tutorials.html

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<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>