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<!DOCTYPE html>
<html>
<head>
<meta charset="utf-8" />
<title>README</title>
<style>.markdown-preview:not([data-use-github-style]) { padding: 2em; font-size: 1.2em; color: rgb(56, 58, 66); background-color: rgb(250, 250, 250); overflow: auto; }
.markdown-preview:not([data-use-github-style]) > :first-child { margin-top: 0px; }
.markdown-preview:not([data-use-github-style]) h1, .markdown-preview:not([data-use-github-style]) h2, .markdown-preview:not([data-use-github-style]) h3, .markdown-preview:not([data-use-github-style]) h4, .markdown-preview:not([data-use-github-style]) h5, .markdown-preview:not([data-use-github-style]) h6 { line-height: 1.2; margin-top: 1.5em; margin-bottom: 0.5em; color: rgb(0, 0, 0); }
.markdown-preview:not([data-use-github-style]) h1 { font-size: 2.4em; font-weight: 300; }
.markdown-preview:not([data-use-github-style]) h2 { font-size: 1.8em; font-weight: 400; }
.markdown-preview:not([data-use-github-style]) h3 { font-size: 1.5em; font-weight: 500; }
.markdown-preview:not([data-use-github-style]) h4 { font-size: 1.2em; font-weight: 600; }
.markdown-preview:not([data-use-github-style]) h5 { font-size: 1.1em; font-weight: 600; }
.markdown-preview:not([data-use-github-style]) h6 { font-size: 1em; font-weight: 600; }
.markdown-preview:not([data-use-github-style]) strong { color: rgb(0, 0, 0); }
.markdown-preview:not([data-use-github-style]) del { color: rgb(94, 97, 110); }
.markdown-preview:not([data-use-github-style]) a, .markdown-preview:not([data-use-github-style]) a code { color: rgb(82, 111, 255); }
.markdown-preview:not([data-use-github-style]) img { max-width: 100%; }
.markdown-preview:not([data-use-github-style]) > p { margin-top: 0px; margin-bottom: 1.5em; }
.markdown-preview:not([data-use-github-style]) > ul, .markdown-preview:not([data-use-github-style]) > ol { margin-bottom: 1.5em; }
.markdown-preview:not([data-use-github-style]) blockquote { margin: 1.5em 0px; font-size: inherit; color: rgb(94, 97, 110); border-color: rgb(209, 209, 210); border-width: 4px; }
.markdown-preview:not([data-use-github-style]) hr { margin: 3em 0px; border-top: 2px dashed rgb(209, 209, 210); background: none; }
.markdown-preview:not([data-use-github-style]) table { margin: 1.5em 0px; }
.markdown-preview:not([data-use-github-style]) th { color: rgb(0, 0, 0); }
.markdown-preview:not([data-use-github-style]) th, .markdown-preview:not([data-use-github-style]) td { padding: 0.66em 1em; border: 1px solid rgb(209, 209, 210); }
.markdown-preview:not([data-use-github-style]) code { color: rgb(0, 0, 0); background-color: rgb(234, 234, 235); }
.markdown-preview:not([data-use-github-style]) pre.editor-colors { margin: 1.5em 0px; padding: 1em; font-size: 0.92em; border-radius: 3px; background-color: rgb(240, 240, 240); }
.markdown-preview:not([data-use-github-style]) kbd { color: rgb(0, 0, 0); border-width: 1px 1px 2px; border-style: solid; border-color: rgb(209, 209, 210) rgb(209, 209, 210) rgb(193, 193, 194); border-image: initial; background-color: rgb(234, 234, 235); }
.markdown-preview[data-use-github-style] { font-family: "Helvetica Neue", Helvetica, "Segoe UI", Arial, freesans, sans-serif; line-height: 1.6; overflow-wrap: break-word; padding: 30px; font-size: 16px; color: rgb(51, 51, 51); background-color: rgb(255, 255, 255); overflow: scroll; }
.markdown-preview[data-use-github-style] > :first-child { margin-top: 0px !important; }
.markdown-preview[data-use-github-style] > :last-child { margin-bottom: 0px !important; }
.markdown-preview[data-use-github-style] a:not([href]) { color: inherit; text-decoration: none; }
.markdown-preview[data-use-github-style] .absent { color: rgb(204, 0, 0); }
.markdown-preview[data-use-github-style] .anchor { position: absolute; top: 0px; left: 0px; display: block; padding-right: 6px; padding-left: 30px; margin-left: -30px; }
.markdown-preview[data-use-github-style] .anchor:focus { outline: none; }
.markdown-preview[data-use-github-style] h1, .markdown-preview[data-use-github-style] h2, .markdown-preview[data-use-github-style] h3, .markdown-preview[data-use-github-style] h4, .markdown-preview[data-use-github-style] h5, .markdown-preview[data-use-github-style] h6 { position: relative; margin-top: 1em; margin-bottom: 16px; font-weight: bold; line-height: 1.4; }
.markdown-preview[data-use-github-style] h1 .octicon-link, .markdown-preview[data-use-github-style] h2 .octicon-link, .markdown-preview[data-use-github-style] h3 .octicon-link, .markdown-preview[data-use-github-style] h4 .octicon-link, .markdown-preview[data-use-github-style] h5 .octicon-link, .markdown-preview[data-use-github-style] h6 .octicon-link { display: none; color: rgb(0, 0, 0); vertical-align: middle; }
.markdown-preview[data-use-github-style] h1:hover .anchor, .markdown-preview[data-use-github-style] h2:hover .anchor, .markdown-preview[data-use-github-style] h3:hover .anchor, .markdown-preview[data-use-github-style] h4:hover .anchor, .markdown-preview[data-use-github-style] h5:hover .anchor, .markdown-preview[data-use-github-style] h6:hover .anchor { padding-left: 8px; margin-left: -30px; text-decoration: none; }
.markdown-preview[data-use-github-style] h1:hover .anchor .octicon-link, .markdown-preview[data-use-github-style] h2:hover .anchor .octicon-link, .markdown-preview[data-use-github-style] h3:hover .anchor .octicon-link, .markdown-preview[data-use-github-style] h4:hover .anchor .octicon-link, .markdown-preview[data-use-github-style] h5:hover .anchor .octicon-link, .markdown-preview[data-use-github-style] h6:hover .anchor .octicon-link { display: inline-block; }
.markdown-preview[data-use-github-style] h1 tt, .markdown-preview[data-use-github-style] h2 tt, .markdown-preview[data-use-github-style] h3 tt, .markdown-preview[data-use-github-style] h4 tt, .markdown-preview[data-use-github-style] h5 tt, .markdown-preview[data-use-github-style] h6 tt, .markdown-preview[data-use-github-style] h1 code, .markdown-preview[data-use-github-style] h2 code, .markdown-preview[data-use-github-style] h3 code, .markdown-preview[data-use-github-style] h4 code, .markdown-preview[data-use-github-style] h5 code, .markdown-preview[data-use-github-style] h6 code { font-size: inherit; }
.markdown-preview[data-use-github-style] h1 { padding-bottom: 0.3em; font-size: 2.25em; line-height: 1.2; border-bottom: 1px solid rgb(238, 238, 238); }
.markdown-preview[data-use-github-style] h1 .anchor { line-height: 1; }
.markdown-preview[data-use-github-style] h2 { padding-bottom: 0.3em; font-size: 1.75em; line-height: 1.225; border-bottom: 1px solid rgb(238, 238, 238); }
.markdown-preview[data-use-github-style] h2 .anchor { line-height: 1; }
.markdown-preview[data-use-github-style] h3 { font-size: 1.5em; line-height: 1.43; }
.markdown-preview[data-use-github-style] h3 .anchor { line-height: 1.2; }
.markdown-preview[data-use-github-style] h4 { font-size: 1.25em; }
.markdown-preview[data-use-github-style] h4 .anchor { line-height: 1.2; }
.markdown-preview[data-use-github-style] h5 { font-size: 1em; }
.markdown-preview[data-use-github-style] h5 .anchor { line-height: 1.1; }
.markdown-preview[data-use-github-style] h6 { font-size: 1em; color: rgb(119, 119, 119); }
.markdown-preview[data-use-github-style] h6 .anchor { line-height: 1.1; }
.markdown-preview[data-use-github-style] p, .markdown-preview[data-use-github-style] blockquote, .markdown-preview[data-use-github-style] ul, .markdown-preview[data-use-github-style] ol, .markdown-preview[data-use-github-style] dl, .markdown-preview[data-use-github-style] table, .markdown-preview[data-use-github-style] pre { margin-top: 0px; margin-bottom: 16px; }
.markdown-preview[data-use-github-style] hr { height: 4px; padding: 0px; margin: 16px 0px; background-color: rgb(231, 231, 231); border: 0px none; }
.markdown-preview[data-use-github-style] ul, .markdown-preview[data-use-github-style] ol { padding-left: 2em; }
.markdown-preview[data-use-github-style] ul.no-list, .markdown-preview[data-use-github-style] ol.no-list { padding: 0px; list-style-type: none; }
.markdown-preview[data-use-github-style] ul ul, .markdown-preview[data-use-github-style] ul ol, .markdown-preview[data-use-github-style] ol ol, .markdown-preview[data-use-github-style] ol ul { margin-top: 0px; margin-bottom: 0px; }
.markdown-preview[data-use-github-style] li > p { margin-top: 16px; }
.markdown-preview[data-use-github-style] dl { padding: 0px; }
.markdown-preview[data-use-github-style] dl dt { padding: 0px; margin-top: 16px; font-size: 1em; font-style: italic; font-weight: bold; }
.markdown-preview[data-use-github-style] dl dd { padding: 0px 16px; margin-bottom: 16px; }
.markdown-preview[data-use-github-style] blockquote { padding: 0px 15px; color: rgb(119, 119, 119); border-left: 4px solid rgb(221, 221, 221); }
.markdown-preview[data-use-github-style] blockquote > :first-child { margin-top: 0px; }
.markdown-preview[data-use-github-style] blockquote > :last-child { margin-bottom: 0px; }
.markdown-preview[data-use-github-style] table { display: block; width: 100%; overflow: auto; word-break: keep-all; }
.markdown-preview[data-use-github-style] table th { font-weight: bold; }
.markdown-preview[data-use-github-style] table th, .markdown-preview[data-use-github-style] table td { padding: 6px 13px; border: 1px solid rgb(221, 221, 221); }
.markdown-preview[data-use-github-style] table tr { background-color: rgb(255, 255, 255); border-top: 1px solid rgb(204, 204, 204); }
.markdown-preview[data-use-github-style] table tr:nth-child(2n) { background-color: rgb(248, 248, 248); }
.markdown-preview[data-use-github-style] img { max-width: 100%; box-sizing: border-box; }
.markdown-preview[data-use-github-style] .emoji { max-width: none; }
.markdown-preview[data-use-github-style] span.frame { display: block; overflow: hidden; }
.markdown-preview[data-use-github-style] span.frame > span { display: block; float: left; width: auto; padding: 7px; margin: 13px 0px 0px; overflow: hidden; border: 1px solid rgb(221, 221, 221); }
.markdown-preview[data-use-github-style] span.frame span img { display: block; float: left; }
.markdown-preview[data-use-github-style] span.frame span span { display: block; padding: 5px 0px 0px; clear: both; color: rgb(51, 51, 51); }
.markdown-preview[data-use-github-style] span.align-center { display: block; overflow: hidden; clear: both; }
.markdown-preview[data-use-github-style] span.align-center > span { display: block; margin: 13px auto 0px; overflow: hidden; text-align: center; }
.markdown-preview[data-use-github-style] span.align-center span img { margin: 0px auto; text-align: center; }
.markdown-preview[data-use-github-style] span.align-right { display: block; overflow: hidden; clear: both; }
.markdown-preview[data-use-github-style] span.align-right > span { display: block; margin: 13px 0px 0px; overflow: hidden; text-align: right; }
.markdown-preview[data-use-github-style] span.align-right span img { margin: 0px; text-align: right; }
.markdown-preview[data-use-github-style] span.float-left { display: block; float: left; margin-right: 13px; overflow: hidden; }
.markdown-preview[data-use-github-style] span.float-left span { margin: 13px 0px 0px; }
.markdown-preview[data-use-github-style] span.float-right { display: block; float: right; margin-left: 13px; overflow: hidden; }
.markdown-preview[data-use-github-style] span.float-right > span { display: block; margin: 13px auto 0px; overflow: hidden; text-align: right; }
.markdown-preview[data-use-github-style] code, .markdown-preview[data-use-github-style] tt { padding: 0.2em 0px; margin: 0px; font-size: 85%; background-color: rgba(0, 0, 0, 0.04); border-radius: 3px; }
.markdown-preview[data-use-github-style] code::before, .markdown-preview[data-use-github-style] tt::before, .markdown-preview[data-use-github-style] code::after, .markdown-preview[data-use-github-style] tt::after { letter-spacing: -0.2em; content: " "; }
.markdown-preview[data-use-github-style] code br, .markdown-preview[data-use-github-style] tt br { display: none; }
.markdown-preview[data-use-github-style] del code { text-decoration: inherit; }
.markdown-preview[data-use-github-style] pre > code { padding: 0px; margin: 0px; font-size: 100%; word-break: normal; white-space: pre; background: transparent; border: 0px; }
.markdown-preview[data-use-github-style] .highlight { margin-bottom: 16px; }
.markdown-preview[data-use-github-style] .highlight pre, .markdown-preview[data-use-github-style] pre { padding: 16px; overflow: auto; font-size: 85%; line-height: 1.45; background-color: rgb(247, 247, 247); border-radius: 3px; }
.markdown-preview[data-use-github-style] .highlight pre { margin-bottom: 0px; word-break: normal; }
.markdown-preview[data-use-github-style] pre { overflow-wrap: normal; }
.markdown-preview[data-use-github-style] pre code, .markdown-preview[data-use-github-style] pre tt { display: inline; max-width: initial; padding: 0px; margin: 0px; overflow: initial; line-height: inherit; overflow-wrap: normal; background-color: transparent; border: 0px; }
.markdown-preview[data-use-github-style] pre code::before, .markdown-preview[data-use-github-style] pre tt::before, .markdown-preview[data-use-github-style] pre code::after, .markdown-preview[data-use-github-style] pre tt::after { content: normal; }
.markdown-preview[data-use-github-style] kbd { display: inline-block; padding: 3px 5px; font-size: 11px; line-height: 10px; color: rgb(85, 85, 85); vertical-align: middle; background-color: rgb(252, 252, 252); border-width: 1px; border-style: solid; border-color: rgb(204, 204, 204) rgb(204, 204, 204) rgb(187, 187, 187); border-image: initial; border-radius: 3px; box-shadow: rgb(187, 187, 187) 0px -1px 0px inset; }
.markdown-preview[data-use-github-style] a { color: rgb(51, 122, 183); }
.markdown-preview[data-use-github-style] code { color: inherit; }
.markdown-preview[data-use-github-style] pre.editor-colors { padding: 0.8em 1em; margin-bottom: 1em; font-size: 0.85em; border-radius: 4px; overflow: auto; }
.markdown-preview pre.editor-colors { user-select: auto; }
.scrollbars-visible-always .markdown-preview pre.editor-colors .vertical-scrollbar, .scrollbars-visible-always .markdown-preview pre.editor-colors .horizontal-scrollbar { visibility: hidden; }
.scrollbars-visible-always .markdown-preview pre.editor-colors:hover .vertical-scrollbar, .scrollbars-visible-always .markdown-preview pre.editor-colors:hover .horizontal-scrollbar { visibility: visible; }
.markdown-preview .task-list-item input[type="checkbox"] { position: absolute; margin: 0.25em 0px 0px -1.4em; }
.markdown-preview .task-list-item { list-style-type: none; }
.bracket-matcher .region {
border-bottom: 1px dotted lime;
position: absolute;
}
.line-number.bracket-matcher.bracket-matcher {
color: #383a42;
background-color: #e5e5e6;
}
.spell-check-misspelling .region {
border-bottom: 2px dotted rgba(255, 51, 51, 0.75);
}
.spell-check-corrections {
width: 25em !important;
}
pre.editor-colors {
background-color: #fafafa;
color: #383a42;
}
pre.editor-colors .line.cursor-line {
background-color: rgba(56, 58, 66, 0.05);
}
pre.editor-colors .invisible {
color: #383a42;
}
pre.editor-colors .cursor {
border-left: 2px solid #526fff;
}
pre.editor-colors .selection .region {
background-color: #e5e5e6;
}
pre.editor-colors .bracket-matcher .region {
border-bottom: 1px solid #526fff;
box-sizing: border-box;
}
pre.editor-colors .invisible-character {
color: rgba(56, 58, 66, 0.2);
}
pre.editor-colors .indent-guide {
color: rgba(56, 58, 66, 0.2);
}
pre.editor-colors .wrap-guide {
background-color: rgba(56, 58, 66, 0.2);
}
pre.editor-colors .find-result .region.region.region,
pre.editor-colors .current-result .region.region.region {
border-radius: 2px;
background-color: rgba(82, 111, 255, 0.2);
transition: border-color 0.4s;
}
pre.editor-colors .find-result .region.region.region {
border: 2px solid transparent;
}
pre.editor-colors .current-result .region.region.region {
border: 2px solid #526fff;
transition-duration: .1s;
}
pre.editor-colors .gutter .line-number {
color: #9d9d9f;
-webkit-font-smoothing: antialiased;
}
pre.editor-colors .gutter .line-number.cursor-line {
color: #383a42;
background-color: #e5e5e6;
}
pre.editor-colors .gutter .line-number.cursor-line-no-selection {
background-color: transparent;
}
pre.editor-colors .gutter .line-number .icon-right {
color: #383a42;
}
pre.editor-colors .gutter:not(.git-diff-icon) .line-number.git-line-removed.git-line-removed::before {
bottom: -3px;
}
pre.editor-colors .gutter:not(.git-diff-icon) .line-number.git-line-removed::after {
content: "";
position: absolute;
left: 0px;
bottom: 0px;
width: 25px;
border-bottom: 1px dotted rgba(255, 20, 20, 0.5);
pointer-events: none;
}
pre.editor-colors .gutter .line-number.folded,
pre.editor-colors .gutter .line-number:after,
pre.editor-colors .fold-marker:after {
color: #383a42;
}
.syntax--comment {
color: #a0a1a7;
font-style: italic;
}
.syntax--comment .syntax--markup.syntax--link {
color: #a0a1a7;
}
.syntax--entity.syntax--name.syntax--type {
color: #c18401;
}
.syntax--entity.syntax--other.syntax--inherited-class {
color: #c18401;
}
.syntax--keyword {
color: #a626a4;
}
.syntax--keyword.syntax--control {
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</head>
<body class='markdown-preview' data-use-github-style><h1 id="readme">README</h1>
<h2 id="system-requirements">System Requirements</h2>
<p>The scripts should run on any operating system, though they were only tested on Windows 10 and Linux.</p>
<p>The following tools are required:</p>
<ul>
<li>ilastik (1.3.3post3, <a href="https://www.ilastik.org">https://www.ilastik.org</a>)</li>
<li>Anaconda Python distribution (2020.07, <a href="https://www.anaconda.com">https://www.anaconda.com</a>)</li>
<li>read_lif (install via <code style="font-family: Menlo, Consolas, "DejaVu Sans Mono", monospace;">pip install read_lif</code>)</li>
</ul>
<p>All Python code is in the form of Jupyter notebooks that can be run in the Browser after starting Jupyter (<code style="font-family: Menlo, Consolas, "DejaVu Sans Mono", monospace;">jupyter notebook</code> or <code style="font-family: Menlo, Consolas, "DejaVu Sans Mono", monospace;">jupyter lab</code> in a terminal). <strong>Not all cells in the notebooks are necessary, so we suggest to run them one after another</strong>, skipping sections marked as <code style="font-family: Menlo, Consolas, "DejaVu Sans Mono", monospace;">test</code> or <code style="font-family: Menlo, Consolas, "DejaVu Sans Mono", monospace;">old data</code>.</p>
<h2 id="1-data-conversion-and-metadata-extraction">1) data conversion and metadata extraction</h2>
<p>Our raw files are Leica LIF files containing multiple image series, each a 3-color confocal z-stack.
Using <code style="font-family: Menlo, Consolas, "DejaVu Sans Mono", monospace;">extract_metadata_from_lif.ipynb</code>, the metadata (especially pixel size) is read from the .lif files and saved in JSON format.
In this script, the input .lif images (<code style="font-family: Menlo, Consolas, "DejaVu Sans Mono", monospace;">files</code>) and the output path (<code style="font-family: Menlo, Consolas, "DejaVu Sans Mono", monospace;">outfile</code>) can be specified.</p>
<p>Furthermore, we have a set of manual crops around single cells, saved as 3-channel TIFF stacks. These are placed in subfolders of the folder containing the LIF files, with the folder name specifying the S-phase stage.
Cropped images follow the naming convention: <code style="font-family: Menlo, Consolas, "DejaVu Sans Mono", monospace;">[original LIF filename] - [Series name]-[index].tif</code>
Using <code style="font-family: Menlo, Consolas, "DejaVu Sans Mono", monospace;">replication_data_export.ipynb</code>, we generate single channel TIFF stacks named <code style="font-family: Menlo, Consolas, "DejaVu Sans Mono", monospace;">[channel name]_[stage]_[chase duration]_[index].tif</code> and split the metadata generated earlier into a <code style="font-family: Menlo, Consolas, "DejaVu Sans Mono", monospace;">metadata_[stage]_[chase duration]_[index].json</code> for each crop.
In the notebook, the folder containing the raw LIF files and TIF crops (<code style="font-family: Menlo, Consolas, "DejaVu Sans Mono", monospace;">rootdir</code>), the folder to save results to (<code style="font-family: Menlo, Consolas, "DejaVu Sans Mono", monospace;">outdir</code>), the channel names (<code style="font-family: Menlo, Consolas, "DejaVu Sans Mono", monospace;">channel_names</code>) and the metadata file generated above (<code style="font-family: Menlo, Consolas, "DejaVu Sans Mono", monospace;">metadata_file</code>) can be specified.</p>
<h2 id="2-semantic-segmentation-and-manual-annotation-using-ilastik">2) semantic segmentation and manual annotation using ilastik</h2>
<p>Using the singlechannel images created above, in ilastik, we created 3 pixel classification projects for the following tasks:</p>
<ul>
<li>3-class segmentation (background-nuclear border-nuclear interior) using the DAPI channel</li>
<li>2-class segmentation (background-RFi) for the EdU and PCNA channels</li>
</ul>
<p>The segmentation results (probabilites) for each file were exported as HDF5 files (dataset name <code style="font-family: Menlo, Consolas, "DejaVu Sans Mono", monospace;">probs</code>) to subfolders (<code style="font-family: Menlo, Consolas, "DejaVu Sans Mono", monospace;">classification_[channel name]</code>) of the single-channel TIFF folder under the same name as the input TIF file.</p>
<p>Using another 2-class pixel classification project, we manually annotated the center of each nucleus in the DAPI images as foreground. The manual labels are exported as HDF5 to a subfolder called <code style="font-family: Menlo, Consolas, "DejaVu Sans Mono", monospace;">markers</code>.</p>
<h2 id="3-feature-extraction">3) Feature extraction</h2>
<p>Using <code style="font-family: Menlo, Consolas, "DejaVu Sans Mono", monospace;">replication_feature_extraction.ipynb</code>, an instance segmentation is performed and features for RFi are extracted and saved in tabular form.
Since the pixel sizes in our images were not equal, we need the metadata JSON files (<code style="font-family: Menlo, Consolas, "DejaVu Sans Mono", monospace;">metadata_files</code>) to use equal dimensions in the features.
For the feature extraction, if the steps above were followed, only the marker folder (<code style="font-family: Menlo, Consolas, "DejaVu Sans Mono", monospace;">marker_dir</code>) has to be changed in the script.</p>
<p>Fine adjustment of parameters (e.g. blur radii, quantiles for normalization, ...) could be done in the function definitions for <code style="font-family: Menlo, Consolas, "DejaVu Sans Mono", monospace;">segment()</code> and <code style="font-family: Menlo, Consolas, "DejaVu Sans Mono", monospace;">get_features()</code>.</p>
<p>The path of the output CSV files can be specified in the <code style="font-family: Menlo, Consolas, "DejaVu Sans Mono", monospace;">df_edu.to_csv()</code> and <code style="font-family: Menlo, Consolas, "DejaVu Sans Mono", monospace;">df_agg.to_csv()</code> calls.</p>
<h2 id="4-visualization-and-analysis-on-features">4) Visualization and analysis on features</h2>
<p>Code for plotting histograms of RFi volume and Distance from periphery can be found at the end of <code style="font-family: Menlo, Consolas, "DejaVu Sans Mono", monospace;">replication_feature_extraction.ipynb</code>.</p>
<p>Code for t-SNE visualization, S-phase stage classification, feature importance assessment and creation of boxplots for single features can be found in <code style="font-family: Menlo, Consolas, "DejaVu Sans Mono", monospace;">replication_cluster_feature_importance.ipynb</code>. The path to the CSV file containing aggregated features (<code style="font-family: Menlo, Consolas, "DejaVu Sans Mono", monospace;">df_agg = pd.read_csv(...)</code>) or, alternatively, single RFi features (<code style="font-family: Menlo, Consolas, "DejaVu Sans Mono", monospace;">df_edu = pd.read_csv(...)</code>) can be specified in the code.</p></body>
</html>