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tutorials.html
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---
layout: default
redirect_from: "/tutorials.shtml"
---
<h1>Tutorials</h1>
<p style="font-size:11px">Documents are in PDF and PPS (self-starting
Powerpoint slide) format.</p>
<p>Technical descriptions of CellProfiler and CellProfiler Analyst software
can be found in <a href="citations.html">our papers</a>.</p>
<p>Our introduction to automated image analysis principles and
practicalities is published as an <a href=
"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000603">
educational article</a> at PLoS.</p>
<p>The NIH has published a introductory <a href=
"http://www.ncbi.nlm.nih.gov/books/NBK100913/">chapter</a> of "best
practices" for image-based high-content screening (in which CellProfiler is
mentioned) as part of the <a href=
"http://www.ncbi.nlm.nih.gov/books/NBK53196/">Assay Guidance Manual</a>,
and our group has published a more advanced follow-up <a href=
"http://www.ncbi.nlm.nih.gov/books/n/assayguide/hcsimage/">chapter</a> on
image analysis methods.</p>
<h3><a id="CPVideoTutorials" name="CPVideoTutorials">CellProfiler Video
Tutorials</a>
</h3>
<div style="list-style: none; margin-left: 2em">
<div class="column">
<center>
<iframe allowfullscreen="" frameborder="0" height="315" src=
"https://www.youtube.com/embed/OEHYXdOINg0" width=
"560"></iframe><br>
CellProfiler: Getting Started. Demonstrates some of
CellProfiler's features.<br>
<iframe allowfullscreen="" frameborder="0" height="315" src=
"https://www.youtube.com/embed/J0JPUrDNHJ0" width=
"560"></iframe><br>
Pipeline example to find individual worms. [<a href=
"http://d1zymp9ayga15t.cloudfront.net/Pipeline1.pdf">PDF</a>]
</center>
</div>
<br>
<ul style="list-style:none">
<li>For an introductory tutorial to construct pipelines, visit
<a href=
"https://youtu.be/PEaiGs18AF0?list=PL7CC87670239B4D10">CellProfiler:
Constructing pipelines</a>. [<a href=
"http://d1zymp9ayga15t.cloudfront.net/Constructing_Pipelines.pdf">PDF</a>]
</li>
<li style="list-style: none"><br>
</li>
<li>
<a href="https://www.youtube.com/embed/WTHY4Rbf49M">Using
CellProfiler and FCS Express 4 Image Cytometry</a>: joint
webinar with <a href=
"http://denovosoftware.com/site/recordedWebinars.shtml">DeNovo
Software</a> on using CellProfiler to peform basic image assays
and generate data compatible with export into FCS Express.
</li>
</ul>
<h3><a id="CPWrittenTutorials" name="CPWrittenTutorials">CellProfiler
Written Tutorials</a>
</h3>
<ul style="list-style:none">
<li>Using CellProfiler for Quantitative Image Analysis <a href=
"http://d1zymp9ayga15t.cloudfront.net/content/Using_CellProfiler_for_quantitative_analysis.pptx">
[PPT]</a>
</li>
<li>Using the Input modules in CellProfiler 2.1:
<ul>
<li>Images <a href=
"http://d1zymp9ayga15t.cloudfront.net/tutorials/Using%20the%20Images%20module.pdf">
[PDF]</a>
</li>
<li>Metadata <a href=
"http://d1zymp9ayga15t.cloudfront.net/tutorials/Using%20the%20Metadata%20module.pdf">
[PDF]</a>
</li>
<li>NamesAndTypes <a href=
"http://d1zymp9ayga15t.cloudfront.net/tutorials/Using%20the%20NamesAndTypes%20module.pdf">
[PDF]</a>
</li>
<li>Groups <a href=
"http://d1zymp9ayga15t.cloudfront.net/tutorials/Using%20the%20Groups%20module.pdf">
[PDF]</a>
</li>
<li>Loading image stacks and movies <a href=
"http://d1zymp9ayga15t.cloudfront.net/tutorials/Loading_image_stacks_and_movies.pdf">
[PDF]</a>
</li>
</ul>
</li>
<li>Identifying, measuring, and classifying yeast colonies
<a href="http://d1zymp9ayga15t.cloudfront.net/content/papers/85-Bray_CurrentProtocols_2015.pdf">
[PDF]</a> (<a href="examples.html#YeastColonies">relevant
example pipeline</a>)
</li>
<li>Identifying and measuring cells: Cytoplasm-nucleus
translocation assay <a href=
"http://d1zymp9ayga15t.cloudfront.net/content/papers/29-Carpenter_MethodsMolBio_2009.pdf">
[PDF]</a> (<a href="examples.html#SBS_Bioimage_CNT">relevant
example pipeline</a>)
</li>
<li>Calculating and applying illumination correction for images
<a href=
"http://d1zymp9ayga15t.cloudfront.net/content/ExampleIlluminationCorrection_Tutorial.pdf">
[PDF]</a> (<a href=
"examples.html#IlluminationCorrection">relevant example
pipeline</a>)
</li>
<li>Using the <a href="http://dx.doi.org/10.1038/nmeth.1984">Worm
Toolbox</a> for image analysis of <i>C. elegans</i> phenotypes
<a href=
"http://d1zymp9ayga15t.cloudfront.net/content/WormToolbox_How_to_get_started.pdf">
[PDF]</a> (<a href="examples.html#WormToolbox">relevant example
pipelines</a>)
</li>
<li>Performing a colocalization assay <a href=
"http://d1zymp9ayga15t.cloudfront.net/content/ExampleColocalization_Tutorial.pdf">
[PDF]</a> (<a href="examples.html#Colocalization">relevant
example pipeline</a>)
</li>
<li>Simple nuclei identification tutorial <a href=
"http://d1zymp9ayga15t.cloudfront.net/content/CellProfiler_BasicIntroduction.pdf">
[PDF]</a> (<a href=
"http://d1zymp9ayga15t.cloudfront.net/Example-RawData_CountNuclei.zip">sample
data</a>) (courtesy of the <a href=
"http://germanbioimaging.org/wiki/index.php/Main_Page">German
BioImaging</a> network)
</li>
</ul>
<ul style="list-style:none">
<li>We also post guided exercises as part of our educational
outreach effort <a href="outreach.html">here</a>.
</li>
</ul>
<h3><a id="CPAVideoTutorials" name="CPAVideoTutorials">CellProfiler
Analyst Video Tutorials</a>
</h3>
<div style="list-style: none; margin-left: 2em">
<div class="column">
<iframe allowfullscreen="" frameborder="0" height="315" src=
"https://www.youtube.com/embed/g7rMdA44fZ0?list=PL7CC87670239B4D10"
width="560"></iframe><br>
Demonstrates some of CellProfiler Analyst's data exploration
features. [<a href="http://d1zymp9ayga15t.cloudfront.net/Exploring_Image_Data.pdf">PDF</a>]
<iframe allowfullscreen="" frameborder="0" height="315" src=
"https://www.youtube.com/embed/9mKrR9J3n2w?list=PL7CC87670239B4D10"
width="560"></iframe><br>
Provides an example of selecting phenotypes using gating.
</div>
<br>
For applying the machine learning tool to identify a phenotype of
interest, vist <a href=
"https://youtu.be/XMKgiRGb4IY?list=PL7CC87670239B4D10">Classifying
cells with machine learning</a>. [<a href=
"http://d1zymp9ayga15t.cloudfront.net/Classifying_Cells.pdf">PDF</a>]<br>
For all CellProfiler tutorials, visit <a href=
"https://www.youtube.com/user/broadinstitute/search?query=cellprofiler">
our YouTube channel</a>.
</div>