a name=VerticalPrep></a><b><span lang=EN-US
style='font-size:16.0pt'>Vertical Slice preparation (for Surface Structure
Analysis):<o:p></o:p></span></b></p>
<p class=MsoNormal><span lang=EN-US style='font-size:14.0pt'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:14.0pt'>Below is a sample
of a .bmp image file used in Surface Structure analysis.<span
style='mso-spacerun:yes'> </span>This represents one slice of many
required to reconstruct a porous 3D structure.<span
style='mso-spacerun:yes'> </span>Opposed to the horizontal slices, the
vertical one is the side view of a sample, and therefore often requires many
more slices to get an adequate sample.<span style='mso-spacerun:yes'>
</span>From a given sample set (example:<span style='mso-spacerun:yes'>
</span>oak_0000 to oak_1000), it is recommended to use as many slices as
possible.<span style='mso-spacerun:yes'> </span>Find the subset that
represents the largest consistent cube of the sample (perhaps oak_0400 to
oak_0600).<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:14.0pt;color:black'><o:p> </o:p></span></p>
<p class=MsoNormal align=center style='text-align:center'><a
name="Vertical_Slice"><span lang=EN-US style='font-size:14.0pt;color:black'><!--[if gte vml 1]><v:shape
id="_x0000_i1029" type="#_x0000_t75" style='width:642.75pt;height:129.75pt'>
<v:imagedata src="PoroMedia%20Help_files/image014.gif" o:title="Side-View"/>
</v:shape><![endif]--><![if !vml]><img border=0 width=857 height=173
src="PoroMedia%20Help_files/image014.gif" v:shapes="_x0000_i1029"><![endif]></span></a><span
lang=EN-US style='font-size:14.0pt;color:black'><o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:14.0pt;color:black'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:14.0pt'>There are several
required coordinates that need to be extracted from this image as input to
Surface Structure Analysis.<span style='mso-spacerun:yes'> </span>This
can be done using any image editing software (such as Microsoft Paint, or Adobe
Photoshop).<span style='mso-spacerun:yes'> </span>Keep in mind that these
coordinates need to be valid for all slices of this sample (it is recommended
to look at the first slice, middle and last slice, and confirm the coordinates
are valid for all).<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:14.0pt'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:14.0pt'>First, find the
X-coordinates that represent the <span style='color:lime'>left most</span>
valid point and the <span style='color:lime'>right most</span> valid
point.<span style='mso-spacerun:yes'> </span>These should represent a
section of the sample that is fairly level (samples that are scanned at an
angle other than flat horizontal are not as good).<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:14.0pt'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:14.0pt'>Next, <i>estimate</i>
the highest point of the sample (<span style='color:blue'>Top-Upper Limit</span>).<span
style='mso-spacerun:yes'> </span>It is beneficial to add a few extra
pixel layers for a safe margin, since other slices might have higher points (it
is impractical to scan all slices looking for highest point). Also, estimate
the lowest point on the top layer of the sample (<span style='color:blue'>Top-Lower
Limit</span>).<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:14.0pt'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:14.0pt'>Finally, repeat
this for the bottom layer of the sample.<span style='mso-spacerun:yes'>
</span>The <span style='color:fuchsia'>Bottom-Upper Limit</span> and <span
style='color:fuchsia'>Bottom-Lower Limit</span> represent these estimates for
the above sample.<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:14.0pt'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:14.0pt'>The following is a
more detailed description of running Surface Structure Analysis.<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:14.0pt;color:black'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:14.0pt;color:black'><o:p> </o:p></span></p>
<p class=MsoNormal><!--[if gte vml 1]><v:line id="_x0000_s1059" style='position:absolute;
z-index:2' from="-32.95pt,7.2pt" to="1155.05pt,7.2pt"/><![endif]--><![if !vml]><span
style='mso-ignore:vglayout;position:relative;z-index:2;left:-45px;top:9px;
width:1586px;height:11px'><img width=1586 height=2
src="PoroMedia%20Help_files/image020.png" v:shapes="_x0000_s1059"></span><![endif]><span
lang=EN-US style='font-size:14.0pt;color:black'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:14.0pt;color:black'><o:p> </o:p></span></p>
<br style='mso-ignore:vglayout' clear=ALL>
<p class=MsoNormal><a name=SurfaceStructure></a><b><span lang=EN-US
style='font-size:14.0pt'>Surface Structure Analysis:<o:p></o:p></span></b></p>
<p class=MsoNormal><span lang=EN-US style='font-size:14.0pt'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:14.0pt'>Below is the
dialog for Surface Structure analysis. It is accessed through <i>Analysis</i>
-> <i>Surface Structure</i> menu.<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:14.0pt;color:black'><o:p> </o:p></span></p>
<p class=MsoNormal align=center style='text-align:center'><span lang=EN-US
style='font-size:14.0pt;color:black'><!--[if gte vml 1]><v:shape id="_x0000_i1030"
type="#_x0000_t75" style='width:534pt;height:420.75pt'>
<v:imagedata src="PoroMedia%20Help_files/image017.jpg" o:title="SurfaceStructure"/>
</v:shape><![endif]--><![if !vml]><img border=0 width=712 height=561
src="PoroMedia%20Help_files/image021.jpg" v:shapes="_x0000_i1030"><![endif]><o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:14.0pt;color:black'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:14.0pt;color:black'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:14.0pt'><o:p> </o:p></span></p>
<p class=MsoNormal style='margin-left:54.0pt;text-indent:-36.0pt;mso-list:l3 level1 lfo8;
tab-stops:list 54.0pt'><![if !supportLists]><span lang=EN-US style='font-size:
14.0pt;mso-fareast-font-family:"Times New Roman";color:red'><span
style='mso-list:Ignore'>1)<span style='font:7.0pt "Times New Roman"'>
</span></span></span><![endif]><span lang=EN-US style='font-size:14.0pt'>Click
to pick the directory with sample images.<o:p></o:p></span></p>
<p class=MsoNormal style='margin-left:54.0pt;text-indent:-36.0pt;mso-list:l3 level1 lfo8;
tab-stops:list 54.0pt'><![if !supportLists]><span lang=EN-US style='font-size:
14.0pt;mso-fareast-font-family:"Times New Roman";color:red'><span
style='mso-list:Ignore'>2)<span style='font:7.0pt "Times New Roman"'>
</span></span></span><![endif]><span lang=EN-US style='font-size:14.0pt'>Displays
image directory, can copy/paste.<o:p></o:p></span></p>
<p class=MsoNormal style='margin-left:54.0pt;text-indent:-36.0pt;mso-list:l3 level1 lfo8;
tab-stops:list 54.0pt'><![if !supportLists]><span lang=EN-US style='font-size:
14.0pt;mso-fareast-font-family:"Times New Roman";color:red'><span
style='mso-list:Ignore'>3)<span style='font:7.0pt "Times New Roman"'>
</span></span></span><![endif]><span lang=EN-US style='font-size:14.0pt'>Enter
the <i>constant</i> part of all image files.<span
style='mso-spacerun:yes'> </span>For example, if a sample set contains
imagesvert_oak_0200.bmp to vert_oak_0300.bmp, vert_oak_0 must be entered into
this field.<o:p></o:p></span></p>
<p class=MsoNormal style='margin-left:54.0pt;text-indent:-36.0pt;mso-list:l3 level1 lfo8;
tab-stops:list 54.0pt'><![if !supportLists]><span lang=EN-US style='font-size:
14.0pt;mso-fareast-font-family:"Times New Roman";color:red'><span
style='mso-list:Ignore'>4)<span style='font:7.0pt "Times New Roman"'>
</span></span></span><![endif]><span lang=EN-US style='font-size:14.0pt'>Click
to pick the directory for run results.<o:p></o:p></span></p>
<p class=MsoNormal style='margin-left:54.0pt;text-indent:-36.0pt;mso-list:l3 level1 lfo8;
tab-stops:list 54.0pt'><![if !supportLists]><span lang=EN-US style='font-size:
14.0pt;mso-fareast-font-family:"Times New Roman";color:red'><span
style='mso-list:Ignore'>5)<span style='font:7.0pt "Times New Roman"'>
</span></span></span><![endif]><span lang=EN-US style='font-size:14.0pt'>Displays
result directory, can copy/paste.<o:p></o:p></span></p>
<p class=MsoNormal><i style='mso-bidi-font-style:normal'><span lang=EN-US
style='font-size:14.0pt'>Sample Properties:<o:p></o:p></span></i></p>
<p class=MsoNormal style='margin-left:54.0pt;text-indent:-36.0pt;mso-list:l3 level1 lfo8;
tab-stops:list 54.0pt'><![if !supportLists]><span lang=EN-US style='font-size:
14.0pt;mso-fareast-font-family:"Times New Roman";color:red'><span
style='mso-list:Ignore'>6)<span style='font:7.0pt "Times New Roman"'>
</span></span></span><![endif]><span lang=EN-US style='font-size:14.0pt'>Enter
the first slice number (the number that is attached to the constant part of
image file).<span style='mso-spacerun:yes'> </span>Continuing on the
previous example, 200 would be entered here (from vert_oak_0200.bmp).<o:p></o:p></span></p>
<p class=MsoNormal style='margin-left:54.0pt;text-indent:-36.0pt;mso-list:l3 level1 lfo8;
tab-stops:list 54.0pt'><![if !supportLists]><span lang=EN-US style='font-size:
14.0pt;mso-fareast-font-family:"Times New Roman";color:red'><span
style='mso-list:Ignore'>7)<span style='font:7.0pt "Times New Roman"'>
</span></span></span><![endif]><span lang=EN-US style='font-size:14.0pt'>Enter
the last slice number.<span style='mso-spacerun:yes'> </span>Continuing
on the previous example, 300 would be entered here (from vert_oak_0300.bmp).<o:p></o:p></span></p>
<p class=MsoNormal style='margin-left:54.0pt;text-indent:-36.0pt;mso-list:l3 level1 lfo8;
tab-stops:list 54.0pt'><![if !supportLists]><span lang=EN-US style='font-size:
14.0pt;mso-fareast-font-family:"Times New Roman";color:red'><span
style='mso-list:Ignore'>8)<span style='font:7.0pt "Times New Roman"'>
</span></span></span><![endif]><span lang=EN-US style='font-size:14.0pt;
color:black'>Left end limit (<a href="#VerticalPrep">description</a>).<o:p></o:p></span></p>
<p class=MsoNormal style='margin-left:54.0pt;text-indent:-36.0pt;mso-list:l3 level1 lfo8;
tab-stops:list 54.0pt'><![if !supportLists]><span lang=EN-US style='font-size:
14.0pt;mso-fareast-font-family:"Times New Roman";color:red'><span
style='mso-list:Ignore'>9)<span style='font:7.0pt "Times New Roman"'>
</span></span></span><![endif]><span lang=EN-US style='font-size:14.0pt;
color:black'>Right end limit (<a href="#VerticalPrep">description</a>).<o:p></o:p></span></p>
<p class=MsoNormal style='margin-left:54.0pt;text-indent:-36.0pt;mso-list:l3 level1 lfo8;
tab-stops:list 54.0pt'><![if !supportLists]><span lang=EN-US style='font-size:
14.0pt;mso-fareast-font-family:"Times New Roman";color:red'><span
style='mso-list:Ignore'>10)<span style='font:7.0pt "Times New Roman"'>
</span></span></span><![endif]><span lang=EN-US style='font-size:14.0pt;
color:black'>Upper top end limit (<a href="#VerticalPrep">description</a>).<o:p></o:p></span></p>
<p class=MsoNormal style='margin-left:54.0pt;text-indent:-36.0pt;mso-list:l3 level1 lfo8;
tab-stops:list 54.0pt'><![if !supportLists]><span lang=EN-US style='font-size:
14.0pt;mso-fareast-font-family:"Times New Roman";color:red'><span
style='mso-list:Ignore'>11)<span style='font:7.0pt "Times New Roman"'>
</span></span></span><![endif]><span lang=EN-US style='font-size:14.0pt;
color:black'>Lower top end limit (<a href="#VerticalPrep">description</a>).<o:p></o:p></span></p>
<p class=MsoNormal style='margin-left:54.0pt;text-indent:-36.0pt;mso-list:l3 level1 lfo8;
tab-stops:list 54.0pt'><![if !supportLists]><span lang=EN-US style='font-size:
14.0pt;mso-fareast-font-family:"Times New Roman";color:red'><span
style='mso-list:Ignore'>12)<span style='font:7.0pt "Times New Roman"'>
</span></span></span><![endif]><span lang=EN-US style='font-size:14.0pt;
color:black'>Upper bottom end limit (<a href="#VerticalPrep">description</a>).<o:p></o:p></span></p>
<p class=MsoNormal style='margin-left:54.0pt;text-indent:-36.0pt;mso-list:l3 level1 lfo8;
tab-stops:list 54.0pt'><![if !supportLists]><span lang=EN-US style='font-size:
14.0pt;mso-fareast-font-family:"Times New Roman";color:red'><span
style='mso-list:Ignore'>13)<span style='font:7.0pt "Times New Roman"'>
</span></span></span><![endif]><span lang=EN-US style='font-size:14.0pt;
color:black'>Lower bottom end limit (<a href="#VerticalPrep">description</a>).<o:p></o:p></span></p>
<p class=MsoNormal><i style='mso-bidi-font-style:normal'><span lang=EN-US
style='font-size:14.0pt;color:black'>Threshold:<o:p></o:p></span></i></p>
<p class=MsoNormal style='margin-left:54.0pt;text-indent:-36.0pt;mso-list:l3 level1 lfo8;
tab-stops:list 54.0pt'><![if !supportLists]><span lang=EN-US style='font-size:
14.0pt;mso-fareast-font-family:"Times New Roman";color:red'><span
style='mso-list:Ignore'>14)<span style='font:7.0pt "Times New Roman"'>
</span></span></span><![endif]><span lang=EN-US style='font-size:14.0pt;
color:black'>Check this box if the image is inverted (pores are white, fiber is
black).<span style='mso-spacerun:yes'> </span><a href="#Vertical_Slice">This
is an inverted image.</a><o:p></o:p></span></p>
<p class=MsoNormal style='margin-left:54.0pt;text-indent:-36.0pt;mso-list:l3 level1 lfo8;
tab-stops:list 54.0pt'><![if !supportLists]><span lang=EN-US style='font-size:
14.0pt;mso-fareast-font-family:"Times New Roman";color:red'><span
style='mso-list:Ignore'>15)<span style='font:7.0pt "Times New Roman"'>
</span></span></span><![endif]><span lang=EN-US style='font-size:14.0pt;
color:black'>Check this box to enable field </span><span lang=EN-US
style='font-size:14.0pt;color:red'>16</span><span lang=EN-US style='font-size:
14.0pt;color:black'> for entering a desired threshold.<span
style='mso-spacerun:yes'> </span>If this box is not checked, the
threshold is automatically computed as part of the run.<span
style='mso-spacerun:yes'> </span>It may sometimes be necessary to use a
manual threshold for certain samples for desired results.<o:p></o:p></span></p>
<p class=MsoNormal style='margin-left:54.0pt;text-indent:-36.0pt;mso-list:l3 level1 lfo8;
tab-stops:list 54.0pt'><![if !supportLists]><span lang=EN-US style='font-size:
14.0pt;mso-fareast-font-family:"Times New Roman";color:red'><span
style='mso-list:Ignore'>16)<span style='font:7.0pt "Times New Roman"'>
</span></span></span><![endif]><span lang=EN-US style='font-size:14.0pt;
color:black'>Enter a threshold if field </span><span lang=EN-US
style='font-size:14.0pt;color:red'>15</span><span lang=EN-US style='font-size:
14.0pt;color:black'> is checked.<span style='mso-spacerun:yes'>
</span>The threshold determines how the .bmp images are converted to binary
form.<span style='mso-spacerun:yes'> </span>A brief explanation is as
follows.<span style='mso-spacerun:yes'> </span>The .bmp images are
first converted to raw form, with each pixel having intensity between 0 and
255.<span style='mso-spacerun:yes'> </span>Then, any value greater than
the threshold value becomes a binary 1 (fiber), and any value less than the
threshold value becomes a binary 0 (pore).<span
style='mso-spacerun:yes'> </span>If there are problems such as .bmp
images being converted to an all black binary files, the threshold should be
raised to a higher value, and vice versa.<o:p></o:p></span></p>
<p class=MsoNormal><i style='mso-bidi-font-style:normal'><span lang=EN-US
style='font-size:14.0pt;color:black'>Run Settings:<o:p></o:p></span></i></p>
<p class=MsoNormal style='margin-left:54.0pt;text-indent:-36.0pt;mso-list:l3 level1 lfo8;
tab-stops:list 54.0pt'><![if !supportLists]><span lang=EN-US style='font-size:
14.0pt;mso-fareast-font-family:"Times New Roman";color:red'><span
style='mso-list:Ignore'>17)<span style='font:7.0pt "Times New Roman"'>
</span></span></span><![endif]><span lang=EN-US style='font-size:14.0pt;
color:black'>Run thickness distribution analysis.<span
style='mso-spacerun:yes'> </span><a href="#thickness_result">Result
description.</a><o:p></o:p></span></p>
<p class=MsoNormal style='margin-left:54.0pt;text-indent:-36.0pt;mso-list:l3 level1 lfo8;
tab-stops:list 54.0pt'><![if !supportLists]><span lang=EN-US style='font-size:
14.0pt;mso-fareast-font-family:"Times New Roman";color:red'><span
style='mso-list:Ignore'>18)<span style='font:7.0pt "Times New Roman"'>
</span></span></span><![endif]><span lang=EN-US style='font-size:14.0pt;
color:black'>Run surface volume distribution analysis.<span
style='mso-spacerun:yes'> </span><a href="#surfaceVolume_result">Result
description.</a><o:p></o:p></span></p>
<p class=MsoNormal style='margin-left:54.0pt;text-indent:-36.0pt;mso-list:l3 level1 lfo8;
tab-stops:list 54.0pt'><![if !supportLists]><span lang=EN-US style='font-size:
14.0pt;mso-fareast-font-family:"Times New Roman";color:red'><span
style='mso-list:Ignore'>19)<span style='font:7.0pt "Times New Roman"'>
</span></span></span><![endif]><span lang=EN-US style='font-size:14.0pt;
color:black'>Run contact fraction and surface pit distribution analysis for the
</span><b style='mso-bidi-font-weight:normal'><i><span lang=EN-US
style='font-size:14.0pt;color:#3366FF'>top</span></i></b><span lang=EN-US
style='font-size:14.0pt;color:black'> layer.<span
style='mso-spacerun:yes'> </span><a href="#contactFractTop_result">Result
description.</a><o:p></o:p></span></p>
<p class=MsoNormal style='margin-left:54.0pt;text-indent:-36.0pt;mso-list:l3 level1 lfo8;
tab-stops:list 54.0pt'><![if !supportLists]><span lang=EN-US style='font-size:
14.0pt;mso-fareast-font-family:"Times New Roman";color:red'><span
style='mso-list:Ignore'>20)<span style='font:7.0pt "Times New Roman"'>
</span></span></span><![endif]><span lang=EN-US style='font-size:14.0pt;
color:black'>Run contact fraction and surface pit distribution analysis for the
</span><b style='mso-bidi-font-weight:normal'><i><span lang=EN-US
style='font-size:14.0pt;color:fuchsia'>bottom</span></i></b><span lang=EN-US
style='font-size:14.0pt;color:black'> layer.<span
style='mso-spacerun:yes'> </span><a href="#contactFractBottom_result">Result
description.</a><o:p></o:p></span></p>
<p class=MsoNormal><i style='mso-bidi-font-style:normal'><span lang=EN-US
style='font-size:14.0pt;color:black'>Advanced:<o:p></o:p></span></i></p>
<p class=MsoNormal style='margin-left:54.0pt;text-indent:-36.0pt;mso-list:l3 level1 lfo8;
tab-stops:list 54.0pt'><![if !supportLists]><span lang=EN-US style='font-size:
14.0pt;mso-fareast-font-family:"Times New Roman";color:red'><span
style='mso-list:Ignore'>21)<span style='font:7.0pt "Times New Roman"'>
</span></span></span><![endif]><span lang=EN-US style='font-size:14.0pt;
color:black'>This determines how many buckets are in the final surface pit distribution
result.<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:14.0pt;color:black'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:14.0pt;color:black'>Press
OK to start the run, the window will be minimized until the run is complete.<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:14.0pt;color:black'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:14.0pt;color:black'><o:p> </o:p></span></p>
<p class=MsoNormal><b style='mso-bidi-font-weight:normal'><span lang=EN-US
style='font-size:14.0pt;color:black'>Surface Structure Analysis Output Files:<o:p></o:p></span></b></p>
<p class=MsoNormal><span lang=EN-US style='font-size:14.0pt;color:black'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:14.0pt;color:black'>All
output files will be in the user specified Results Directory (</span><span
lang=EN-US style='font-size:14.0pt;color:red'>5</span><span lang=EN-US
style='font-size:14.0pt;color:black'>).<span style='mso-spacerun:yes'>
</span>Depending on what Runs are specified, the following outputs files are
possible.<span style='mso-spacerun:yes'> </span>Any .<span class=SpellE>csv</span>
file can be examined using Microsoft Excel.<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:14.0pt;color:black'><o:p> </o:p></span></p>
<p class=MsoNormal><a name="thickness_result"></a><i style='mso-bidi-font-style:
normal'><span lang=EN-US style='font-size:14.0pt;color:black'>Run thickness
distribution analysis </span></i><span lang=EN-US style='font-size:14.0pt;
color:black'>is checked<i style='mso-bidi-font-style:normal'>:<o:p></o:p></i></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:14.0pt;color:black'><span
style='mso-tab-count:1'> </span><span
class=SpellE>thickness_distribution.csv</span>:<span style='mso-tab-count:1'> </span><span
style='mso-tab-count:1'> </span>Contains
the sample thickness distribution results, and all of the specific run
parameters.<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:14.0pt;color:black'><span
style='mso-tab-count:1'> </span><span
class=SpellE><span class=GramE>resultThickness</span></span>:<span
style='mso-tab-count:3'> </span><span
style='mso-tab-count:1'> </span>This
directory contains the raw thickness data for every sample slice.<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:14.0pt;color:black'><o:p> </o:p></span></p>
<p class=MsoNormal><a name="surfaceVolume_result"></a><i style='mso-bidi-font-style:
normal'><span lang=EN-US style='font-size:14.0pt;color:black'>Run surface
volume distribution analysis</span></i><span lang=EN-US style='font-size:14.0pt;
color:black'> is checked:<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:14.0pt;color:black'><span
style='mso-tab-count:1'> </span><span
class=SpellE>surface_volume_distribution.csv</span>:<span style='mso-tab-count:
1'> </span>Contains the sample volume
distribution results, and all of the specific run parameters.<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:14.0pt;color:black'><span
style='mso-tab-count:1'> </span><span
class=SpellE><span class=GramE>resultSurfaceVolume</span></span>:<span
style='mso-tab-count:3'> </span>This
directory contains the raw data of surface volume run.<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:14.0pt;color:black'><o:p> </o:p></span></p>
<p class=MsoNormal><a name="contactFractTop_result"></a><i style='mso-bidi-font-style:
normal'><span lang=EN-US style='font-size:14.0pt;color:black'>Run contact
fraction for Top</span></i><span lang=EN-US style='font-size:14.0pt;color:black'>
is checked:<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:14.0pt;color:black'><span
style='mso-tab-count:1'> </span><span
class=SpellE>contact_fraction_Top.csv</span>:<o:p></o:p></span></p>
<p class=MsoNormal style='text-indent:36.0pt'><span class=SpellE><span
lang=EN-US style='font-size:14.0pt;color:black'>surfacepit_distribution_Top.csv</span></span><span
lang=EN-US style='font-size:14.0pt;color:black'>:<o:p></o:p></span></p>
<p class=MsoNormal style='text-indent:36.0pt'><span class=SpellE><span
class=GramE><span lang=EN-US style='font-size:14.0pt;color:black'>resultContactFractTop</span></span></span><span
lang=EN-US style='font-size:14.0pt;color:black'>:<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:14.0pt;color:black'><o:p> </o:p></span></p>
<p class=MsoNormal><a name="contactFractBottom_result"></a><i style='mso-bidi-font-style:
normal'><span lang=EN-US style='font-size:14.0pt;color:black'>Run contact
fraction for Bottom</span></i><span lang=EN-US style='font-size:14.0pt;
color:black'> is checked: <o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:14.0pt;color:black'><span
style='mso-tab-count:1'> </span><span
class=SpellE>contact_fraction_Bottom.csv</span>:<o:p></o:p></span></p>
<p class=MsoNormal style='text-indent:36.0pt'><span class=SpellE><span
lang=EN-US style='font-size:14.0pt;color:black'>surfacepit_distribution_Bottom.csv</span></span><span
lang=EN-US style='font-size:14.0pt;color:black'>:<o:p></o:p></span></p>
<p class=MsoNormal style='text-indent:36.0pt'><span class=SpellE><span
class=GramE><span lang=EN-US style='font-size:14.0pt;color:black'>resultContactFractBottom</span></span></span><span
lang=EN-US style='font-size:14.0pt;color:black'>:<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:14.0pt;color:black'><o:p> </o:p></span></p>
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