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Medical Image Segmentation Synthesis (MISS) Tool User Guide.html
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Medical Image Segmentation Synthesis (MISS) Tool User Guide.html
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<p class=MsoTocHeading align=center style='text-align:center'><b><span
style='font-family:"Times New Roman",serif'>Medical Image Segmentation
Synthesis (MISS) Tool User Guide</span></b></p>
<p class=MsoNormal> </p>
<p class=MsoTocHeading>Contents</p>
<p class=MsoToc1><a href="#_Toc174976501">Introduction<span style='color:windowtext;
display:none;text-decoration:none'>. </span><span
style='color:windowtext;display:none;text-decoration:none'>3</span></a></p>
<p class=MsoToc2><a href="#_Toc174976502">Version (last update): <b>8/19/2024</b><span
style='color:windowtext;display:none;text-decoration:none'>. </span><span
style='color:windowtext;display:none;text-decoration:none'>3</span></a></p>
<p class=MsoToc1><a href="#_Toc174976503">The Use of GUI<span style='color:
windowtext;display:none;text-decoration:none'> </span><span
style='color:windowtext;display:none;text-decoration:none'>3</span></a></p>
<p class=MsoToc2><a href="#_Toc174976504">Main options<span style='color:windowtext;
display:none;text-decoration:none'>. </span><span
style='color:windowtext;display:none;text-decoration:none'>3</span></a></p>
<p class=MsoToc2><a href="#_Toc174976505">Segmentation Performance Metrics<span
style='color:windowtext;display:none;text-decoration:none'>. </span><span
style='color:windowtext;display:none;text-decoration:none'>4</span></a></p>
<p class=MsoToc3><a href="#_Toc174976506">Evaluation of a single case<span
style='color:windowtext;display:none;text-decoration:none'>. </span><span
style='color:windowtext;display:none;text-decoration:none'>4</span></a></p>
<p class=MsoToc4><a href="#_Toc174976507">Load data<span style='color:windowtext;
display:none;text-decoration:none'>. </span><span
style='color:windowtext;display:none;text-decoration:none'>4</span></a></p>
<p class=MsoToc4><a href="#_Toc174976508">To view result<span style='color:
windowtext;display:none;text-decoration:none'>. </span><span
style='color:windowtext;display:none;text-decoration:none'>5</span></a></p>
<p class=MsoToc4><a href="#_Toc174976509">Results output<span style='color:
windowtext;display:none;text-decoration:none'>. </span><span
style='color:windowtext;display:none;text-decoration:none'>5</span></a></p>
<p class=MsoToc3><a href="#_Toc174976510">Other options<span style='color:windowtext;
display:none;text-decoration:none'>. </span><span
style='color:windowtext;display:none;text-decoration:none'>6</span></a></p>
<p class=MsoToc3><a href="#_Toc174976511">Performance metrics computation on
multiple cases<span style='color:windowtext;display:none;text-decoration:none'>. </span><span
style='color:windowtext;display:none;text-decoration:none'>7</span></a></p>
<p class=MsoToc4><a href="#_Toc174976512">Load data<span style='color:windowtext;
display:none;text-decoration:none'>. </span><span
style='color:windowtext;display:none;text-decoration:none'>7</span></a></p>
<p class=MsoToc4><a href="#_Toc174976513">Results output<span style='color:
windowtext;display:none;text-decoration:none'>. </span><span
style='color:windowtext;display:none;text-decoration:none'>7</span></a></p>
<p class=MsoToc2><a href="#_Toc174976514">Segmentation synthesis<span
style='color:windowtext;display:none;text-decoration:none'>. </span><span
style='color:windowtext;display:none;text-decoration:none'>8</span></a></p>
<p class=MsoToc3><a href="#_Toc174976515">Load data<span style='color:windowtext;
display:none;text-decoration:none'>. </span><span
style='color:windowtext;display:none;text-decoration:none'>8</span></a></p>
<p class=MsoToc3><a href="#_Toc174976516">Synthesis Tools<span
style='color:windowtext;display:none;text-decoration:none'>. </span><span
style='color:windowtext;display:none;text-decoration:none'>9</span></a></p>
<p class=MsoToc4><a href="#_Toc174976517">Add spiculations<span
style='color:windowtext;display:none;text-decoration:none'>. </span><span
style='color:windowtext;display:none;text-decoration:none'>10</span></a></p>
<p class=MsoToc4><a href="#_Toc174976518">Change contour by Fourier Descriptor<span
style='color:windowtext;display:none;text-decoration:none'>. </span><span
style='color:windowtext;display:none;text-decoration:none'>11</span></a></p>
<p class=MsoToc4><a href="#_Toc174976519">Affine transformation<span
style='color:windowtext;display:none;text-decoration:none'>. </span><span
style='color:windowtext;display:none;text-decoration:none'>12</span></a></p>
<p class=MsoToc3><a href="#_Toc174976520">Results Output<span style='color:
windowtext;display:none;text-decoration:none'>. </span><span
style='color:windowtext;display:none;text-decoration:none'>13</span></a></p>
<p class=MsoToc3><a href="#_Toc174976521">Batch Processing<span
style='color:windowtext;display:none;text-decoration:none'>. </span><span
style='color:windowtext;display:none;text-decoration:none'>13</span></a></p>
<p class=MsoToc4><a href="#_Toc174976522">Parameters<span style='color:windowtext;
display:none;text-decoration:none'>. </span><span
style='color:windowtext;display:none;text-decoration:none'>14</span></a></p>
<p class=MsoToc4><a href="#_Toc174976523">Editing operations for modification
plan<span style='color:windowtext;display:none;text-decoration:none'>. </span><span
style='color:windowtext;display:none;text-decoration:none'>15</span></a></p>
<p class=MsoToc4><a href="#_Toc174976524">Applying modifications to mask(s)<span
style='color:windowtext;display:none;text-decoration:none'>. </span><span
style='color:windowtext;display:none;text-decoration:none'>17</span></a></p>
<p class=MsoToc4><a href="#_Toc174976525">Save & load modifications plan<span
style='color:windowtext;display:none;text-decoration:none'>. </span><span
style='color:windowtext;display:none;text-decoration:none'>18</span></a></p>
<p class=MsoToc1><a href="#_Toc174976526">The Use of Command (Code)<span
style='color:windowtext;display:none;text-decoration:none'>. </span><span
style='color:windowtext;display:none;text-decoration:none'>19</span></a></p>
<p class=MsoToc2><a href="#_Toc174976527">Main functions<span style='color:
windowtext;display:none;text-decoration:none'>. </span><span
style='color:windowtext;display:none;text-decoration:none'>19</span></a></p>
<p class=MsoToc3><a href="#_Toc174976528">Function for segmentation evaluation
metrics: <b>seg_measures</b><span style='color:windowtext;display:none;
text-decoration:none'>. </span><span
style='color:windowtext;display:none;text-decoration:none'>19</span></a></p>
<p class=MsoToc3><a href="#_Toc174976529">Functions for segmentation synthesis<span
style='color:windowtext;display:none;text-decoration:none'>. </span><span
style='color:windowtext;display:none;text-decoration:none'>20</span></a></p>
<p class=MsoToc4><a href="#_Toc174976530">Add spiculations: <b>mod_spike</b><span
style='color:windowtext;display:none;text-decoration:none'>. </span><span
style='color:windowtext;display:none;text-decoration:none'>20</span></a></p>
<p class=MsoToc4><a href="#_Toc174976531">Change contour by Fourier Descriptor:
<b>mod_fourier</b><span style='color:windowtext;display:none;text-decoration:
none'>. </span><span
style='color:windowtext;display:none;text-decoration:none'>20</span></a></p>
<p class=MsoToc4><a href="#_Toc174976532">Affine transformation: <b>mod_affine</b><span
style='color:windowtext;display:none;text-decoration:none'>. </span><span
style='color:windowtext;display:none;text-decoration:none'>21</span></a></p>
<p class=MsoToc1><a href="#_Toc174976533">An example of segmentation evaluation<span
style='color:windowtext;display:none;text-decoration:none'>. </span><span
style='color:windowtext;display:none;text-decoration:none'>22</span></a></p>
<p class=MsoToc2><a href="#_Toc174976534">Implement by GUI<span
style='color:windowtext;display:none;text-decoration:none'> </span><span
style='color:windowtext;display:none;text-decoration:none'>22</span></a></p>
<p class=MsoToc2><a href="#_Toc174976535">Implement by Command (Code)<span
style='color:windowtext;display:none;text-decoration:none'>. </span><span
style='color:windowtext;display:none;text-decoration:none'>22</span></a></p>
<p class=MsoToc1><a href="#_Toc174976536">An example of segmentation synthesis<span
style='color:windowtext;display:none;text-decoration:none'>. </span><span
style='color:windowtext;display:none;text-decoration:none'>22</span></a></p>
<p class=MsoToc2><a href="#_Toc174976537">Implement by GUI<span
style='color:windowtext;display:none;text-decoration:none'> </span><span
style='color:windowtext;display:none;text-decoration:none'>23</span></a></p>
<p class=MsoToc2><a href="#_Toc174976538">Implement by Command (Code)<span
style='color:windowtext;display:none;text-decoration:none'>. </span><span
style='color:windowtext;display:none;text-decoration:none'>23</span></a></p>
<p class=MsoNormal> </p>
<span style='font-size:11.0pt;line-height:107%;font-family:"Calibri",sans-serif'><br
clear=all style='page-break-before:always'>
</span>
<p class=MsoNormal> </p>
<h1><a name="_Toc174976501">Introduction</a></h1>
<p class=paragraph><span class=normaltextrun><span style='font-family:"Calibri",sans-serif'>The
Medical Image Segmentation Synthesis (MISS) Tool is a program written in MATLAB
for emulating segmentation contours by adjusting the input (truth) mask through
synthesizing various types of segmentation errors. The tool also implemented
the computation of performance metrics for segmentation evaluation, including
the Dice coefficient, Jaccard index (IoU), Medical Similarity Index (MSI), and
several distance-based metrics. The MISS tool supports two ways to use: through
its graphical user interface (GUI) or using command-line functions. The GUI
allows for visualization of the synthesis results, interactively tuning
synthesis parameters, evaluation results, and also limited support to run batch
jobs. The command-line mode allows for processing images in batches as well as
providing flexible ways for users to integrate the MISS tool with their
applications.</span></span></p>
<p class=paragraph><span class=normaltextrun><span style='font-family:"Calibri",sans-serif'>The
MISS tool provides the following components:</span></span></p>
<p class=paragraph style='margin-left:.5in;text-indent:-.25in'><span
class=normaltextrun><span style='font-family:Symbol'>·<span style='font:7.0pt "Times New Roman"'>
</span></span></span><span class=normaltextrun><b><span style='font-family:
"Calibri",sans-serif'>Image segmentation synthesis</span></b></span><span
class=normaltextrun><span style='font-family:"Calibri",sans-serif'>: the user
inputs a truth mask, and the program outputs a segmentation contour with
controlled segmentation errors.</span></span></p>
<p class=paragraph style='margin-left:.5in;text-indent:-.25in'><span
class=normaltextrun><span style='font-family:Symbol'>·<span style='font:7.0pt "Times New Roman"'>
</span></span></span><span class=normaltextrun><b><span style='font-family:
"Calibri",sans-serif'>Segmentation performance evaluation</span></b></span><span
class=normaltextrun><span style='font-family:"Calibri",sans-serif'>: the user
provides a truth and a segmentation result, and the program outputs performance
metrics chosen by the user.</span></span></p>
<h2><a name="_Toc174976502">Version (last update): </a><b><span style='color:#4472C4'>8/19/2024</span></b></h2>
<h1><a name="_Toc174976503">The Use of GUI</a></h1>
<p class=MsoNormal>The GUI contains two options: </p>
<p class=MsoListParagraphCxSpFirst style='text-indent:-.25in'><span
style='font-family:Symbol'>·<span style='font:7.0pt "Times New Roman"'>
</span></span>Segmentation performance evaluation </p>
<p class=MsoListParagraphCxSpLast style='text-indent:-.25in'><span
style='font-family:Symbol'>·<span style='font:7.0pt "Times New Roman"'>
</span></span>Image segmentation contour synthesis </p>
<p class=MsoNormal><span style='font-family:Consolas;color:#0070C0'>To start
the GUI, open the file “main_option.mlapp” and run it in MATLAB.</span></p>
<h2><a name="_Toc174976504">Main options</a></h2>
<p class=MsoNormal>When running the MISS tool MATLAB-GUI, the Main Options
window pops up.</p>
<p class=MsoNormal><img width=278 height=233 id="Picture 33"
src="Medical%20Image%20Segmentation%20Synthesis%20(MISS)%20Tool%20User%20Guide_files/image001.jpg"></p>
<p class=MsoNormal>If you have truth masks and binary segmentation results, to calculate
segmentation performance metrics, select <b>1: Computing Segmentation Metrics</b>.</p>
<p class=MsoNormal>If you have truth masks, to generate synthetic segmentation
contours based on the truth masks, select <b>2: Synthesis of Segmentation
Contours</b>.</p>
<p class=MsoNormal>When either option is selected, the Main Options window is closed,
and a new window will be shown. There is a “Return to main window” button on
the new window to go back to the Main Options window.</p>
<h2><a name="_Hlk149648453"></a><a name="_Toc174976505">Segmentation
Performance Metrics</a> </h2>
<p class=MsoNormal><img width=624 height=412 id="Picture 1"
src="Medical%20Image%20Segmentation%20Synthesis%20(MISS)%20Tool%20User%20Guide_files/image002.png">After
<a name="_Hlk172647084">clicking the “Computing Segmentation Metrics” on the
main options window</a>, you will see the window for <b>Metrics Computation</b>.
</p>
<p class=MsoNormal><b>“Return to main window” </b>button on the new window is for
going back to the main window.</p>
<h3><a name="_Toc174976506">Evaluation of a single case</a> </h3>
<h4><a name="_Toc174976507">Load data</a></h4>
<p class=MsoNormal>For evaluating segmentation performance of a single case, you
click the “<b>Segmentation contour</b>” and “<b>Reference contour</b>” buttons
in the “<b>User Input (Single)</b>” panel to input one segmentation contour and
one (reference) truth mask. </p>
<p class=MsoNormal><span style='font-family:Consolas;color:#4472C4'>The
supported input file formats are: '*.jpg; *.tif; *.png; *.gif'. The image
should have only one object (connected component) as the segmentation or truth
mask (filled contour image). </span></p>
<p class=MsoNormal><span style='font-family:Consolas;color:#C00000'>Note: input
images must have the same size.</span></p>
<p class=MsoNormal><img width=145 height=118 id="Picture 34"
src="Medical%20Image%20Segmentation%20Synthesis%20(MISS)%20Tool%20User%20Guide_files/image003.png"></p>
<p class=MsoNormal>After inputting an image, the file name of the image will
show below the input button, the metrics values and images will display
automatically.</p>
<h4><a name="_Toc174976508">To view result</a></h4>
<p class=MsoNormal>The values of 24 metrics show in the “Segmentation Metrics”
frame. On the Segmentation Viewer, the segmentation truth is shown as a blue mask,
and the segmentation is shown as a green contour.</p>
<p class=MsoNormal><span style='font-family:Consolas;color:#C00000'>Note: by default,
on Metrics Computation window the calculations of Hausdorff Distance (HD) and Average
Hausdorff Distance (AVD) metrics are enabled. If you want to exclude the two
metrics, uncheck the “Compute Hausdorff Distances (Slow)” box under the “Comparison”
frame.</span></p>
<p class=MsoNormal><img width=624 height=413 id="Picture 5"
src="Medical%20Image%20Segmentation%20Synthesis%20(MISS)%20Tool%20User%20Guide_files/image004.png">More
details of these metrics are in the “<a href="#_Function_for_segmentation">Functions
of segmentation evaluation metrics</a>” section.</p>
<h4><a name="_Toc174976509">Results output</a></h4>
<p class=MsoNormal>The values of 24 metrics auto-save in the “<b>Workspace</b>”
of MATLAB, it is a MATLAB <b><i>struct</i></b> value named “<b>metrics_value</b>”.</p>
<p class=MsoNormal><img border=0 width=193 height=53 id="Picture 9"
src="Medical%20Image%20Segmentation%20Synthesis%20(MISS)%20Tool%20User%20Guide_files/image005.jpg"></p>
<p class=MsoNormal><img border=0 width=241 height=316 id="Picture 10"
src="Medical%20Image%20Segmentation%20Synthesis%20(MISS)%20Tool%20User%20Guide_files/image006.jpg"></p>
<p class=MsoNormal>By clicking the “<b>Save metrics values</b>” button, these
values will be saved in a <b><i>CSV</i></b> file specified by the user.</p>
<h3><a name="_Toc174976510"></a><a name="_Other_options"></a>Other options</h3>
<p class=MsoListParagraphCxSpFirst style='text-indent:-.25in'><span
style='font-family:Symbol'>·<span style='font:7.0pt "Times New Roman"'>
</span></span><b>“Compute Hausdorff Distances (slower)” </b>check box: on/off
the calculations of Hausdorff Distance (HD) and Average Hausdorff Distance
(AVD) metrics.</p>
<p class=MsoListParagraphCxSpMiddle><img border=0 width=190 height=53
id="Picture 37"
src="Medical%20Image%20Segmentation%20Synthesis%20(MISS)%20Tool%20User%20Guide_files/image007.png"><span
style='font-family:Wingdings'>ßà</span> <img border=0 width=186 height=50
id="Picture 38"
src="Medical%20Image%20Segmentation%20Synthesis%20(MISS)%20Tool%20User%20Guide_files/image008.png"></p>
<p class=MsoListParagraphCxSpMiddle> </p>
<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in'><span
style='font-family:Symbol'>·<span style='font:7.0pt "Times New Roman"'>
</span></span><b>“Display in filled contour” </b>check box: on/off filling the
area of segmentation. If checked the truth mask shows in filled red area, and
the segmentation shows in filled blue area with green contour. Their
overlapping area shows in purple. </p>
<p class=MsoListParagraphCxSpLast><img border=0 width=253 height=262
id="Picture 39"
src="Medical%20Image%20Segmentation%20Synthesis%20(MISS)%20Tool%20User%20Guide_files/image009.png"> <span
style='font-family:Wingdings'>ßà</span> <img border=0 width=250 height=265
id="Picture 40"
src="Medical%20Image%20Segmentation%20Synthesis%20(MISS)%20Tool%20User%20Guide_files/image010.png"></p>
<h3><a name="_Toc174976511">Performance metrics computation on multiple cases</a></h3>
<h4><a name="_Toc174976512">Load data</a></h4>
<p class=MsoNormal>To <a name="_Hlk172546465">load images and masks for </a>multiple
cases, you click the “<b>Segmentation contours</b>” and “<a name="_Hlk172647187"><b>Reference
contours</b></a>” buttons in the “<b>User Input (Multiple cases)</b>” panel to specify
segmentation masks and truth (reference) masks. </p>
<p class=MsoNormal><span style='font-family:Consolas;color:#4472C4'>The
supported image formats are: '*.jpg; *.tif; *.png; *.gif'. The image should
have only one object (connected component) as the segmentation or truth mask. </span></p>
<p class=MsoNormal><span style='font-family:Consolas;color:#C00000'>Note: 1) the
numbers of segmentations and truth masks must be same and non-zero; 2) all
input images must have the same size; 3) the program assumes one-to-one
correspondence between the two lists, i.e., the first segmentation mask
corresponds to the first truth mask, and so on.</span></p>
<p class=MsoNormal><img border=0 width=150 height=174 id="Picture 44"
src="Medical%20Image%20Segmentation%20Synthesis%20(MISS)%20Tool%20User%20Guide_files/image011.png"> <img
border=0 width=212 height=174 id="Picture 43"
src="Medical%20Image%20Segmentation%20Synthesis%20(MISS)%20Tool%20User%20Guide_files/image012.png"></p>
<p class=MsoNormal>After loading the image files, the number of image files
will show below the buttons, and files’ names will print in <b>MATLAB Command
Window</b>.</p>
<h4><a name="_Toc174976513">Results output</a></h4>
<p class=MsoNormal>After loading the image files, you click the “<b>Performance
Metrics</b>” button to start computing the 24 metrics values for each pair of segmentations
and truth masks, and the results will be saved in a <b><i>CSV</i></b> file
specified by the user.</p>
<h2><a name="_Toc174976514">Segmentation synthesis</a></h2>
<h3><a name="_Toc174976515">Load data</a></h3>
<p class=MsoNormal><img border=0 width=624 height=411 id="Picture 2"
src="Medical%20Image%20Segmentation%20Synthesis%20(MISS)%20Tool%20User%20Guide_files/image013.jpg"></p>
<p class=MsoNormal>First, you click the “<b>Load Truth Mask</b>” button (the blue
arrow on above picture) to input a truth mask. </p>
<p class=MsoNormal><span style='font-family:Consolas;color:#4472C4'>The
supported image formats are: '*.jpg; *.tif; *.png; *.gif'. The image should
have only one object (connected component) as the truth mask. </span></p>
<p class=MsoNormal><img border=0 width=624 height=415 id="Picture 4"
src="Medical%20Image%20Segmentation%20Synthesis%20(MISS)%20Tool%20User%20Guide_files/image014.png"></p>
<p class=MsoNormal>After loading a mask, the metrics values and images will
display automatically, where the metrics reflect the segmentation error of the
synthetic contour against the input truth contour. Without any modification, the
synthetic segmentation is identical to the truth mask. </p>
<p class=MsoNormal><span style='font-family:Consolas;color:#C00000'>Note: by default,
on Synthesis of Contour window the calculations of Hausdorff Distance (HD) and Average
Hausdorff Distance (AVD) metrics are disabled due to a slow processing. If you
want to include the two metrics, check the “Compute Hausdorff Distances (Slow)”
box under the “Comparison” frame.</span></p>
<p class=MsoNormal>The “<b>Recover</b>” button is to undo all changes and
recover the original mask image. For details of the “Compute Hausdorff
Distances (slower)” check box and “Display in filled contour” check box, please
see in the <a href="#_Other_options">“Other options” section</a>.</p>
<p class=MsoNormal> </p>
<h3><a name="_Toc174976516">Synthesis Tools</a></h3>
<p class=MsoNormal>Our tool provides three methods to modify the input truth
mask and generate synthetic segmentation contours:</p>
<p class=MsoListParagraphCxSpFirst style='text-indent:-.25in'><span
style='font-family:Symbol'>·<span style='font:7.0pt "Times New Roman"'>
</span></span>Add spiculations – <b>“Spiculation” </b>button. An example:</p>
<p class=MsoListParagraphCxSpMiddle><img border=0 width=109 height=109
id="Picture 14"
src="Medical%20Image%20Segmentation%20Synthesis%20(MISS)%20Tool%20User%20Guide_files/image015.jpg"> <span
style='font-family:Wingdings'>à</span> <img border=0 width=110 height=109
id="Picture 15"
src="Medical%20Image%20Segmentation%20Synthesis%20(MISS)%20Tool%20User%20Guide_files/image016.jpg"></p>
<p class=MsoListParagraphCxSpMiddle> </p>
<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in'><span
style='font-family:Symbol'>·<span style='font:7.0pt "Times New Roman"'>
</span></span>Contour change by Fourier Descriptor – <b>“Fourier” </b>button.
An example:</p>
<p class=MsoListParagraphCxSpMiddle><img border=0 width=109 height=109
id="Picture 18"
src="Medical%20Image%20Segmentation%20Synthesis%20(MISS)%20Tool%20User%20Guide_files/image017.jpg"> <span
style='font-family:Wingdings'>à</span> <img border=0 width=110 height=109
id="Picture 16"
src="Medical%20Image%20Segmentation%20Synthesis%20(MISS)%20Tool%20User%20Guide_files/image018.jpg"></p>
<p class=MsoListParagraphCxSpMiddle> </p>
<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in'><span
style='font-family:Symbol'>·<span style='font:7.0pt "Times New Roman"'>
</span></span>Affine transformation – <b>“Affine” </b>button. An example:</p>
<p class=MsoListParagraphCxSpMiddle><img border=0 width=109 height=109
id="Picture 19"
src="Medical%20Image%20Segmentation%20Synthesis%20(MISS)%20Tool%20User%20Guide_files/image017.jpg"> <span
style='font-family:Wingdings'>à</span> <img border=0 width=109 height=109
id="Picture 17"
src="Medical%20Image%20Segmentation%20Synthesis%20(MISS)%20Tool%20User%20Guide_files/image019.jpg"></p>
<p class=MsoListParagraphCxSpLast> </p>
<p class=MsoNormal>Each method has several parameters for the user to tune in
order to generate different synthetic segmentations. For more details of these
methods, please see in the “<a href="#_Functions_for_segmentation">Functions of
segmentation synthesis</a>” section.</p>
<h4><a name="_Toc174976517"></a><a name="_Add_spiculations"></a>Add spiculations</h4>
<p class=MsoNormal><img border=0 width=358 height=238 id="Picture 6"
src="Medical%20Image%20Segmentation%20Synthesis%20(MISS)%20Tool%20User%20Guide_files/image020.png"></p>
<p class=MsoNormal><b><u><span style='color:#0070C0'>Parameters</span></u></b></p>
<p class=MsoListParagraphCxSpFirst style='text-indent:-.25in'><a
name="_Hlk155529742"><span style='font-family:Symbol'>·<span style='font:7.0pt "Times New Roman"'>
</span></span><b>Angle</b>: angular location to put the spiculation, it is an
angle value ranging from 0 to 359 degree.</a></p>
<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in'><span
style='font-family:Symbol'>·<span style='font:7.0pt "Times New Roman"'>
</span></span><b>Height</b>:<b> </b>the height of the spiculation, in terms of the
number of pixels.</p>
<p class=MsoListParagraphCxSpLast style='text-indent:-.25in'><span
style='font-family:Symbol'>·<span style='font:7.0pt "Times New Roman"'>
</span></span><b>Width</b>: the width of the spiculation, in terms of the
number of pixels.</p>
<p class=MsoNormal style='margin-left:.25in'>For technical details of these
parameters, please see in the “<b><i>2.3 Spiculations</i></b>” section of the
paper: </p>
<p class=MsoNormal style='margin-left:.25in'><span style='font-size:10.0pt;
line-height:107%;font-family:"Arial",sans-serif;color:#222222;background:white'>Guan,
S., Samala, R. K., Arab, A., & Chen, W. (2023, April). MISS-tool: medical
image segmentation synthesis tool to emulate segmentation errors. In <i>Medical
Imaging 2023: Computer-Aided Diagnosis</i> (Vol. 12465, pp. 273-281).
SPIE. </span><a href="https://doi.org/10.1117/12.2653650"><span
style='font-size:10.0pt;line-height:107%;font-family:"Arial",sans-serif;
background:white'>https://doi.org/10.1117/12.2653650</span></a><span
style='font-size:10.0pt;line-height:107%;font-family:"Arial",sans-serif;
color:#222222;background:white'> </span></p>
<p class=MsoNormal><b><u><span style='color:#0070C0'>Operations (note these
apply to the other </span></u></b></p>
<p class=MsoListParagraphCxSpFirst style='text-indent:-.25in'><span
style='font-family:Symbol'>·<span style='font:7.0pt "Times New Roman"'>
</span></span><b>Close</b>: close the window.</p>
<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in'><span
style='font-family:Symbol'>·<span style='font:7.0pt "Times New Roman"'>
</span></span><b>Apply to original</b>: add the spiculation to the input mask.
This operation will reset the mask that has been modified by other methods
before adding a spiculation.</p>
<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in'><span
style='font-family:Symbol'>·<span style='font:7.0pt "Times New Roman"'>
</span></span><b>Apply to current</b>: add the spiculation to the current mask.
This operation is to add a spiculation to a mask that has been modified by
other methods (or to add multiple spiculations to a mask). </p>
<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in'><span
style='font-family:Symbol'>·<span style='font:7.0pt "Times New Roman"'>
</span></span><b>Add params to Batch Processing</b>: send and add all
parameters of this modification to the Batch Processing window. For more
details, please see in the “<a href="#_Batch_Processing">Batch Processing</a>”
section.</p>
<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in'><span
style='font-family:Symbol'>·<span style='font:7.0pt "Times New Roman"'>
</span></span><b>Undo once</b>: This operation will undo the last modification
and recover the previous mask. When multiple changes have been applied, this operation
can only undo the last change. </p>
<p class=MsoListParagraphCxSpLast><span style='font-family:Consolas;color:#C00000'>Note:
changes by all the three Synthesis methods are counted, i.e., after the “undo
once” in one Synthesis Tool window, the “undo once” function in other Synthesis
Tool windows will not work anymore before the next modification is executed.</span></p>
<p class=MsoNormal>After clicking the “Apply to original” or “Apply to current”,
the result will show on the Segmentation Viewer. Here we show an example of:</p>
<table class=MsoTableGrid border=0 cellspacing=0 cellpadding=0
style='border-collapse:collapse;border:none'>
<tr>
<td width=312 valign=top style='width:233.75pt;padding:0in 5.4pt 0in 5.4pt'>
<p class=MsoNormal style='margin-bottom:0in;line-height:200%'><b>Angle</b>:
270 (degree)</p>
<p class=MsoNormal style='margin-bottom:0in;line-height:200%'><b>Height</b>:
20 (pixels)</p>
<p class=MsoNormal style='margin-bottom:0in;line-height:200%'><b>Width</b>: 6
(pixels)</p>
<p class=MsoNormal style='margin-bottom:0in;line-height:200%'><b>Apply to
original.</b></p>
</td>
<td width=312 style='width:233.75pt;padding:0in 5.4pt 0in 5.4pt'>
<p class=MsoNormal align=center style='margin-bottom:0in;text-align:center;
line-height:normal'><img border=0 width=109 height=109 id="Picture 22"
src="Medical%20Image%20Segmentation%20Synthesis%20(MISS)%20Tool%20User%20Guide_files/image021.jpg">
<span style='font-family:Wingdings'>à</span> <img border=0 width=109
height=109 id="Picture 21"
src="Medical%20Image%20Segmentation%20Synthesis%20(MISS)%20Tool%20User%20Guide_files/image022.jpg"></p>
</td>
</tr>
</table>
<h4><a name="_Toc174976518"></a><a name="_Change_contour_by"></a>Change contour
by Fourier Descriptor</h4>
<p class=MsoNormal><img border=0 width=405 height=233 id="Picture 7"
src="Medical%20Image%20Segmentation%20Synthesis%20(MISS)%20Tool%20User%20Guide_files/image023.png"></p>
<p class=MsoNormal> </p>
<p class=MsoNormal><b><u><span style='color:#0070C0'>Parameters</span></u></b></p>
<p class=MsoListParagraphCxSpFirst style='text-indent:-.25in'><a
name="_Hlk155548020"><span style='font-family:Symbol'>·<span style='font:7.0pt "Times New Roman"'>
</span></span><b>Detail</b>: the<b> </b>number of<b> lower-frequency </b>Fourier
Descriptors to be kept (FDs beyond this will be set to zero); the larger value
for this parameter the more detail of the contour (high-frequency components)
will be kept; ranging from 1 to the “<b>Total #</b>”, which is the total number
of Fourier Descriptors for this contour.</a></p>
<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in'><span
style='font-family:Symbol'>·<span style='font:7.0pt "Times New Roman"'>
</span></span><b>Range</b>:<b> </b>the<b> </b>number of<b> </b>Fourier
Descriptors to be modified; ranging from 0 to (<i>Detail value</i> – 1); the
larger value for this parameter the greater change is applied to the contour.</p>
<p class=MsoListParagraphCxSpLast style='text-indent:-.25in'><span
style='font-family:Symbol'>·<span style='font:7.0pt "Times New Roman"'>
</span></span><b>Magnitude</b>: the magnitude of modification to the Fourier
Descriptors to be made according to the <i>Range</i>; the larger value for this
parameter the greater change is applied to the contour.</p>
<p class=MsoNormal style='margin-left:.25in'>For technical details of these
parameters, please see in the “<b><i>2.4 Fourier Descriptor</i></b>” section of
the paper: </p>
<p class=MsoNormal style='margin-left:.25in'><span style='font-size:10.0pt;
line-height:107%;font-family:"Arial",sans-serif;color:#222222;background:white'>Guan,
S., Samala, R. K., Arab, A., & Chen, W. (2023, April). MISS-tool: medical
image segmentation synthesis tool to emulate segmentation errors. In <i>Medical
Imaging 2023: Computer-Aided Diagnosis</i> (Vol. 12465, pp. 273-281).
SPIE. </span><a href="https://doi.org/10.1117/12.2653650"><span
style='font-size:10.0pt;line-height:107%;font-family:"Arial",sans-serif;
background:white'>https://doi.org/10.1117/12.2653650</span></a><span
style='font-size:10.0pt;line-height:107%;font-family:"Arial",sans-serif;
color:#222222;background:white'> </span></p>
<p class=MsoNormal>After clicking the “Apply to original” or “Apply to current”,
the result will show on the Segmentation Viewer. Here is an example:</p>
<table class=MsoTableGrid border=0 cellspacing=0 cellpadding=0
style='border-collapse:collapse;border:none'>
<tr>
<td width=312 valign=top style='width:233.75pt;padding:0in 5.4pt 0in 5.4pt'>
<p class=MsoNormal style='margin-bottom:0in;line-height:200%'><b>Detail</b>:
20</p>
<p class=MsoNormal style='margin-bottom:0in;line-height:200%'><b>Range</b>: 12</p>
<p class=MsoNormal style='margin-bottom:0in;line-height:200%'><b>Magnitude</b>:
6</p>
<p class=MsoNormal style='margin-bottom:0in;line-height:200%'><b>Apply to
original.</b></p>
</td>
<td width=312 style='width:233.75pt;padding:0in 5.4pt 0in 5.4pt'>
<p class=MsoNormal align=center style='margin-bottom:0in;text-align:center;
line-height:normal'><img border=0 width=109 height=109 id="Picture 24"
src="Medical%20Image%20Segmentation%20Synthesis%20(MISS)%20Tool%20User%20Guide_files/image024.png">
<span style='font-family:Wingdings'>à</span> <img border=0 width=111
height=111 id="Picture 11"
src="Medical%20Image%20Segmentation%20Synthesis%20(MISS)%20Tool%20User%20Guide_files/image025.jpg"></p>
</td>
</tr>
</table>
<h4><a name="_Toc174976519"></a><a name="_Affine_transformation"></a>Affine transformation</h4>
<p class=MsoNormal><img border=0 width=334 height=206 id="Picture 8"
src="Medical%20Image%20Segmentation%20Synthesis%20(MISS)%20Tool%20User%20Guide_files/image026.png"></p>
<p class=MsoNormal><b><u><span style='color:#0070C0'>Parameters</span></u></b></p>
<p class=MsoListParagraphCxSpFirst style='text-indent:-.25in'><a
name="_Hlk155550261"><span style='font-family:Symbol'>·<span style='font:7.0pt "Times New Roman"'>
</span></span><b>Resize</b>: the ratio of size change on x-axis (vertical) and
y-axis (horizontal). Here we show an example for x = 1.5, y=2 applying to
original mask, without other changes:</a></p>
<p class=MsoListParagraphCxSpMiddle><img border=0 width=109 height=109
id="Picture 26"
src="Medical%20Image%20Segmentation%20Synthesis%20(MISS)%20Tool%20User%20Guide_files/image027.jpg"><b> </b><span
style='font-family:Wingdings'>à</span> <img border=0 width=109 height=110
id="Picture 29"
src="Medical%20Image%20Segmentation%20Synthesis%20(MISS)%20Tool%20User%20Guide_files/image028.jpg"></p>
<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in'><span
style='font-family:Symbol'>·<span style='font:7.0pt "Times New Roman"'>
</span></span><b>Rotation</b>:<b> </b>the degree of<b> counter-clockwise </b>rotation
around the center. Here is an example for rotation of90 degrees:</p>
<p class=MsoListParagraphCxSpMiddle><img border=0 width=109 height=109
id="Picture 27"
src="Medical%20Image%20Segmentation%20Synthesis%20(MISS)%20Tool%20User%20Guide_files/image029.jpg"><b> </b><span
style='font-family:Wingdings'>à</span> <img border=0 width=110 height=110
id="Picture 30"
src="Medical%20Image%20Segmentation%20Synthesis%20(MISS)%20Tool%20User%20Guide_files/image030.jpg"></p>
<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in'><span
style='font-family:Symbol'>·<span style='font:7.0pt "Times New Roman"'>
</span></span><b>translation</b>: in terms of the number of pixels. Here is an
example:</p>
<p class=MsoListParagraphCxSpLast><img border=0 width=109 height=109
id="Picture 28"
src="Medical%20Image%20Segmentation%20Synthesis%20(MISS)%20Tool%20User%20Guide_files/image027.jpg"><b> </b><span
style='font-family:Wingdings'>à</span> <img border=0 width=110 height=110
id="Picture 31"
src="Medical%20Image%20Segmentation%20Synthesis%20(MISS)%20Tool%20User%20Guide_files/image031.jpg"></p>
<p class=MsoNormal style='margin-left:.25in'>For technical details of these
parameters, please see in the “<b><i>2.1 Affine Transformation</i></b>” section
of the paper: </p>
<p class=MsoNormal style='margin-left:.25in'><span style='font-size:10.0pt;
line-height:107%;font-family:"Arial",sans-serif;color:#222222;background:white'>Guan,
S., Samala, R. K., Arab, A., & Chen, W. (2023, April). MISS-tool: medical
image segmentation synthesis tool to emulate segmentation errors. In <i>Medical
Imaging 2023: Computer-Aided Diagnosis</i> (Vol. 12465, pp. 273-281).
SPIE. </span><a href="https://doi.org/10.1117/12.2653650"><span
style='font-size:10.0pt;line-height:107%;font-family:"Arial",sans-serif;
background:white'>https://doi.org/10.1117/12.2653650</span></a><span
style='font-size:10.0pt;line-height:107%;font-family:"Arial",sans-serif;
color:#222222;background:white'> </span></p>
<h3><a name="_Toc174976520">Results Output</a></h3>
<p class=MsoNormal>After all changes have been applied to the mask, by clicking
the “<b>Save syn mask & metrics values</b>” button, two files will be
created: 1) the modified mask will be saved in a <b><i>PNG</i></b> file
specified by the user, 2) and results of 24 segmentation metrics between the
input truth mask and synthetic masks will be saved in a <b><i>CSV</i></b> file
with a name <i>PNG file name_Metrics.csv</i>. The values of 24 metrics also
auto-save in the “Workspace” of MATLAB, it is a MATLAB <i>struct</i> value
named “<b>metrics_value</b>”.</p>
<h3><a name="_Toc174976521"></a><a name="_Batch_Processing"></a>Batch
Processing</h3>
<p class=MsoNormal> “<b>Batch Processing</b>” button allows you to apply
several modifications, including Fourier Descriptor (<b>FD</b>), Spiculation (<b>SP</b>),
and Affine transformation (<b>AF</b>), to one or many masks all at once. </p>
<p class=MsoNormal><img border=0 width=618 height=446 id="Picture 12"
src="Medical%20Image%20Segmentation%20Synthesis%20(MISS)%20Tool%20User%20Guide_files/image032.png"></p>
<p class=MsoNormal><span style='font-family:Consolas;color:#C00000'>Note: 1) To
apply functions in the “Batch Processing” window, a truth mask must have been
loaded from the main “Segmentation Viewer” window. 2) To click the “Return to
main window” button in main “Segmentation Viewer” window, the “Batch Processing”
window must be closed. 3) The modifications plan (MOD) will be deleted once the
“Batch Processing” window is closed. To keep it, please click “Save to MOD file”.</span></p>
<h4><a name="_Toc174976522"></a><a name="_Parameters"></a>Parameters</h4>
<p class=MsoNormal>The parameters are grouped by the three types of modifications
to masks, as shown in the “Synthesis Tools” before. To look at the details of the
parameters for each type of modifications, please use their links: <a
name="_Hlk171428579"></a><a href="#_Change_contour_by">Fourier Descriptor (FD)</a>,
<a href="#_Add_spiculations">Spiculation (SP)</a>, and <a
href="#_Affine_transformation">Affine transformation (AF)</a>.</p>
<p class=MsoNormal><span style='font-family:Consolas;color:#0070C0'>The
parameters: <a name="_Hlk172725797"><b>Detail</b> and <b>Range</b> for Fourier