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<title>OpenMicroanatomy Handbook</title>
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<body class="article toc2 toc-left">
<div id="header">
<h1>OpenMicroanatomy Handbook</h1>
<div class="details">
<span id="author" class="author">v1.0 draft, 22.9.2023</span><br>
</div>
<div id="toc" class="toc2">
<div id="toctitle">Table of Contents</div>
<ul class="sectlevel1">
<li><a href="#_introduction_to_openmicroanatomy">Introduction to OpenMicroanatomy</a>
<ul class="sectlevel2">
<li><a href="#_what_is_openmicroanatomy">What is OpenMicroanatomy</a></li>
<li><a href="#_hierarchy">Hierarchy</a></li>
</ul>
</li>
<li><a href="#_getting_started">Getting started</a>
<ul class="sectlevel2">
<li><a href="#_feature_comparison">Feature comparison</a></li>
<li><a href="#_prerequisites">Prerequisites</a></li>
<li><a href="#_installing_qupath_edu_extension">Installing QuPath Edu Extension</a></li>
</ul>
</li>
<li><a href="#_qupath_edu_extension">QuPath Edu Extension</a>
<ul class="sectlevel2">
<li><a href="#_connecting_authenticating">Connecting & authenticating</a>
<ul class="sectlevel3">
<li><a href="#_first_time_setup">First time setup</a></li>
<li><a href="#_logging_in">Logging in</a></li>
<li><a href="#_password_recovery">Password recovery</a></li>
</ul>
</li>
<li><a href="#_creating_content">Creating content</a>
<ul class="sectlevel3">
<li><a href="#_creating_workspaces_courses_and_lessons">Creating workspaces, courses and lessons</a></li>
<li><a href="#_adding_slides_to_a_lesson">Adding slides to a lesson</a></li>
<li><a href="#_making_changes_to_slides">Making changes to slides</a></li>
<li><a href="#_modify_lesson_information">Modify Lesson Information</a></li>
<li><a href="#_creating_slide_tours">Creating slide tours</a></li>
</ul>
</li>
<li><a href="#_administrative_tasks">Administrative tasks</a>
<ul class="sectlevel3">
<li><a href="#_users_roles">Users & Roles</a></li>
<li><a href="#_slides">Slides</a></li>
<li><a href="#_backups">Backups</a></li>
<li><a href="#_organizations">Organizations</a></li>
<li><a href="#_permissions">Permissions</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#_openmicroanatomy_web">OpenMicroanatomy Web</a></li>
<li><a href="#_openmicroanatomy_server">OpenMicroanatomy Server</a>
<ul class="sectlevel2">
<li><a href="#_installation_docker">Installation (Docker)</a>
<ul class="sectlevel4">
<li><a href="#_prerequisites_2">Prerequisites</a></li>
<li><a href="#_installation">Installation</a></li>
<li><a href="#_updating">Updating</a></li>
</ul>
</li>
<li><a href="#_configuration">Configuration</a></li>
<li><a href="#_ssl">SSL</a>
<ul class="sectlevel3">
<li><a href="#_setting_up_ssl_using_caddy_server_with_docker">Setting up SSL using Caddy server with Docker</a></li>
<li><a href="#_reverse_proxy">Reverse proxy</a></li>
</ul>
</li>
<li><a href="#_installation_manually">Installation (Manually)</a>
<ul class="sectlevel4">
<li><a href="#_prerequisites_3">Prerequisites</a></li>
<li><a href="#_installation_2">Installation</a></li>
<li><a href="#_running_the_server">Running the server</a></li>
<li><a href="#_updating_2">Updating</a></li>
<li><a href="#_systemd_service">Systemd service</a></li>
</ul>
</li>
<li><a href="#_troubleshooting">Troubleshooting</a>
<ul class="sectlevel3">
<li><a href="#_fixing_incorrect_slide_paths">Fixing Incorrect Slide Paths</a></li>
</ul>
</li>
<li><a href="#_http_api">HTTP API</a></li>
</ul>
</li>
</ul>
</div>
</div>
<div id="content">
<div id="preamble">
<div class="sectionbody">
<div class="paragraph">
<p><em>This documentation is partly work in progress</em></p>
</div>
</div>
</div>
<div class="sect1">
<h2 id="_introduction_to_openmicroanatomy">Introduction to OpenMicroanatomy</h2>
<div class="sectionbody">
<div class="sect2">
<h3 id="_what_is_openmicroanatomy">What is OpenMicroanatomy</h3>
<div class="paragraph">
<p>OpenMicroanatomy is a project built on top of QuPath which contains three components: <strong>OpenMicroanatomy Server</strong>, <strong>OpenMicroanatomy Web</strong> and <strong>QuPath Edu Extension</strong>.</p>
</div>
<div class="paragraph">
<p><a href="https://github.com/openmicroanatomy/qupath-extension"><strong>QuPath Edu Extension</strong></a> is an extension for <a href="https://qupath.github.io/">QuPath</a>, which allows QuPath projects (called <em>Lessons</em> in QuPath Edu) to be synced between multiple users via an <a href="https://github.com/openmicroanatomy/server"><strong>OpenMicroanatomy Server</strong></a>. The <strong>OpenMicroanatomy Server</strong> handles all the heavy lifting required to authenticate users, upload new slides, manage data and so on. <em>QuPath Edu</em> is also compatible with other data sources, such as <a href="https://github.com/qupath/qupath-extension-omero">Omero</a>.</p>
</div>
<div class="paragraph">
<p>OpenMicroanatomy also includes <a href="https://github.com/openmicroanatomy/web"><strong>OpenMicroanatomy Web</strong></a>, which is a web application that communicates with a <strong>OpenMicroanatomy Server</strong> and can be used for <strong>viewing</strong> projects.</p>
</div>
<div id="img-components" class="imageblock">
<div class="content">
<img src="images/Components.png" alt="Components">
</div>
<div class="title">Figure 1. Visual representation of different OpenMicroanatomy components and how they communicate with each other. Green components are downloaded by the end-user and the blue components are set up by the system administrator. Red are optional third-party features.</div>
</div>
</div>
<div class="sect2">
<h3 id="_hierarchy">Hierarchy</h3>
<div class="paragraph">
<p>A <strong>OpenMicroanatomy Server</strong> is <em>“compartmentalized”</em> as shown in <strong>Figure 2.</strong> Each server can host one or multiple <em>Organizations</em>. Each organization has its own <em>Workspaces</em>, which hold <em>Classes</em>, which contain the <em>Lessons</em>. See <strong>Table 1</strong> for how to think about these.</p>
</div>
<div id="img-hierarchy" class="imageblock">
<div class="content">
<img src="images/Hierarchy.png" alt="Hierarchy">
</div>
<div class="title">Figure 2. A demonstration of the OpenMicroanatomy hierarchy, with a server with three different organizations.</div>
</div>
<table class="tableblock frame-all grid-all stretch">
<caption class="title">Table 1. Translations for different OpenMicroanatomy components</caption>
<colgroup>
<col style="width: 25%;">
<col style="width: 75%;">
</colgroup>
<thead>
<tr>
<th class="tableblock halign-left valign-top">Name</th>
<th class="tableblock halign-left valign-top">Translation</th>
</tr>
</thead>
<tbody>
<tr>
<td class="tableblock halign-left valign-top"><p class="tableblock">Organization</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">Represents a university, school, department, or such – depending on your needs</p></td>
</tr>
<tr>
<td class="tableblock halign-left valign-top"><p class="tableblock">Workspace</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">A course, such as <em>Histology</em> or <em>Pathology</em>.</p></td>
</tr>
<tr>
<td class="tableblock halign-left valign-top"><p class="tableblock">Class</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">A class such as <em>Basic Histology</em> or <em>Advanced Histology</em>.</p></td>
</tr>
<tr>
<td class="tableblock halign-left valign-top"><p class="tableblock">Lesson</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">A lesson within that class, such as <em>Epithelium</em> or <em>Connective tissue</em>.</p></td>
</tr>
</tbody>
</table>
</div>
</div>
</div>
<div class="sect1">
<h2 id="_getting_started">Getting started</h2>
<div class="sectionbody">
<div class="sect2">
<h3 id="_feature_comparison">Feature comparison</h3>
<div class="paragraph">
<p>✅ = supported ❌ = not supported <em>(and currently no plans to implement)</em> 👷♀ = work in progress</p>
</div>
<table class="tableblock frame-all grid-all stretch">
<colgroup>
<col style="width: 33.3333%;">
<col style="width: 33.3333%;">
<col style="width: 33.3334%;">
</colgroup>
<thead>
<tr>
<th class="tableblock halign-left valign-top">Feature</th>
<th class="tableblock halign-left valign-top">Browser / Mobile</th>
<th class="tableblock halign-left valign-top">Desktop app</th>
</tr>
</thead>
<tbody>
<tr>
<td class="tableblock halign-left valign-top"><p class="tableblock">View slides</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">✅</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">✅</p></td>
</tr>
<tr>
<td class="tableblock halign-left valign-top"><p class="tableblock">Slide tours</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">✅️</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">✅</p></td>
</tr>
<tr>
<td class="tableblock halign-left valign-top"><p class="tableblock"><a href="#_creating_content">Creating content</a></p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">❌</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">✅</p></td>
</tr>
<tr>
<td class="tableblock halign-left valign-top"><p class="tableblock"><a href="#_administrative_tasks">Administrative tasks</a></p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">❌</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">✅</p></td>
</tr>
<tr>
<td class="tableblock halign-left valign-top"><p class="tableblock">Authentication</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">👷♀️</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">✅</p></td>
</tr>
</tbody>
</table>
</div>
<div class="sect2">
<h3 id="_prerequisites">Prerequisites</h3>
<div class="paragraph">
<p><strong>QuPath & QuPath Edu Extension</strong></p>
</div>
<div class="ulist">
<ul>
<li>
<p>A 64-bit Windows, macOS or Linux machine, with at least 250 MB of disk space</p>
</li>
</ul>
</div>
<div class="paragraph">
<p><strong>OpenMicroanatomy Web</strong></p>
</div>
<div class="ulist">
<ul>
<li>
<p>None</p>
</li>
</ul>
</div>
<div class="paragraph">
<p><strong>OpenMicroanatomy Server</strong></p>
</div>
<div class="ulist">
<ul>
<li>
<p>See <a href="#_openmicroanatomy_server">OpenMicroanatomy Server</a> chapter.</p>
</li>
</ul>
</div>
</div>
<div class="sect2">
<h3 id="_installing_qupath_edu_extension">Installing QuPath Edu Extension</h3>
<div class="olist arabic">
<ol class="arabic">
<li>
<p>Install <a href="https://qupath.readthedocs.io/en/stable/docs/intro/installation.html">QuPath</a> by following the instructions on the QuPath website</p>
</li>
<li>
<p>Download the <a href="https://github.com/yli-hallila/qupath-edu-extension/releases">QuPath Edu extension</a></p>
</li>
<li>
<p>Install the extension by drag and dropping the downloaded <code>.jar</code> file to the QuPath viewer</p>
</li>
</ol>
</div>
<div class="paragraph">
<p><em>See <a href="https://github.com/qupath/qupath/wiki/Creating-extensions#installing-extensions">here</a> for more detailed instructions on how to install QuPath extensions</em></p>
</div>
</div>
</div>
</div>
<div class="sect1">
<h2 id="_qupath_edu_extension">QuPath Edu Extension</h2>
<div class="sectionbody">
<div class="sect2">
<h3 id="_connecting_authenticating">Connecting & authenticating</h3>
<div class="sect3">
<h4 id="_first_time_setup">First time setup</h4>
<div class="paragraph">
<p>When starting QuPath Edu for the first time, you’ll see the <em>First-time setup</em> dialog. You must either select a <em>public host</em> or enter your <strong>QuPath Edu Servers</strong> address to continue. If you are unsure what your institutions address is, try contacting your IT-services. Public hosts are QuPath Edu Servers which can be freely viewed by anyone. Currently the only public host is the demo server provided by the University of Oulu.</p>
</div>
<div id="img-setup" class="imageblock">
<div class="content">
<img src="images/Setup.png" alt="First Time Setup">
</div>
<div class="title">Figure 3. First-time setup dialog</div>
</div>
<div class="paragraph">
<p>You can change your host later by clicking the <strong>Change host …​</strong> link on the <strong>Login dialog</strong> (see <a href="#img-login">Figure 4</a>) or from the QuPath settings <span class="menuseq"><b class="menu">Edit</b> <b class="caret">›</b> <b class="submenu">Preferences</b> <b class="caret">›</b> <b class="menuitem">Edu</b></span></p>
</div>
</div>
<div class="sect3">
<h4 id="_logging_in">Logging in</h4>
<div class="paragraph">
<p>You can continue either <strong>Continue as a guest</strong> <em>(only read permissions)</em> or authenticate using <strong>Credentials</strong> <em>(regular email & password combination)</em> or a <strong>Microsoft account</strong>.</p>
</div>
<div class="admonitionblock note">
<table>
<tr>
<td class="icon">
<div class="title">Note</div>
</td>
<td class="content">
Logging in using Credentials and/or Microsoft Authentication may not be available on your organization depending on your <em>OpenMicroanatomy Server</em> setup.
</td>
</tr>
</table>
</div>
<div id="img-login" class="imageblock">
<div class="content">
<img src="images/Login.png" alt="Login dialog">
</div>
<div class="title">Figure 4. Login dialog. Change host by pressing the <b class="button">Change host …​</b> on the bottom-right hand corner.</div>
</div>
</div>
<div class="sect3">
<h4 id="_password_recovery">Password recovery</h4>
<div class="paragraph">
<p>If you forgot your password, you can recover your password by pressing <b class="button">Login with credentials</b> and then <b class="button">Forgot password</b> from the bottom right-hand corner.</p>
</div>
</div>
</div>
<div class="sect2">
<h3 id="_creating_content">Creating content</h3>
<div class="paragraph">
<p>Going further, it’s assumed the reader is already familiar with QuPath. If you have never used QuPath before, it’s advised to read the <a href="https://qupath.readthedocs.io/en/stable/">QuPath documentation</a> first.</p>
</div>
<div class="paragraph">
<p>Before making changes anywhere, confirm that you have <strong>Editing mode enabled</strong> by pressing <b class="button">Turn editing on</b> on the QuPath toolbar (see <a href="#img-toolbar">Figure 5</a> below). If any button is disabled, try checking first that <strong>a)</strong> edit mode is enabled, <strong>b)</strong> you’re logged in <strong>b)</strong>, you have the required permissions to make changes (see <a href="#_users_roles">Users & Roles</a>).</p>
</div>
<div id="img-toolbar" class="imageblock">
<div class="content">
<img src="images/Toolbar.png" alt="Toolbar">
</div>
<div class="title">Figure 5. QuPath Toolbar. Notice how the annotation tools are disabled because editing mode is not turned on.</div>
</div>
<div class="sect3">
<h4 id="_creating_workspaces_courses_and_lessons">Creating workspaces, courses and lessons</h4>
<div class="paragraph">
<p>Begin by opening the <strong>Select lesson</strong> (see <a href="#img-select-lesson">Figure 7</a> below) interface by pressing either <b class="button">Open lesson</b> or <b class="button">Create lesson</b> buttons in the main QuPath interface on the left sidebar (see <a href="#img-create-lesson">Figure 6</a> below).</p>
</div>
<div id="img-create-lesson" class="imageblock">
<div class="content">
<img src="images/Left-Sidebar.png" alt="Open or create lesson">
</div>
<div class="title">Figure 6. Buttons to open and create lesson, and add images</div>
</div>
<div id="img-select-lesson" class="imageblock">
<div class="content">
<img src="images/Select-Lesson.png" alt="Select lesson dialog">
</div>
<div class="title">Figure 7. <strong>1</strong>: A workspace named <em>Anatomy</em>. <strong>2</strong>: Two courses named <em>Course materials</em> and <em>Additional materials</em>. <strong>3</strong>: Five lessons belonging to the <em>Course materials</em> course. <strong>4</strong>: Create a workspace, course or a lesson.</div>
</div>
<div class="paragraph">
<p>Create new workspaces by pressing <b class="button">Create …​</b> and selecting either <code>Workspace</code>, <code>Course</code> or <code>Lesson</code>. <code>Course</code> and <code>Lesson</code> are disabled until you select a <code>Workspace</code>.</p>
</div>
<div class="paragraph">
<p><strong>Delete or rename</strong> any <code>Workspace</code>, <code>Lesson</code> or <code>Class</code> by right-clicking on it. You can also <strong>hide</strong> Classes or set a <strong>description</strong>. Hiding a Class will hide that Class from guests and users without write permissions. Deleting a Workspace will delete all Lessons and Classes belonging to that Workspace and similarly deleting a Lesson will delete all Classes belonging to that Lesson.</p>
</div>
<div class="admonitionblock warning">
<table>
<tr>
<td class="icon">
<div class="title">Warning</div>
</td>
<td class="content">
Deleting a workspace, lesson or class is currently not reversible. See <a href="#_backups">Backups</a> for more details.
</td>
</tr>
</table>
</div>
</div>
<div class="sect3">
<h4 id="_adding_slides_to_a_lesson">Adding slides to a lesson</h4>
<div class="paragraph">
<p>To add a new slide click on <b class="button">Add images</b> (next to <b class="button">Open lesson</b>, see <a href="#img-create-lesson">Figure 6</a> above) to open the <strong>Slide manager</strong> interface. From here, select any slide you wish to add and click on <b class="button">Add selected</b>. This will open the <strong>QuPath Image Import</strong> interface. These settings are important if you’re planning on doing any analysis on the slides later. The default options and setting the <strong>Image type</strong> to <strong>Brightfield (H-DAB)</strong> is usually enough for teaching purposes. Clicking on <b class="button">Import</b> will add the slide to the lesson.</p>
</div>
</div>
<div class="sect3">
<h4 id="_making_changes_to_slides">Making changes to slides</h4>
<div class="paragraph">
<p>Adding annotations, modifying slide description or such work identically as in QuPath, just make sure you have <strong>enabled editing mode</strong> (see <a href="#img-toolbar">Figure 5</a>). Read the <a href="https://qupath.readthedocs.io/en/stable/docs/starting/annotating.html">QuPath documentation</a> for detailed information on annotating and such.</p>
</div>
<div class="paragraph">
<p>Any changes will be saved when either <strong>a)</strong> clicking on <span class="menuseq"><b class="menu">File</b> <b class="caret">›</b> <b class="menuitem">Save</b></span> or <span class="menuseq"><b class="menu">File</b> <b class="caret">›</b> <b class="menuitem">Save as</b></span>, <strong>b)</strong> changing slides, <strong>c)</strong> closing the lesson.</p>
</div>
</div>
<div class="sect3">
<h4 id="_modify_lesson_information">Modify Lesson Information</h4>
<div class="paragraph">
<p>Edit the <strong>Lesson Information</strong> by either <strong>a)</strong> double-click anywhere on the <strong>Lesson Information</strong> tab <strong>b)</strong> <span class="menuseq"><b class="menu">File</b> <b class="caret">›</b> <b class="submenu">Project…​</b> <b class="caret">›</b> <b class="menuitem">Edit lesson information</b></span>.</p>
</div>
<div class="paragraph">
<p>Lesson Information supports <strong>rich text</strong>, which includes custom fonts, colors, tables, images, videos, hyperlinks and much more.</p>
</div>
<div id="img-wysiwyg-editor" class="imageblock">
<div class="content">
<img src="images/WYSIWYG-Editor.png" alt="Rich text editor">
</div>
<div class="title">Figure 8. Rich text editor.</div>
</div>
</div>
<div class="sect3">
<h4 id="_creating_slide_tours">Creating slide tours</h4>
<div class="paragraph">
<p><strong>Slide tours</strong> are a feature introduced by QuPath Edu, it allows teachers to create short guided tours of slides, going through the key points of a slide.</p>
</div>
<div id="img-create-slidetour" class="imageblock">
<div class="content">
<img src="images/Create-Slide-Tour.png" alt="Create Slide tour">
</div>
<div class="title">Figure 9. Create slide tour button on viewers top-left corner.</div>
</div>
<div class="paragraph">
<p>Slide tours consists of <strong>"frames"</strong>, which the user views one-by-one. To create a <strong>Slide tour</strong>, press on <b class="button">Create tour</b> tour on the Viewers top-left corner. Next click on <span class="menuseq"><b class="menu">More ⋮</b> <b class="caret">›</b> <b class="menuitem">Create new frame</b></span>, and pan & zoom on the point of interest, make any annotations you wish. Set a description for this frame by pressing <span class="menuseq"><b class="menu">More ⋮</b> <b class="caret">›</b> <b class="menuitem">Edit text</b></span>. Save changes by clicking on <span class="menuseq"><b class="menu">More ⋮</b> <b class="caret">›</b> <b class="menuitem">Save changes</b></span>. Create as many frames you wish by clicking <span class="menuseq"><b class="menu">More ⋮</b> <b class="caret">›</b> <b class="menuitem">Create new frame</b></span> and again making any annotations, panning & zooming, setting a description and saving the changes with <span class="menuseq"><b class="menu">More ⋮</b> <b class="caret">›</b> <b class="menuitem">Save changes</b></span>. Preview your slide tour by clicking on <b class="button">Previous</b> and <b class="button">Next</b>.</p>
</div>
<div id="img-slidetour" class="imageblock">
<div class="content">
<img src="images/Slide-Tour.png" alt="Slide tour">
</div>
<div class="title">Figure 10. Slide tour editing interface</div>
</div>
</div>
</div>
<div class="sect2">
<h3 id="_administrative_tasks">Administrative tasks</h3>
<div class="paragraph">
<p>Most administrative tools are available by selecting <span class="menuseq"><b class="menu">QuPath Edu</b> <b class="caret">›</b> <b class="menuitem">…​</b></span> from the QuPath top bar. Some administrative tasks requires access to the server and are detailed in the <a href="#_openmicroanatomy_server">OpenMicroanatomy Server</a> chapter.</p>
</div>
<div class="sect3">
<h4 id="_users_roles">Users & Roles</h4>
<div class="paragraph">
<p>Manage users by opening the <strong>User management</strong> interface using <span class="menuseq"><b class="menu">QuPath Edu</b> <b class="caret">›</b> <b class="menuitem">Manage users</b></span>.</p>
</div>
<div id="img-user-management" class="imageblock">
<div class="content">
<img src="images/User-Management.png" alt="User management interface">
</div>
<div class="title">Figure 11. User management interface</div>
</div>
<div class="paragraph">
<p>Users with the <strong>Administrative tasks</strong> role are able to view & modify all users regardless of organization. Users with only the <strong>Manage users</strong> roles can only view & modify users that belong to the users organization.</p>
</div>
<div class="paragraph">
<p>Only users with the <strong>Administrative tasks</strong> role are able to migrate users to a different organization.</p>
</div>
<div class="paragraph">
<p>Passwords are required to have at least 3 characters, no other requirements.</p>
</div>
<table class="tableblock frame-all grid-all stretch">
<caption class="title">Table 2. Explanation for different roles</caption>
<colgroup>
<col style="width: 25%;">
<col style="width: 75%;">
</colgroup>
<thead>
<tr>
<th class="tableblock halign-left valign-top">Role</th>
<th class="tableblock halign-left valign-top">Explanation</th>
</tr>
</thead>
<tbody>
<tr>
<td class="tableblock halign-left valign-top"><p class="tableblock">Manage slides</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">Upload new slides and delete / modify slides that are owned by the users organization.</p></td>
</tr>
<tr>
<td class="tableblock halign-left valign-top"><p class="tableblock">Manage users</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">Create new users and edit existing users on the users organization.</p></td>
</tr>
<tr>
<td class="tableblock halign-left valign-top"><p class="tableblock">Moderator tasks</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">Create new workspaces, courses and lessons on the users organization.</p></td>
</tr>
<tr>
<td class="tableblock halign-left valign-top"><p class="tableblock">Administrative tasks</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">All permissions, regardless of organization.</p></td>
</tr>
</tbody>
</table>
</div>
<div class="sect3">
<h4 id="_slides">Slides</h4>
<div class="paragraph">
<p>Manage slides by opening the <strong>Slide management</strong> interface using <span class="menuseq"><b class="menu">QuPath Edu</b> <b class="caret">›</b> <b class="menuitem">Manage slides</b></span>.</p>
</div>
<div id="img-slide-management" class="imageblock">
<div class="content">
<img src="images/Slide-Management.png" alt="Slide management interface">
</div>
<div class="title">Figure 12. Slide management interface. Each slide has an UUID <em>(Universal Unique Identifier)</em> which distinguishes it from others.</div>
</div>
<div class="paragraph">
<p>Users with the <strong>Administrative tasks</strong> roles are able to view & modify all slides regardless of organization. Users with only the <strong>Manage slides</strong> roles can only view & modify slides that belong to the users organization.</p>
</div>
<div class="paragraph">
<p><strong>Import new slides</strong> by clicking the <b class="button">Import slide</b> button. QuPath verifies that the selected slide is compatible with QuPath Edu and starts uploading it. After upload the OpenMicroanatomy Server processes the slide which can take up to 30 minutes depending on the slide size and server performance.</p>
</div>
<div class="paragraph">
<p><strong>Deleting</strong> a slide will make it inaccessible from any Lesson that contains it but <strong>will not</strong> remove it from the slide listing. Deleted slides must be removed manually from each lesson also. <strong>Renaming</strong> a slide will only affect slides added in the future.</p>
</div>
<div class="admonitionblock warning">
<table>
<tr>
<td class="icon">
<div class="title">Warning</div>
</td>
<td class="content">
In OpenMicroanatomy Server <strong>version 1.0</strong> deleting slides only makes them inaccessible but <strong>does not</strong> remove the data stored. It is up to the server administrator to delete any associated data.
</td>
</tr>
</table>
</div>
<div class="paragraph">
<p>You can view any slide by clicking on <b class="button">Open selected</b>. If you have a lesson open, you will be prompted to add that slide to the current project.</p>
</div>
</div>
<div class="sect3">
<h4 id="_backups">Backups</h4>
<div class="paragraph">
<p>Manage <strong>lesson</strong> backups by opening the <strong>Backup management</strong> interface using <span class="menuseq"><b class="menu">QuPath Edu</b> <b class="caret">›</b> <b class="menuitem">Manage backups</b></span>.</p>
</div>
<div class="paragraph">
<p>Restore a lesson by selecting the lesson and pressing <b class="button">Restore backup</b> or preview it first by pressing <b class="button">Preview backup</b>. Backups are automatically deleted after 30 days.</p>
</div>
<div class="admonitionblock warning">
<table>
<tr>
<td class="icon">
<div class="title">Warning</div>
</td>
<td class="content">
Currently there’s no way to restore a deleted workspace / class or a lesson without administrative tools. A whole database backup is performed every 24 hours, which can be used to restore any deleted workspace / class or lesson.
</td>
</tr>
</table>
</div>
<div class="admonitionblock note">
<table>
<tr>
<td class="icon">
<div class="title">Note</div>
</td>
<td class="content">
In QuPath Edu Server version 1.0 a bug exists, which allows users with write permissions to preview all backups regardless of organization. Restoring backups is still limited to users with proper write permissions to a specific workspace.
</td>
</tr>
</table>
</div>
<div id="img-edit-organization" class="imageblock">
<div class="content">
<img src="images/Backup-Management.png" alt="Backup management dialog">
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<div class="title">Figure 13. Backup management interface.</div>
</div>
</div>
<div class="sect3">
<h4 id="_organizations">Organizations</h4>
<div class="paragraph">
<p>Manage organizations by opening the <strong>Organization management</strong> interface using <span class="menuseq"><b class="menu">QuPath Edu</b> <b class="caret">›</b> <b class="menuitem">Manage organizations</b></span>.</p>
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<div id="img-organization-management" class="imageblock">
<div class="content">
<img src="images/Organization-Management.png" alt="Organization management interface">
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<div class="title">Figure 14. Organization management interface. Each organization has an UUID <em>(Universal Unique Identifier)</em> which distinguishes it from others.</div>
</div>
<div class="paragraph">
<p><strong>Making any changes to an organization requires the <em>Administrative tasks</em> role</strong>.</p>