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<!DOCTYPE html>
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<html lang="en" data-bs-theme="light">
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<head>
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<meta charset="utf-8">
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<meta http-equiv="X-UA-Compatible" content="IE=edge">
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<meta name="viewport" content="width=device-width, initial-scale=1.0">
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<link rel="shortcut icon" href="/img/favicon.ico">
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<title>StarryNight Documentation</title>
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<link href="/css/bootstrap.min.css" rel="stylesheet">
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<link href="/css/fontawesome.min.css" rel="stylesheet">
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<link href="/css/brands.min.css" rel="stylesheet">
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<link href="/css/v4-font-face.min.css" rel="stylesheet">
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<link href="/css/base.css" rel="stylesheet">
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<link id="hljs-light" rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/highlight.js/11.8.0/styles/github.min.css" >
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<link id="hljs-dark" rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/highlight.js/11.8.0/styles/github-dark.min.css" disabled>
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<script src="https://cdnjs.cloudflare.com/ajax/libs/highlight.js/11.8.0/highlight.min.js"></script>
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<script>hljs.highlightAll();</script>
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</head>
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<body>
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<div class="navbar fixed-top navbar-expand-lg navbar-dark bg-primary">
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<div class="container">
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<a class="navbar-brand" href="/.">StarryNight Documentation</a>
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<!-- Expander button -->
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<button type="button" class="navbar-toggler" data-bs-toggle="collapse" data-bs-target="#navbar-collapse" aria-controls="navbar-collapse" aria-expanded="false" aria-label="Toggle navigation">
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<span class="navbar-toggler-icon"></span>
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</button>
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<!-- Expanded navigation -->
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<div id="navbar-collapse" class="navbar-collapse collapse">
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<!-- Main navigation -->
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<ul class="nav navbar-nav">
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<li class="nav-item">
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<a href="/." class="nav-link">Home</a>
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</li>
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<li class="nav-item dropdown">
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<a href="#" class="nav-link dropdown-toggle" role="button" data-bs-toggle="dropdown" aria-expanded="false">Getting Started</a>
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<ul class="dropdown-menu">
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<li>
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<a href="/getting-started/installation/" class="dropdown-item">Installation</a>
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</li>
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<li>
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<a href="/getting-started/quickstart/" class="dropdown-item">Quick Start Guide</a>
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</li>
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</ul>
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</li>
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<li class="nav-item dropdown">
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<a href="#" class="nav-link dropdown-toggle" role="button" data-bs-toggle="dropdown" aria-expanded="false">User Guide</a>
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<ul class="dropdown-menu">
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<li>
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<a href="/user/core-concepts/" class="dropdown-item">Core Concepts</a>
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</li>
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<li>
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<a href="/user/parser-configuration/" class="dropdown-item">Parser Configuration</a>
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</li>
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<li>
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<a href="/user/modules/" class="dropdown-item">Processing Modules</a>
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</li>
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<li>
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<a href="/user/example-pipeline-cli/" class="dropdown-item">Example CLI Pipeline</a>
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</li>
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</ul>
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</li>
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<li class="nav-item dropdown">
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<a href="#" class="nav-link dropdown-toggle" role="button" data-bs-toggle="dropdown" aria-expanded="false">Algorithms</a>
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<ul class="dropdown-menu">
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<li>
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<a href="/user/algorithms/" class="dropdown-item">Overview</a>
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</li>
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<li>
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<a href="/user/algorithms/DOCUMENTATION_GUIDE/" class="dropdown-item">Documentation Guide</a>
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</li>
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</li>
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<li>
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<a href="/user/algorithms/illum_apply/" class="dropdown-item">Illumination Apply</a>
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</li>
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<li>
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<a href="/user/algorithms/presegcheck/" class="dropdown-item">Pre-segmentation Check</a>
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<a href="/user/algorithms/segcheck/" class="dropdown-item">Segmentation Check</a>
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<a href="/user/algorithms/align/" class="dropdown-item">Alignment</a>
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<a href="/user/algorithms/preprocess/" class="dropdown-item">Preprocessing</a>
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<a href="/user/algorithms/stitchcrop/" class="dropdown-item">Stitch and Crop</a>
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<a href="/user/algorithms/analysis/" class="dropdown-item">Analysis</a>
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</li>
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</ul>
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</li>
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<li class="nav-item dropdown">
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<a href="#" class="nav-link dropdown-toggle" role="button" data-bs-toggle="dropdown" aria-expanded="false">Development</a>
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<a href="/misc/faq/" class="nav-link">FAQ</a>
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<a href="https://github.com/broadinstitute/starrynight" class="nav-link"><i class="fa-brands fa-github"></i> GitHub</a>
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<div id="main-content" class="span12">
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<h1 id="404-page-not-found" style="text-align: center">404</h1>
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<p style="text-align: center"><strong>Page not found</strong></p>
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<footer class="col-md-12">
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<p>Documentation built with <a href="https://www.mkdocs.org/">MkDocs</a>.</p>
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<script>
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var base_url = "/",
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shortcuts = {"help": 191, "next": 78, "previous": 80, "search": 83};
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</script>
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<script src="/js/base.js"></script>
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<button type="button" class="btn-close" data-bs-dismiss="modal" aria-label="Close"></button>
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<table class="table">
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<thead>
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<tr>
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<th style="width: 20%;">Keys</th>
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<th>Action</th>
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</tr>
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</thead>
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<tbody>
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<tr>
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<td class="help shortcut"><kbd>?</kbd></td>
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<td>Open this help</td>
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</tr>
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<td class="next shortcut"><kbd>n</kbd></td>
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<td>Next page</td>
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</tr>
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<td class="prev shortcut"><kbd>p</kbd></td>
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<td>Previous page</td>
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<td class="search shortcut"><kbd>s</kbd></td>
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</body>
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</html>
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export INPUT_DIR='./scratch/starrynight_example_input'
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export OUTPUT_BASELINE_DIR='./scratch/starrynight_example_output_baseline'
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# Compress files to reduce disk usage after downloading
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echo "Compressing files to reduce disk usage..."
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## Compress all TIFF files
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find ${OUTPUT_BASELINE_DIR} -type f -name "*.tiff" | parallel 'magick {} -compress jpeg -quality 80 {}'
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find ${INPUT_DIR} -type f -name "*.tiff" | parallel 'magick {} -compress jpeg -quality 80 {}'
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# Compress CSV files
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find ${OUTPUT_BASELINE_DIR} -type f -name "*.csv" | parallel 'gzip -9 {}'

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