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<p><h3>Getting Started</h3></p>
<li><a href="#intro">Introduction</a>
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<li><a href="#intro_pipeline">Modeling Pipeline</a></li>
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<a href="https://simtk.org/frs/download_confirm.php/latestzip/2256/SimVascularTutorialProject-latest.zip?group_id=930">Tutorial</a>
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<div class="manQuickGuide"><section id="getting_started" class="group"><h1>Getting Started</h1>
<p>This document provides beginning users with the basic knowledge needed to get started using the SimVascular suite of software
applications. The SimVascular software suite comprises the following applications</p>
<ul style="list-style-type:none;">
<li> <b> SimVascular </b> - Interactive image-based modeling pipeline application </li>
<li> <b> svZeroDSolver </b> - 0D (lumped parameter) solver </li>
<li> <b> svOneDSolver </b> - 1D fluids solver </li>
<li> <b> svSolver </b> - Computational fluid dynamics (CFD) solver </li>
<li> <b> svFSI </b> - Coupled fluid-solid solver </li>
</ul>
<p>Throughout this document the interactive image-based modeling pipeline application is referred to as just SimVascular.
Input files for all of the solver applications can be created and optionally executed from the SimVascular GUI.</p>
<p>The <a href="#introduction"> Introduction </a> section describes important SimVascular concepts.
The following <a href="#gui"> GUI </a> section then describes the SimVascular graphical user interface (GUI) and its basic functionality.
The <a href="#tutorial"> Tutorial</a> section demonstrates the steps in the SimVascular image-based modeling pipeline,
from medical image data segmentation to patient-specific blood flow simulation. A model of an aorta and two iliac
arteries is created from medical imaging data. A finite element mesh is then generated from the model and used in a
CFD simulation of blood flow in the aorta and iliac arteries. </p>
<p>Another useful resource for learning how to use SimVascular are the
<a href="https://www.youtube.com/playlist?list=PL1CBZ8Wh-xvSKUsuBA4MM4Jba-psVdxXT">SimVascular Online Tutorials</a>. This series
of recent videos demonstrate all the steps in the modeling pipeline presented in the <a href="#tutorial"> Tutorial</a> below. </p>
<p>Images taken of the
<a href="https://simtk.org/frs/download_confirm.php/file/5113/DemoProject.zip?group_id=930"> Demo Project </a>
are used to illustrate certain concepts throughout this document.</p>
</section>
<section id="intro" class="group"><h1 href="#introduction"> Introduction </h1>
<p>SimVascular is an interactive application used to created patient-specific geometric models of human vasculature from 3D medical
imaging data acquired for a specific anatomical region. These models are then used as the basis for blood flow simulations using
various numerical methods. The sequence of steps used by SimVascular to do this is called the <i>image-based modeling pipeline</i>. </p>
<p>The SimVascular graphical user interface (GUI) is used to interactively manage each step in the image-based modeling pipeline.
The <a href="#gui"> GUI </a> provides different graphical controls (e.g. buttons) used to input the data required to generate
the output (e.g. geometric model) of each step. The display of image and geometrical data in a graphics window can be interactively
controlled using the mouse. Information from image and geometrical data can also be queried using the mouse and allows selecting,
for example, a point in 3D space</p>
</section>
<section id="intro_pipeline" class="group"><h2>Modeling Pipeline</h2>
<p>The SimVascular image-based modeling pipeline comprises the following steps </p>
<ol>
<li> <b>Image visualization</b> - Identify anatomic features in the imaging data </li>
<li> <b>Path planning</b> - Vessel centerlines geometry is created using 2D image slices to identify vessel lumens </li>
<li> <b>Segmentation</b> - Vessel lumens are segmented from 2D slice probes of 3D image data oriented perpendicular to positions along paths</li>
<li> <b>Modeling</b> - A geometric model of a vessel is created by generating a surface fitted to groups of 2D segmentations. Individual
vessels are then joined together to form a complete 3D solid model of vascular anatomy. </li>
<li> <b>Meshing</b> - A finite element mesh is generated from the 3D solid model </li>
<li> <b>Simulation</b> - Perform a finite element computational fluid dynamics (CFD) simulation of blood flow in the vascular anatomy</li>
</ol>
<p><br></p>
<p>Each step in the pipeline uses data created by the preceding steps. For example, the <i>Segmentation</i> step uses path geometry created
in the <i>Path planning</i> step to position and orient 2D image slices used to segment a vessel lumen.</p>
<p>A visual representation of the pipeline steps (Fig. 1) provides a sense of the (primarily geometric) data created in each step.
<br> <br></p>
<figure>
<img class="svImg svImgXl" src="documentation/quickguide/images/sv-pipeline.png">
<figcaption class="svCaption">Fig. 1   The SimVascular image-based modeling pipeline</figcaption>
</figure>
</section>
<section id="intro_tools" class="group"><h2 id="intro_tools"> Tools </h2>
<p>The SimVascular application provides a set of core <i>Tools</i> (aka plugins) implementing methods for each step in the
SimVascular image-based modeling pipeline. The follow lists each core <i>Tool</i> type and primary function</p>
<ol>
<li> <b>Paths</b> - Interactively creates paths based on image data
<li> <b>Segmentations</b> - Segments 2D slices along path geometry using various segmentation techniques
<li> <b>Models</b> - Generates surface and solid models from segmentations
<li> <b>Meshes</b> - Generates a finite element mesh from a solid model
<li> <b>Simulations</b> - Performs a CFD simulation
<li> <b>svFSI</b> - Performs a coupled fluid-solid interaction simulation
<li> <b>ROMSimulations</b> - Performs a reduced-order model (ROM) simulation
</ol>
<p>One or more instances of these <i>Tool</i> types are created to implement an image-based modeling pipeline for a particular
application. An instance of a <i>Tool</i> is called a <i>Data Node</i>.</p>
<p><i>Tools</i> typically use data from other tools to perform their functions. For example, the <i>Segmentations Tool</i> uses
paths created by the <i>Paths Tool</i> to position and orient 2D slices in the 3D image volume. The data used by a
<i>Tool</i> is specified by the user.</p>
<p>The geometry created by each <i>Tool</i> is typically stored in <a href="https://vtk.org"> Visualization Toolkit (VTK) </a>
VTP and VTU <a href="https://vtk.org/wp-content/uploads/2015/04/file-formats.pdf"> VTK File Formats </a>.</p>
<p>Each <i>Tool</i> has a panel containing GUI controls (i.e. widgets) used to specify the parameters that control tool behavior.
A <i>Tool</i> panel is displayed using the <a href="#data_manager"> Data Manager </a>.</p>
<p><br>
<h3 id="intro_tools_instances"> Creating Tool Instances</h3>
An instance of a particular <i>Tool</i> type is created using options selected from <a href="#data_manager_menus">Data Manager Menus</a>.
Some <i>Tool</i> instances can be created in two ways based on the source of the data used by the <i>Tool</i> </p>
<ol>
<li> <b>Internal</b> - Data used by the <i>Tool</i> is obtained from another <i>Tool</i>.<br><br>
Example: A <i>Models Tool</i> uses segmentations created by a <i>Segmentations Tool</i>. </li> <br>
<li> <b>External</b> - Data used by the <i>Tool</i> is read in (imported) from a file. The instances of <i>Paths</i>,
<i>Segmentations</i> and <i>Models</i> <i>Tools</i> can be created by reading data from a file. <br><br>
Example: <i>Models Tool</i> geometry is read in from a VTK VTP file.</li>
</ol>
</section>
<section id="intro_projects" class="group"><h2>Projects</h2>
<p>The <i>Tools</i> that comprise a SimVascular pipeline and the data they create are organized as a SimVascular <i>Project</i>.
<i>Tools</i> are added to a <i>Project</i> interactively using the GUI. Multiple instances of most <i>Tools</i> can be
added to a <i>Project</i>. </p>
<p>A SimVascular <i>Project</i> is stored in a directory on disk using the location and name provided by the user when creating a <i>Project</i>.
The <i>Project</i> directory contains sub-directories for each core <i>Tool</i>. Each <i>Tool</i> sub-directory in turn stores data
created by each <i>Tool</i> instance in files named by the instance. The data stored in <i>Tool</i> sub-directories are typically of
two types</p>
<ol>
<li> <b>Geometry Data</b> - The geometry created by the <i>Tool</i> stored in VTK VTP and VTU format files.
<li> <b>GUI State Data</b> - The values of the <i>Tool</i> panel GUI controls stored in an XML format file.
</ol>
<p><br></p>
<p>An example <i>Project</i> directory is shown in Fig. 2. The .msh, .mdl, .pth, .ctgr and .sjb files are XML format files
storing values for all GUI controls.</p>
<figure>
<img class="svImg svImgSm" src="documentation/quickguide/images/project-dir.png">
<figcaption class="svCaption">Fig. 2   An example of a <i>Project</i> directory showing core <i>Tool</i>
<b>Images</b>, <b>Segmentations</b>, <b>Models</b>, <b>Meshes</b>, <b>Simulations</b>, <b>svFSI</b>, and
<b>ROMSimulations</b> sub-directories. The data for each <i>Tool</i> instance (e.g. aorta) are shown under each
<i>Tool</i> sub-directory.
</figcaption>
</figure>
<p>The GUI <i> Data Manager </i> is used to view a <i>Project</i> as a hierarchy of <i>Tools</i> and <i>Data Nodes </i>
representing individual <i>Tool</i> data: images, paths, segmentations, models, meshes, and simulation jobs. The <i> Data Manager </i>
provides an interface to interactively manage adding/removing <i>Tool</i> instances and changing some of the properties used to
display the geometric data created by a <i>Tool</i> (e.g. color). </p>
<p>The <i> Data Manager </i> view of the
<a href="https://simtk.org/frs/download_confirm.php/file/5113/DemoProject.zip?group_id=930"> Demo Project </a>
created following the steps demonstrated in the tutorial section is shown in Fig. 3.</p>
<figure>
<img class="svImg svImgSm" src="documentation/quickguide/gui/images/demo-data-manager.png">
<figcaption class="svCaption">Fig. 3   An example of a <i>Project</i> displayed in the <i>Data Manager</i>.
Instances of <i>Tools</i> added to the <i>Project</i> (e.g. aorta) are shown below the core <b>Images</b>, <b>Paths</b>,
<b>Segmentations</b>, <b>Models</b>, <b>Meshes</b>, <b>Simulations</b>, <b>svFSI</b>, and
<b>ROMSimulations</b> <b>Tool</b> names.
</figcaption>
</figure>
<p>A more complete discussion of the <i> Data Manager </i> is given below.
<br></p>
</section>
<section id="intro_mitk" class="group"><h2>MITK Framework</h2>
<p>The SimVascular application uses the <a href="https://www.mitk.org/"> Medical Imaging Interaction Toolkit (MITK)</a>
framework for medical imaging applications incorporating a plugin architecture. Standard <i>MITK</i> tools have been
incorporated into SimVascular: a graphics display window with three orthographic 2D views and one 3D view,
image file readers (e.g. DICOM), an image navigator tool for displaying 2D image planes, image processing, and volume rendering.</p>
<div style="background-color: #F0F0F0; padding: 10px; border: 1px solid #e6e600; border-left: 6px solid #e6e600">
<i>MITK</i> <i>Tools</i> (e.g. image processing) are not integrated with SimVascular <i>Tools</i>. This means that data created by
<i>MITK</i> <i>Tools</i> is not accessible from SimVascular <i>Tools</i>. <i>MITK</i> <i>Tools</i> are therefore of limited use in
the SimVascular modeling pipeline.
</div>
</section>
<section id="gui_intro" class="group"><h1 id="gui"> Graphical User Interface </h1>
<p>The SimVascular GUI provides an interface for interactively managing the input of data needed for each step in the
image-based modeling pipeline. The GUI provides different graphical controls (aka widgets) used to input data values
and methods to interact with and query image and geometrical data in a graphics window.</p>
<p>The following table lists the controls used by the SimVascular GUI</p>
<table class="table table-bordered" style="width:100%">
<tr>
<th> Control </th>
<th> Description </th>
<th> Example </th>
</tr>
<tr>
<td> Button </td>
<td> A rectangular region that typically displays a text label describing its action.
A button performs an action when pressed (clicked on)</td>
<td><img src="documentation/quickguide/gui/images/gui-button.png" width="100" height="25"> </td>
</tr>
<tr>
<td> CheckBox </td>
<td> A rectangular region that permits the user to make a binary choice, i.e. a choice between one of two possible mutually
exclusive options </td>
<td><img src="documentation/quickguide/gui/images/gui-check-box.png" width="100" height="20"> </td>
</tr>
<tr>
<td> ComboBox </td>
<td> A drop-down list that allows the user to select a value from the list. </td>
<td> <img src="documentation/quickguide/gui/images/gui-combo-box.png" width="100" height="30"> </td>
</tr>
<tr>
<td> DialogBox </td>
<td> A popup window that asks a user for input. </td>
<td> <img src="documentation/quickguide/gui/images/gui-dialog.png" width="150" height="125"> </td>
</tr>
<tr>
<td> FileBrowser </td>
<td> A popup window used to select a file or directory. </td>
<td> <img src="documentation/quickguide/gui/images/gui-file-browser.png" width="345" height="186"> </td>
</tr>
<tr>
<td> Icon </td>
<td> A small graphical representation of a <i>Tool</i> or file. </td>
<td> <img src="documentation/quickguide/gui/images/gui-icon.png" width="50" height="40"> </td>
</tr>
<tr>
<td> InformationPopup </td>
<td> A popup window that provides information to the user. </td>
<td> <img src="documentation/quickguide/gui/images/gui-info-popup.png" width="234" height="134"> </td>
</tr>
<tr>
<td> Menu </td>
<td> A list of choices offered to the user for selection. </td>
<td> <img src="documentation/quickguide/gui/images/gui-menu.png" width="100" height="150"> </td>
</tr>
<tr>
<td> MenuBar </td>
<td> A thin, horizontal bar containing the text labels for a group of menus.
<td> <img src="documentation/quickguide/gui/images/gui-menu-bar.png" width="200" height="20"> </td>
</tr>
<tr>
<td> QuestionPopup </td>
<td> A popup window that asks the user to respond to a yes/no question. </td>
<td> <img src="documentation/quickguide/gui/images/gui-quest-popup.png" width="234" height="134"> </td>
</tr>
<tr>
<td> Slider </td>
<td> A horizontal bar used to set a value by moving an indicator on the bar horizontally.
Values can also be entered in the text box. </td>
<td> <img src="documentation/quickguide/gui/images/gui-slider.png" width="400" height="25"> </td>
</tr>
<tr>
<td> SpinBox </td>
<td> A rectangular region used to choose a value by clicking the up/down buttons or pressing up/down on the keyboard
to increase/decrease the value currently displayed.
<td> <img src="documentation/quickguide/gui/images/gui-spin-box.png" width="200" height="25"> </td>
</tr>
<tr>
<td> Table </td>
<td> A rectangular region that arranges data (e.g. text or other widgets) into rows and columns of cells.
Data can be modified by selecting a cell in the table. </td>
<td> <img src="documentation/quickguide/gui/images/gui-table.png" width="300" height="200"> </td>
</tr>
<tr>
<td> TextBox </td>
<td> A rectangular region used to entry string, integer or float values. </td>
<td> <img src="documentation/quickguide/gui/images/gui-text-box.png" width="130" height="24"> </td>
</tr>
<tr>
<td> ToolBar </td>
<td> A row of buttons at the top of window that controls software functions. </td>
<td> <img src="documentation/quickguide/gui/images/gui-tool-bar.png" width="250" height="20"> </td>
</tr>
<tr>
<td> ToolBox </td>
<td> An area of a <i>Tool</i> panel that contains multiple pages of GUI widgets identified by a section
of rectangles with text at the Toolbox bottom. <br> Selecting a rectangle shows another page. </td>
<td> <img src="documentation/quickguide/gui/images/gui-tool-box.png" width="200" height="300"> </td>
</tr>
</table>
<p><br> <br></p>
<p>The SimVascular main window GUI is composed of a <em>MenuBar</em>, <em>ToolBar</em>, <em>Data Manager</em>, <em>Image Navigator</em> and <em>Display</em>.
An additional <em>Tool Panel</em> is displayed on the right side of the window when a <i>Tool</i> is active.</p>
<figure>
<img class="svImg svImgLg" src="documentation/quickguide/gui/images/mainwindow.png">
<figcaption class="svCaption">Fig. 4   The SimVascular GUI layout</figcaption>
</figure>
<p><br></p>
<div style="background-color: #F0F0F0; padding: 10px; border: 1px solid #d0d0d0; border-left: 6px solid #d0d0d0">
The SimVascular GUI may look slightly different on MacOS, Ubuntu and Windows platforms.
</div>
<p><br> <br></p>
</section>
<section id="menubar" class="group"><h2 id="gui_menubar"> MenuBar </h2>
<p>The <i>MenuBar</i> contains <em>File</em>, <em>Edit</em>, <em>Tools</em>, <em>Window</em> and <em>Help</em> menu items. </p>
<figure>
<img class="svImg svImgMd" src="documentation/quickguide/gui/images/menus.png">
<figcaption class="svCaption" ></figcaption>
</figure>
<h3 id="gui_menubar_file"> File Menu </h3>
<p>The <em>File</em> menu is used to create, open and save SimVascular <em>Projects</em>. Creating or opening a <em>Project</em> is typically the first
step when using SimVascular.</p>
<div style="background-color: #F0F0F0; padding: 10px; border: 1px solid #e6e600; border-left: 6px solid #e6e600">
It is not recommended to use the <i>Open File</i> menu item because it is used to read files (e.g. image files) outside of
a SimVascular <i>Project</i>. The data read in from the file can therefore not be used by any SimVascular tools (e.g. Segmentations).
</div>
<p><br></p>
<h3 id="gui_menubar_tools"> Tools Menu </h3>
<p>The <em>Tools</em> menu is used to add a SimVascular <i>Tool</i> to the <i>Tool Panel</i>. It This does not add a new <i>Tool</i>
to the <i>Project</i>. The <i>Level Set</i> menu item creates a level set segmentation <i>Tool</i>
(see <a href="http://simvascular.github.io/docsModelGuide.html#modeling3DSeg"> 3D Level Set Segmentation </a>).
The <i>Python Console</i> menu item opens a panel used to execute Python scripts.
(see <a href="http://simvascular.github.io/docsPythonInterface.html#console"> Python Console </a>).
The other menu items are mostly MITK tools that are typically not often used. </p>
</section>
<section id="toolbar" class="group"><h2 id="gui_toolbar"> ToolBar </h2>
<p>The <i>ToolBar</i> is composed of three sections. The first section contains icons used to save a <i>Project</i>, undo an operation, hide/show
the <i>Image Navigator</i> and toggle the <b>A</b>xial, <b>S</b>agittal and <b>C</b>oronal image scan slices.</p>
<figure>
<img class="svImg svImgMd" src="documentation/quickguide/gui/images/toolbar-1.png">
<figcaption class="svCaption">The first ToolBar section </figcaption>
</figure>
<table class="table table-bordered" style="width:100%">
<tr>
<th> Icon </th>
<th> Description </th>
</tr>
<tr>
<td> <img src="documentation/quickguide/gui/images/gui-save-icon.png" width="40" height="35"> </td>
<td> Save the Project. </td>
</tr>
<tr>
<td> <img src="documentation/quickguide/gui/images/gui-undo-icon.png" width="75" height="32"> </td>
<td> Undo an operation. </td>
</tr>
<tr>
<td> <img src="documentation/quickguide/gui/images/gui-img-nav-icon.png" width="45" height="40"> </td>
<td> Hide/show the <i>Image Navigator</i>. </td>
</tr>
<tr>
<td> <img src="documentation/quickguide/gui/images/gui-a-plane-icon.png" width="40" height="40"> </td>
<td> Hide/show the axial image scan slice. </td>
</tr>
<tr>
<td> <img src="documentation/quickguide/gui/images/gui-s-plane-icon.png" width="40" height="40"> </td>
<td> Hide/show the sagittal image scan slice. </td>
</tr>
<tr>
<td> <img src="documentation/quickguide/gui/images/gui-c-plane-icon.png" width="40" height="40"> </td>
<td> Hide/show the coronal image scan slice. </td>
</tr>
</table>
<div style="background-color: #F0F0F0; padding: 10px; border: 1px solid #e6e600; border-left: 6px solid #e6e600">
SimVascular does not automatically save data created by a <i>Tool</i> to the <i>Project</i>. If a <i>Project</i> is closed without
being saved all newly added data will be lost.
</div>
<p><br></p>
<p>The second section duplicates the <em>Tools</em> menu using icons. </p>
<figure>
<img class="svImg svImgMd" src="documentation/quickguide/gui/images/toolbar-2.png">
<figcaption class="svCaption"> The second ToolBar section</figcaption>
</figure>
<p>The third second section duplicates the <em>Tools</em> menu using icons. </p>
<figure>
<img class="svImg svImgMd" src="documentation/quickguide/gui/images/toolbar-3.png">
<figcaption class="svCaption"> The third ToolBar section</figcaption>
</figure>
</section>
<section id="gui_display" class="group"><h2 id="display"> Display </h2>
<p>The GUI main window <i>Display</i> area uses a four-window view to display 2D and 3D views of image and geometry data as
the standard layout. The four-window view provides an interactive environment to view geometry data created by <i>Tools</i> in
context with medical image data. This enables matching geometric data (e.g. models) to anatomical features present in the imaging data.</p>
<p>The layout of the <i>Display</i> windows and its GUI components are shown in Fig. 5.</p>
<figure>
<img class="svImg svImgMd" src="documentation/quickguide/imgs/display.png">
<figcaption class="svCaption"> Fig. 5   The standard four-window view comprising three 2D and one 3D views.
</figure>
<p>The three 2D views represent the principal planes used in medical imaging to describe the location of anatomical
structures defined as </p>
<ul style="list-style-type:none;">
<li> <b>axial</b> - Divides the body into top and bottom sections. Upper left 2D window. </li>
<li> <b>coronal</b> - Divides the body into back and front, or posterior and anterior, sections. Upper right 2D window. </li>
<li> <b>sagittal</b> - Divides the body into left and right sections. Lower left 2D window. </li>
</ul>
<p><br></p>
<h3 id="navigation"> Navigation </h3>
<p>The principal planes slice is represented by a pair of crosshairs the 2D view windows. Selecting a point with the left
mouse button in a 2D view centers the crosshair on that point. Pressing the right mouse button and moving the mouse zooms
in and out. Scrolling the mouse wheel changes the principal plane slice for which the mouse cursor is in. </p>
<p>Changing the principal planes slice changes the values displayed in the <a href="#image_navigator"> Image Navigator </a>
and vice versa.</p>
<p>The function of the mouse buttons depends on the window the mouse cursor is in.</p>
<table class="table table-bordered" style="width:100%">
<caption> <b> 2D View </b> </caption>
<tr>
<th> Mouse Button </th>
<th> Function </th>
</tr>
<tr>
<td> Left </td>
<td> Moves the crosshairs, select image points and pixel values </td>
</tr>
<tr>
<td> Right </td>
<td> Zooms the 2D view
</tr>
<tr>
<td> Mouse Wheel Scrolling </td>
<td> Changes the principal plane slice
</tr>
</table>
<table class="table table-bordered" style="width:100%">
<caption> <b> 3D View </b> </caption>
<tr>
<th> Mouse Button </th>
<th> Function </th>
</tr>
<tr>
<td> Left </td>
<td> Rotates the 3D view </td>
</tr>
<tr>
<td> Right </td>
<td> Zooms the 3D view
</tr>
<tr>
<td> Shift-left </td>
<td> Translates the 3D view
</tr>
</table>
<div style="background-color: #F0F0F0; padding: 10px; border: 1px solid #d0d0d0; border-left: 6px solid #d0d0d0">
Pressing the <b>F</b> key in the 3D view changes the center of rotation and zoom to be the point under
the mouse cursor.
</div>
<p><br>
<h3 id="window_menus"> Window Menus</h3></p>
<p>The three icons
<img src="documentation/quickguide/gui/images/display_icon_menu.png" width="70" height="30"> </td> displayed in the upper right
corner each window provides options to customize the view and crosshair behavior when selected using the left mouse button. </p>
<table class="table table-bordered" style="width:100%">
<tr>
<th> Icon </th>
<th> Menu or Action </th>
<th> Description </th>
</tr>
<tr>
<td><img src="documentation/quickguide/gui/images/window-icon-1.png" width="28" height="24"> </td>
<td>
<img src="documentation/quickguide/gui/images/window-menu-1.png" width="180" height="180">
</td>
<td>
<ul style="list-style-type:none;">
<li> <b> Reset view </b> - Resets 1) crosshairs to their default position and 2) viewing transformations (e.g. rotations) </li>
<li> <b> Show crosshair </b> - Select to toggle showing crosshairs </li>
<li> <b> No crosshair rotation </b> - Select to toggle using crosshairs to position planes orthogonal to image axes </li>
<li> <b> Crosshair rotation </b> - Select to toggle using crosshairs to rotate two planes </li>
<li> <b> Coupled crosshair rotation </b> - Select to toggle using crosshairs to rotate planes both planes </li>
<li> <b> Swivel mode </b> - Select to toggle using crosshairs to rotate planes in about all three axes </li>
<li> <img src="documentation/quickguide/gui/images/window-ts-slider.png" width="140" height="30">
- The <b>T</b>thicker <b>S</b>slices slider controls how many slices around the current one are used for a maximum intensity projection </li>
</ul>
</td>
</tr>
<tr>
<td><img src="documentation/quickguide/gui/images/window-icon-2.png" width="28" height="24"> </td>
<td> Changes the view layout </td>
<td> The view is changed to a full-screen layout for the window and plane the mouse cursor is in
When selected it changes to <img src="documentation/quickguide/gui/images/window-icon-4.png" width="28" height="24">
</td>
</tr>
<tr>
<td><img src="documentation/quickguide/gui/images/window-icon-4.png" width="28" height="24"> </td>
<td> Changes the view layout </td>
<td> Expands the corresponding window to full screen within the four window view </td>
</tr>
<tr>
<td><img src="documentation/quickguide/gui/images/window-icon-3.png" width="28" height="24"> </td>
<td>
<img src="documentation/quickguide/gui/images/window-menu-2.png" width="180" height="180">
</td>
<td>
<ul style="list-style-type:none;">
<li> <b> standard layout </b> - Resets the display to the four-window view </li>
<li> <b> 2D images top, 3D bottom </b> - Sets the display to all three 2D views on top of the 3D view
<li> <b> 2D images top, 3D right </b> - Sets the display to all 2D and 3D views on top
<li> <b> Big 3D </b> - Sets the display to a single 3D view
<li> <b> Axial plane </b> - Sets the display to a single 2D axial plane view
<li> <b> Sagittal plane </b> - Sets the display to a single 2D sagittal plane view
<li> <b> Coronal plane </b> - Sets the display to a single 2D coronal plane view
<li> <b> Coronal top, 3D bottom </b> - Sets the display to the 2D coronal view on top of the 3D view
<li> <b> Coronal left, 3D right </b> - Sets the display to the 2D coronal view to the left of the 3D view
<li> <b> Sagittal top, Coronal n 3D bottom </b> - Sets the display to the 2D sagittal view on top of the coronal and 3D view
<li> <b> Axial n Sagittal left, 3D right </b> - Sets the display to the 2D axial and sagittal views on top and 3D view right
<li> <b> Axial n 3D left, Sagittal right </b> - Sets the display to the 2D axial and 3D view to the left of the sagittal view
</td>
</tr>
</table>
</section>
<section id="image_windowing" class="group"><p><br>
<h2 id="image_windowing"> Image Windowing </h2></p>
<p>The <i>Image Windowing</i> tool is used to adjust image brightness and contrast using a technique called <i>Windowing</i>,
also known as gray-level mapping, contrast stretching, histogram modification or contrast enhancement.
<i>Windowing</i> manipulates the image greyscale component using image values to change the appearance of the
image to highlight particular structures. The image brightness is adjusted by changing the <i>window center</i>.
The image contrast is adjusted by changing the <i>window width</i>. </p>
<p>A blue region in the <i>Image Windowing</i> tool shows then <i>window center</i> and <i>window width</i>.</p>
<figure>
<img class="svImg svImgXs" src="documentation/quickguide/gui/images/image-window-level-tool.png" style="width:2%">
<figcaption class="svCaption"> The <b>Image Windowing</b> tool. The <b>window width</b> and <b>window center</b> is
represented using a blue region within the tool. The two text boxes at the bottom of the tool show the
<b>window center</b> (upper box) and the <b>window width</b> (lower box).
</figcaption>
</figure>
<p>The <i>window center</i> is changed by selecting the center of the <i>Image Windowing</i> tool blue region with the
left mouse button and moving up or down. </p>
<p>The <i>window width</i> is changed uniformly about the <i>window center</i> by selecting either end of the
<i>Image Windowing</i> tool blue region with the left mouse button and moving up or down. </p>
<p>The <i>window width</i> is changed non-uniformly about the <i>window center</i> by selecting either end of the
<i>Image Windowing</i> tool blue region with using shift-left mouse button and moving up or down. </p>
<table class="table table-bordered" style="width:100%">
<caption> <b> Adjusting image brightness and contrast </b> </caption>
<tr>
<th> Operation </th>
<th> Result </th>
</tr>
<tr>
<td> No operation, original image brightness and contrast </td>
<td> <img src="documentation/quickguide/gui/images/image-window-level-demo-1.png" width="612" height="410"> </td>
</tr>
<tr>
<td> Move the <i>window center</i> up by placing the mouse cursor in the center of the <i>Image Windowing</i> tool
blue region holding the left mouse button down while moving the mouse cursor up </td>
<td> <img src="documentation/quickguide/gui/images/image-window-level-demo-2.png" width="612" height="410"> </td>
</tr>
<tr>
<td> Move the <i>window center</i> down by placing the mouse cursor in the center of the <i>Image Windowing</i> tool
blue region holding the left mouse button down while moving the mouse cursor down
</td>
<td> <img src="documentation/quickguide/gui/images/image-window-level-demo-3.png" width="612" height="410"> </td>
</tr>
<tr>
<td> Reduce the <i>window width</i> uniformly around the <i>window center</i> by placing the mouse cursor in the upper
boundary of the <i>Image Windowing</i> tool blue region holding and mouse button down while moving the mouse cursor down
</td>
<td> <img src="documentation/quickguide/gui/images/image-window-level-demo-4.png" width="612" height="410"> </td>
</tr>
<tr>
<td> Reduce the <i>window width</i> non-informally around the <i>window center</i> by placing the mouse cursor in the upper
boundary of the <i>Image Windowing</i> tool blue region holding and pressing shift-left mouse button down while
moving the mouse cursor down
</td>
<td> <img src="documentation/quickguide/gui/images/image-window-level-demo-5.png" width="612" height="410"> </td>
</tr>
</table>
<p><br></p>
<p>Selecting the <i>Image Window Level</i> tool with the right mouse button pops up the following menu </p>
<figure>
<img class="svImg svImgSm" src="documentation/quickguide/gui/images/image-window-level-menu-1.png">
<figcaption class="svCaption" ></figcaption>
</figure>
<table class="table table-bordered" style="width:100%">
<caption> <b> Image Window Level Tool Menu </b> </caption>
<tr>
<th> Menu Option </th>
<th> Description </th>
</tr>
<tr>
<td> Hide Scale </td>
<td> Hide the <i>Image Windowing</i> tool scale </td>
</tr>
<tr>
<td> Set Slider Fixed </td>
<td> Disables modifying the <i>window width</i> and <i>window center</i>. </td>
</tr>
<tr>
<td> Use whole image grey values </td>
<td> Set the <i>Image Windowing</i> tool use the entire range of image values. </td>
</tr>
<tr>
<td> Use optimized levelwindow </td>
<td> Set the <i>Image Windowing</i> tool to use a range of image values that optimizes contrast and brightness. </td>
</tr>
<tr>
<td> Set Maximum Window </td>
<td> N/A </td>
</tr>
<tr>
<td> Default Level/Window </td>
<td> N/A </td>
</tr>
<tr>
<td> Change Scale Range </td>
<td> Displays a popup window used to manually change the upper and lower <i>window width</i> bounds. </td>
</tr>
<tr>
<td> Default Scale Range </td>
<td> Resets the upper and lower <i>window width</i> bounds to their default values. </td>
</tr>
<tr>
<td> Presets </td>
<td> Displays a menu of preset upper and lower <i>window width</i> bounds for various tissues acquired using CT. </td>
</tr>
<tr>
<td> Images </td>
<td> N/A </td>
</tr>
</table>
</section>
<section id="gui_data_manager" class="group"><h2 id="data_manager"> Data Manager </h2>
<p>The <i> Data Manager </i> is used to view a <i>Project</i> as a hierarchy of <i>Tools</i> and <i>Data Nodes </i>
representing the data created by <i>Tool</i> instances: images, paths, segmentations, models, meshes, and simulation jobs.
Most of the <i>Tools</i> produce geometry that can be interactively viewed in the 2D and 3D views of the
<a href="#display"> Display </a> area of the main window. The <i> Data Manager </i> provides an interface to interactively
manage adding/removing <i>Tool</i> instances and changing some of the properties used to display the geometric data created by a
<i>Tool</i> (e.g. color).</p>
<p>When creating a new <i>Project</i> the <i> Data Manager </i> displays a list of core <i>Tool Types</i> (Fig. 6).</p>
<figure>
<img class="svImg svImgSm" src="documentation/quickguide/gui/images/data-manager-new-project.png">
<figcaption class="svCaption">Fig. 6   The <i>Data Manager</i> of a new <i>Project</i> listing
the core <b>Images</b>, <b>Paths</b>, <b>Segmentations</b>, <b>Models</b>, <b>Meshes</b>, <b>Simulations</b>,
<b>svFSI</b>, and <b>ROMSimulations</b> <b>Tool Types</b>.
</figcaption>
</figure>
<p>Adding a new <i>Tool</i> to the <i>Project</i> creates a new <i>Data Node </i> under the appropriate <i>Tool Type</i>.
The <i> Data Manager </i> view of the
<a href="https://simtk.org/frs/download_confirm.php/file/5113/DemoProject.zip?group_id=930"> Demo Project </a>
created following the steps demonstrated in the <a href="#tutorial"> Tutorial</a> section is shown in Fig. 7.</p>
<figure>
<img class="svImg svImgSm" src="documentation/quickguide/gui/images/demo-data-manager.png">
<figcaption class="svCaption">Fig. 7   An example of a <i>Project</i> displayed in the <i>Data Manager</i>.
Instances of <i>Tools</i> added to the <i>Project</i> (e.g. <b>aorta</b>) are shown below the core <b>Images</b>, <b>Paths</b>,
<b>Segmentations</b>, <b>Models</b>, <b>Meshes</b>, <b>Simulations</b>, <b>svFSI</b>, and
<b>ROMSimulations</b> <b>Tool Types</b>.
</figcaption>
</figure>
<p>The <i> Data Manager </i> hierarchy shown in Fig 7. indicates that the following <i>Tool</i> instances are defined for the
<i>Project</i> as one or more <i>Data Nodes</i></p>
<ul style="list-style-type:none;">
<li> <b>Images</b> - A single <i>Tool</i> instance named <b>sample_data-cm</b>
<li> <b>Paths</b> - Two <i>Tool</i> instances named <b>aorta</b> and <b>right_iliac</b>.
<li> <b>Segmentations</b> - Two <i>Tool</i> instances named <b>aorta</b> and <b>right_iliac</b>
<li> <b>Models</b> - A single <i>Tool</i> instance named <b>demo</b>
<li> <b>Meshes</b> - A single <i>Tool</i> named <b>demomesh</b>
<li> <b>Simulations</b> - A single <i>Tool</i> instance named <b>demojob</b>
</ul>
<p><br></p>
<h3 id="data_manager_interaction"> Interacting with the Data Manager </h3>
<p>Interaction with the <i> Data Manager </i> is performed using the mouse. The resulting action depends on if a
<i>Tool Type</i> or a <i>Data Nodes</i> is selected. The mouse buttons have the following functions </p>
<table class="table table-bordered" style="width:100%">
<caption> <b> Data Manager mouse button function </b> </caption>
<tr>
<th> Mouse Button </th>
<th> Function </th>
</tr>
<tr>
<td> Left </td>
<td> Used to select GUI controls to manage <i>Tool</i> data visibility and expand/collapse <i>Tool</i> hierarchy </td>
</tr>
<tr>
<td> Left, double click </td>
<td>
<b> <i>Tool Type</i></b> - Expand/collapse <i>Tool</i> <i>Data Nodes</i> <br><br>
<b> <i>Tool</i> <i>Data Node</i> </b> - Brings up the <i>Tool</i> panel </td>
</td>