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‎404.html‎

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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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<link rel="shortcut icon" href="/img/favicon.ico">
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<title>StarryNight Documentation</title>
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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/parser-configuration/" class="dropdown-item">Parser Configuration</a>
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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 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="/developer/developer-guide/" class="dropdown-item">Developer Guide</a>
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<li class="nav-item">
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<a href="/misc/faq/" class="nav-link">FAQ</a>
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<ul class="nav navbar-nav ms-md-auto">
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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 class="container">
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<div class="row">
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<div class="row-fluid">
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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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<hr>
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<p>Documentation built with <a href="https://www.mkdocs.org/">MkDocs</a>.</p>
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<script src="/js/bootstrap.bundle.min.js"></script>
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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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<div class="modal" id="mkdocs_keyboard_modal" tabindex="-1" role="dialog" aria-labelledby="keyboardModalLabel" aria-hidden="true">
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<div class="modal-header">
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<h4 class="modal-title" id="keyboardModalLabel">Keyboard Shortcuts</h4>
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<button type="button" class="btn-close" data-bs-dismiss="modal" aria-label="Close"></button>
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<div class="modal-body">
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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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<td class="help shortcut"><kbd>?</kbd></td>
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‎assets/create_starrynight_example.sh‎

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BUCKET=XXXXXX
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PROJECT=XXXXXX
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BATCH=XXXXXX
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export S3_PATH="s3://${BUCKET}/projects/${PROJECT}/${BATCH}"
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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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# Inputs
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## SBS images
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parallel mkdir -p ${INPUT_DIR}/Source1/Batch1/images/Plate1/20X_c{1}_SBS-{1}/ ::: 1 2 3
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parallel --match '.*' --match '(.*) (.*) (.*)' \
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aws s3 cp "${S3_PATH}/images/Plate1/20X_c{1}_SBS-{1}/Well{2.1}_Point{2.1}_{2.2}_ChannelC,A,T,G,DAPI_Seq{2.3}.ome.tiff" \
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"${INPUT_DIR}/Source1/Batch1/images/Plate1/20X_c{1}_SBS-{1}/" ::: \
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1 2 3 ::: \
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"A1 0000 0000" "A1 0001 0001" "A2 0000 1025" "A2 0001 1026" "B1 0000 3075" "B1 0001 3076"
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## Cell Painting images
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mkdir -p ${INPUT_DIR}/Source1/Batch1/images/20X_CP_Plate1_20240319_122800_179
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parallel --match '(.*) (.*) (.*)' \
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aws s3 cp "${S3_PATH}/images/Plate1/20X_CP_Plate1_20240319_122800_179/Well{1.1}_Point{1.1}_{1.2}_ChannelPhalloAF750,ZO1-AF488,DAPI_Seq{1.3}.ome.tiff" \
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"${INPUT_DIR}/Source1/Batch1/images/Plate1/20X_CP_Plate1_20240319_122800_179/" ::: \
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"A1 0000 0000" "A1 0001 0001" "A2 0000 1025" "A2 0001 1026" "B1 0000 3075" "B1 0001 3076"
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# Outputs
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## Illumination correction images
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mkdir -p ${OUTPUT_BASELINE_DIR}/Source1/Batch1/illum/Plate1
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parallel \
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aws s3 cp "${S3_PATH}/illum/Plate1/Plate1_Cycle{1}_Illum{2}.npy" "${OUTPUT_BASELINE_DIR}/Source1/Batch1/illum/Plate1/" ::: \
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1 2 3 ::: \
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DNA A T G C
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parallel \
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aws s3 cp "${S3_PATH}/illum/Plate1/Plate1_Illum{1}.npy" "${OUTPUT_BASELINE_DIR}/Source1/Batch1/illum/Plate1/" ::: \
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DNA Phalloidin ZO1
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## Cell Painting images: Illumination corrected
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parallel \
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aws s3 cp "${S3_PATH}/images_corrected/painting/Plate1-Well{1}/Plate_Plate1_Well_Well{1}_Site_{2}_Corr{3}.tiff" \
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"${OUTPUT_BASELINE_DIR}/Source1/Batch1/images_corrected/painting/Plate1-Well{1}/" ::: \
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A1 A2 B1 ::: 0 1 ::: DNA Phalloidin ZO1
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parallel \
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aws s3 cp "${S3_PATH}/images_corrected/painting/Plate1-Well{1}/PaintingIllumApplication_{2}.csv" \
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"${OUTPUT_BASELINE_DIR}/Source1/Batch1/images_corrected/painting/Plate1-Well{1}/" ::: \
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A1 A2 B1 ::: Cells ConfluentRegions Experiment Image Nuclei
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# SBS images: Illumination aligned
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parallel \
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aws s3 cp "${S3_PATH}/images_aligned/barcoding/Plate1-Well{1}-{2}/Plate_Plate1_Well_{1}_Site_{2}_Cycle0{3}_{4}.tiff" \
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"${OUTPUT_BASELINE_DIR}/Source1/Batch1/images_aligned/barcoding/Plate1-Well{1}-{2}/" ::: \
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A1 A2 B1 ::: 0 1 ::: 1 2 3 ::: A T G C DAPI
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parallel \
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aws s3 cp "${S3_PATH}/images_aligned/barcoding/Plate1-Well{1}-{2}/BarcodingApplication_{3}.csv" \
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"${OUTPUT_BASELINE_DIR}/Source1/Batch1/images_aligned/barcoding/Plate1-Well{1}-{2}/" ::: \
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A1 A2 B1 ::: 0 1 ::: Experiment Image
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## SBS images: Illumination corrected
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parallel \
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aws s3 cp "${S3_PATH}/images_corrected/barcoding/Plate1-Well{1}-{2}/Plate_Plate1_Well_{1}_Site_{2}_Cycle0{3}_{4}.tiff" \
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"${OUTPUT_BASELINE_DIR}/Source1/Batch1/images_corrected/barcoding/Plate1-Well{1}-{2}/" ::: \
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A1 A2 B1 ::: 0 1 ::: 1 2 3 ::: A T G C
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parallel \
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aws s3 cp "${S3_PATH}/images_corrected/barcoding/Plate1-Well{1}-{2}/Plate_Plate1_Well_{1}_Site_{2}_Cycle0{3}_{4}.tiff" \
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"${OUTPUT_BASELINE_DIR}/Source1/Batch1/images_corrected/barcoding/Plate1-Well{1}-{2}/" ::: \
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A1 A2 B1 ::: 0 1 ::: 1 ::: DAPI
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# DAPI is present only in the first cycle
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parallel \
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aws s3 cp "${S3_PATH}/images_corrected/barcoding/Plate1-Well{1}-{2}/BarcodePreprocessing_{3}.csv" \
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"${OUTPUT_BASELINE_DIR}/Source1/Batch1/images_corrected/barcoding/Plate1-Well{1}-{2}/" ::: \
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A1 A2 B1 ::: 0 1 ::: BarcodeFoci PreFoci Experiment Image Nuclei
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## Segmentation images
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parallel \
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aws s3 cp "${S3_PATH}/images_segmentation/Plate1/Plate_Plate1_Well_Well{1}_Site_{2}_Corr{3}_SegmentCheck.png" \
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"${OUTPUT_BASELINE_DIR}/Source1/Batch1/images_segmentation/Plate1/" ::: \
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A1 A2 B1 ::: 0 ::: DNA
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parallel \
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aws s3 cp "${S3_PATH}/images_segmentation/Plate1/Plate_Plate1_Well_Well{1}_Site_{2}_Corr{3}_SegmentCheck.png" \
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"${OUTPUT_BASELINE_DIR}/Source1/Batch1/images_segmentation/Plate1/" ::: \
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A1 A2 B1 ::: 0 ::: DNA
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parallel \
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aws s3 cp "${S3_PATH}/images_segmentation/Plate1/SegmentationCheck_{1}.csv" \
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"${OUTPUT_BASELINE_DIR}/Source1/Batch1/images_segmentation/Plate1/" ::: \
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Experiment Image Nuclei Cells PreCells ConfluentRegions
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## Load Data CSVs
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export S3_PATH_WORKSPACE="s3://${BUCKET}/projects/${PROJECT}/workspace"
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aws s3 sync \
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"${S3_PATH_WORKSPACE}/load_data_csv/${BATCH}/Plate1/" \
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"${OUTPUT_BASELINE_DIR}/Source1/workspace_example/load_data_csv/Batch1/Plate1/"
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## Analysis CSVs
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parallel \
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aws s3 sync \
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"${S3_PATH_WORKSPACE}/analysis/${BATCH}/Plate1-Well{1}-{2}/" \
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"${OUTPUT_BASELINE_DIR}/Source1/workspace_example/analysis/${BATCH}/Plate1-Well{1}-{2}/" \
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--exclude \""*.csv\"" ::: \
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A1 A2 B1 ::: 0 1
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parallel \
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aws s3 sync \
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"${S3_PATH_WORKSPACE}/analysisfix/${BATCH}/Plate1-Well{1}-{2}/" \
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"${OUTPUT_BASELINE_DIR}/Source1/workspace_example/analysis/${BATCH}/Plate1-Well{1}-{2}/" ::: \
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A1 A2 B1 ::: 0 1
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# Note that the analysis files are synced from two different locations: analysis and analysisfix.
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# analysisfix was a rerun of analysis
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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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