

<!DOCTYPE html>

<html>
  <head>
    <meta charset="utf-8" />
    <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="generator" content="Docutils 0.17.1: http://docutils.sourceforge.net/" />

    <title>Segmentation analysis with VollSeg  &#8212; VollSeg  29.9.0 documentation</title>

  <!-- Loaded before other Sphinx assets -->
  <link href="https://github.com/Kapoorlabs-CAPED/VollSeg/blob/main/css/style_0.css" rel="stylesheet">
<link href="https://github.com/Kapoorlabs-CAPED/VollSeg/blob/main/css/style_1.css" rel="stylesheet">


  <link rel="stylesheet"
    href="_static/vendor/fontawesome/5.13.0/css/all.min.css">
  <link rel="preload" as="font" type="font/woff2" crossorigin
    href="_static/vendor/fontawesome/5.13.0/webfonts/fa-solid-900.woff2">
  <link rel="preload" as="font" type="font/woff2" crossorigin
    href="_static/vendor/fontawesome/5.13.0/webfonts/fa-brands-400.woff2">

    <link rel="stylesheet" type="text/css" href="_static/pygments.css" />
    <link rel="stylesheet" type="text/css" href="_static/copybutton.css" />
    <link rel="stylesheet" type="text/css" href="_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" />

  <!-- Pre-loaded scripts that we'll load fully later -->
  <link rel="preload" as="script" href="_static/scripts/pydata-sphinx-theme.js?digest=1999514e3f237ded88cf">

    <script data-url_root="./" id="documentation_options" src="_static/documentation_options.js"></script>
    <script src="_static/jquery.js"></script>
    <script src="_static/underscore.js"></script>
    <script src="_static/doctools.js"></script>
    <script src="_static/clipboard.min.js"></script>
    <script src="_static/copybutton.js"></script>
    <link rel="index" title="Index" href="genindex.html" />
    <link rel="search" title="Search" href="search.html" />
    <link rel="next" title="Getting started" href="getting_started/index.html" />
    <meta name="viewport" content="width=device-width, initial-scale=1" />
    <meta name="docsearch:language" content="None">


    <!-- Google Analytics -->

  </head>
  <body data-spy="scroll" data-target="#bd-toc-nav" data-offset="60">

    <div class="container-fluid" id="banner"></div>


    <nav class="navbar navbar-light navbar-expand-lg bg-light fixed-top bd-navbar" id="navbar-main"><div class="container-xl">

  <div id="navbar-start">


<a class="navbar-brand" href="#">
<p class="title">VollSeg </p>
</a>


  </div>

  <button class="navbar-toggler" type="button" data-toggle="collapse" data-target="#navbar-collapsible" aria-controls="navbar-collapsible" aria-expanded="false" aria-label="Toggle navigation">
    <span class="navbar-toggler-icon"></span>
  </button>


  <div id="navbar-collapsible" class="col-lg-9 collapse navbar-collapse">
    <div id="navbar-center" class="mr-auto">

      <div class="navbar-center-item">
        <ul id="navbar-main-elements" class="navbar-nav">
    <li class="toctree-l1 nav-item">
 <a class="reference internal nav-link" href="getting_started/index.html">
  Getting started
 </a>
</li>

<li class="toctree-l1 nav-item">
 <a class="reference internal nav-link" href="examples/index.html">
  Examples
 </a>
</li>

<li class="toctree-l1 nav-item">
 <a class="reference internal nav-link" href="api/api.html">
  VollSeg API Reference
 </a>
</li>

<li class="toctree-l1 nav-item">
 <a class="reference internal nav-link" href="misc/index.html">
  Miscellaneous
 </a>
</li>


</ul>
      </div>

    </div>

    <div id="navbar-end">

      <div class="navbar-end-item">
        <div class="dropdown" id="version_switcher">
    <button type="button" class="btn btn-primary btn-sm navbar-btn dropdown-toggle" id="version_switcher_button" data-toggle="dropdown">
        29.9.0  <!-- this text may get changed later by javascript -->
        <span class="caret"></span>
    </button>
    <div id="version_switcher_menu" class="dropdown-menu list-group-flush py-0" aria-labelledby="version_switcher_button">
    <!-- dropdown will be populated by javascript on page load -->
    </div>
</div>

<!-- NOTE: this JS must live here (not in our global JS file) because it relies
     on being processed by Jinja before it is run (specifically for replacing
     variables index and {'json_url': 'https://github.com/Kapoorlabs-CAPED/VollSeg/blob/main/version_switcher.json', 'version_match': '29.9.0'}.
-->

<script type="text/javascript">
// Check if corresponding page path exists in other version of docs
// and, if so, go there instead of the homepage of the other docs version
function checkPageExistsAndRedirect(event) {
    const currentFilePath = "index.html",
          tryUrl = event.target.getAttribute("href");
    let otherDocsHomepage = tryUrl.replace(currentFilePath, "");
    $.ajax({
        type: 'HEAD',
        url: tryUrl,
        // if the page exists, go there
        success: function() {
            location.href = tryUrl;
        }
    }).fail(function() {
        location.href = otherDocsHomepage;
    });
    // this prevents the browser from following the href of the clicked node
    // (which is fine because this function takes care of redirecting)
    return false;
}

// Populate the version switcher from the JSON config file
(function () {
    $.getJSON("https://github.com/Kapoorlabs-CAPED/VollSeg/blob/main/version_switcher.json", function(data, textStatus, jqXHR) {
        const currentFilePath = "index.html";
        // create links to the corresponding page in the other docs versions
        $.each(data, function(index, entry) {
            // if no custom name specified (e.g., "latest"), use version string
            if (!("name" in entry)) {
                entry.name = entry.version;
            }
            // create the node
            const node = document.createElement("a");
            node.setAttribute("class", "list-group-item list-group-item-action py-1");
            node.textContent = `${entry.name}`;
            node.setAttribute("href", `${entry.url}${currentFilePath}`);
            // on click, AJAX calls will check if the linked page exists before
            // trying to redirect, and if not, will redirect to the homepage
            // for that version of the docs.
            node.onclick = checkPageExistsAndRedirect;
            // Add dataset values for the version and name in case people want
            // to apply CSS styling based on this information.
            node.dataset["versionName"] = entry.name;
            node.dataset["version"] = entry.version;

            $("#version_switcher_menu").append(node);
            // replace dropdown button text with the preferred display name of
            // this version, rather than using sphinx's 29.9.0 variable.
            // also highlight the dropdown entry for the currently-viewed
            // version's entry
            if (entry.version == "29.9.0") {
                node.classList.add("active");
                let btn = document.getElementById("version_switcher_button");
                btn.innerText = btn.dataset["activeVersionName"] = entry.name;
                btn.dataset["activeVersion"] = entry.version;
            }
        });
    });
})();
</script>
      </div>

      <div class="navbar-end-item">
        <ul id="navbar-icon-links" class="navbar-nav" aria-label="Icon Links">
        <li class="nav-item">
          <a class="nav-link" href="https://github.com/Kapoorlabs-CAPED/VollSeg" rel="noopener" target="_blank" title="GitHub"><span><i class="fa-brands fa-square-github"></i></span>
            <label class="sr-only">GitHub</label></a>
        </li>
      </ul>
      </div>

    </div>
  </div>
</div>
    </nav>


    <div class="container-xl">
      <div class="row">


            <!-- Only show if we have sidebars configured, else just a small margin  -->
            <div class="col-12 col-md-3 bd-sidebar">
              <div class="sidebar-start-items"><form class="bd-search d-flex align-items-center" action="search.html" method="get">
  <i class="icon fas fa-search"></i>
  <input type="search" class="form-control" name="q" id="search-input" placeholder="Search the docs ..." aria-label="Search the docs ..." autocomplete="off" >
</form><nav class="bd-links" id="bd-docs-nav" aria-label="Main navigation">
  <div class="bd-toc-item active">

  </div>
</nav>
              </div>
              <div class="sidebar-end-items">
              </div>
            </div>




          <div class="d-none d-xl-block col-xl-2 bd-toc">


              <div class="toc-item">

<div class="tocsection onthispage mt-5 pt-1 pb-3">
    <i class="fas fa-list"></i> On this page
</div>

<nav id="bd-toc-nav">
    <ul class="visible nav section-nav flex-column">
 <li class="toc-h1 nav-item toc-entry">
  <a class="reference internal nav-link" href="#">
   Segmentation analysis with VollSeg
  </a>
 </li>
 <li class="toc-h1 nav-item toc-entry">
  <a class="reference internal nav-link" href="#indices-and-tables">
   Indices and tables
  </a>
 </li>
</ul>

</nav>
              </div>

              <div class="toc-item">

              </div>


          </div>






          <main class="col-12 col-md-9 col-xl-7 py-md-5 pl-md-5 pr-md-4 bd-content" role="main">

              <div>

  <section id="segmentation-analysis-with-VollSeg">
<h1>Segmentation Analysis with VollSeg <a class="headerlink" href="#segmentation-analysis-with-vollseg" title="Permalink to this headline">#</a></h1>
<p>VollSeg is a pure Python library to segment and analyse images.</p>
<div class="toctree-wrapper compound">
<ul>
<li class="toctree-l1"><a class="reference internal" href="getting_started/index.html">Getting started</a><ul>
<li class="toctree-l2"><a class="reference internal" href="getting_started/install.html">Installing VollSeg</a><ul>
<li class="toctree-l3"><a class="reference internal" href="getting_started/install.html#getting-the-python-package-and-dependencies">Getting the Python package and dependencies</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="getting_started/getting_started.html">Getting started: Segmentation analysis with VollSeg</a><ul>
<li class="toctree-l3"><a class="reference internal" href="getting_started/getting_started.html#choosing-vollseg-segmentation-mode">0. Choosing VollSeg Segmentation Mode</a></li>
<li class="toctree-l3"><a class="reference internal" href="getting_started/getting_started.html#choices-for-each-mode">1. Parameter choices within each mode</a></li>
<li class="toctree-l3"><a class="reference internal" href="getting_started/getting_started.html#comparing-different-modes">2. Comparing different modes</a></li>
</ul>
</li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="examples/index.html">Examples</a><ul>
<li class="toctree-l2"><a class="reference internal" href="examples/complete_analysis.html">Complete analysis with U-NET</a><ul>
<li class="toctree-l3"><a class="reference internal" href="examples/complete_analysis.html#getting-the-data">0. Getting the data</a></li>
<li class="toctree-l3"><a class="reference internal" href="examples/complete_analysis.html#using-unet-only-to-segment-ascadian-embryos">1. Using <code class="docutils literal notranslate"><span class="pre">unet.pipe</span></code> to get segmentation of ascadian embryo cells.</a></li>

</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="examples//complete_analysis.html#stardist-in-roi">StarDist with Region of Interest Model</a></li>
<li class="toctree-l2"><a class="reference internal" href="examples/complete_analysis.html#stardist-with-unet">StarDist with U-Net model</a><ul>
<li class="toctree-l3"><a class="reference internal" href="examples/complete_analysis.html#care-before-segmentation">Using CARE prior to segmentation</a></li>
<li class="toctree-l3"><a class="reference internal" href="examples/visualizing_3d_skeletons.html#using-the-labels-layer">Using the Labels layer</a></li>
</ul>
</li>
</ul>
</li>




</ul>
</li>

</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="misc/citing.html">Citing VollSeg</a></li>
</ul>
</li>
</ul>
</div>
</section>
<section id="indices-and-tables">
<h1>Indices and tables<a class="headerlink" href="#indices-and-tables" title="Permalink to this headline">#</a></h1>
<ul class="simple">
<li><p><a class="reference internal" href="genindex.html"><span class="std std-ref">Index</span></a></p></li>
<li><p><a class="reference internal" href="py-modindex.html"><span class="std std-ref">Module Index</span></a></p></li>
<li><p><a class="reference internal" href="search.html"><span class="std std-ref">Search Page</span></a></p></li>
</ul>
</section>


              </div>


              <!-- Previous / next buttons -->
<div class='prev-next-area'>
    <a class='right-next' id="next-link" href="getting_started/index.html" title="next page">
    <div class="prev-next-info">
        <p class="prev-next-subtitle">next</p>
        <p class="prev-next-title">Getting started</p>
    </div>
    <i class="fas fa-angle-right"></i>
    </a>
</div>

          </main>


      </div>
    </div>

  <!-- Scripts loaded after <body> so the DOM is not blocked -->
  <script src="_static/scripts/pydata-sphinx-theme.js?digest=1999514e3f237ded88cf"></script>
<footer class="footer mt-5 mt-md-0">
  <div class="container">

    <div class="footer-item">
      <p class="copyright">
    &copy; Copyright 2021, Varun Kapoor &amp; VollSeg contributors.<br>
</p>
    </div>

  </div>
</footer>
  </body>
</html>
