interfaces.html

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        <h1>
          Software Interfaces
        </h1>

        <ul>
          <li>
            <a href="#datatools">Software for analyzing CellProfiler-produced
            data</a>
          </li>

          <li>
            <a href="#partners">Software partnerships</a>
          </li>
        </ul>
        <a name="datatools"></a>
        <h2>
          Software for analyzing CellProfiler-produced data
        </h2>

        <table border="0" cellpadding="15">
          <tr>
            <td align="center">
              <b>Software</b>
            </td>
            <td align="center">
              <b>Description</b>
            </td>
            <td align="center">
              <b>Interface</b>
            </td>
          </tr>

          <tr>
            <td align="center">
              <a href="http://www.cellprofiler.org/download.html" style=
              "text-decoration:none"><img src="http://d1zymp9ayga15t.cloudfront.net/images/cp_128.png" vspace="5"
              width="100" /><br />
              <b>CellProfiler</b></a>
            </td>
            <td align="center">
              In addition to performing image analysis to generate
              measurements, CellProfiler has built-in tools in the <i>Data
              Tools</i> menu to generate a few types of plots.
            </td>
            <td>
              CellProfiler output files in MATLAB (.mat) and HDF5 (.h5) can be
              opened by CellProfiler's data tools.
            </td>
          </tr>

          <tr>
            <td align="center">
              <a href="http://www.cellprofiler.org/downloadCPA.html" style=
              "text-decoration:none"><img src="http://d1zymp9ayga15t.cloudfront.net/images/cpa_128.png" vspace="5"
              width="100" /><br />
              <b>CellProfiler Analyst</b></a>
            </td>
            <td>
              CellProfiler Analyst allows analysis, exploration and
              machine-learning for high-dimensional image-based data.
            </td><!--<table cellpadding="5">
<tr><td align="center"><a href="http://www.mysql.com/"><img src="http://d1zymp9ayga15t.cloudfront.net/images/logo_mysql.jpg" height=50></a></td><td align="center"><a href="http://www.sqlite.org/"><img src="http://d1zymp9ayga15t.cloudfront.net/images/logo_sqlite.gif" width=100></a></td></tr>
</table> -->

            <td align="center">
              CellProfiler Analyst can be used with data that follows a simple
              format: One image table with rows of databases produced in
              CellProfiler using the <a href="http://d1zymp9ayga15t.cloudfront.net/CPmanual/ExportToDatabase.html">ExportToDatabase</a>
              module or data tool.
            </td>
          </tr>

          <tr>
            <td align="center">
              <a href="http://accelrys.com/platform/enterprise-platform.html"
              style="text-decoration:none"><img src="http://d1zymp9ayga15t.cloudfront.net/images/logo_accelrys.png"
              vspace="5" width="200" /><br />
              <b>Accelrys</b></a>
            </td>
            <td>
              The Component Collections of the Accelrys Enterprise Platform
              (AEP) allows researchers to build, deploy, analyze and report on
              complex scientific data types within the Accelrys applications
              framework and other third-party applications.
            </td>
            <td align="center">
              The Pipeline Pilot <a href=
              "http://accelrys.com/products/pipeline-pilot/component-collections/imaging.html">
              Imaging Component Collection</a> provides a component,
              'CellProfiler (on Server)', for integration with CellProfiler.
              The user can run a protocol and send images to be analyzed into
              CellProfiler as input, and allows for images and analysis data to
              be retrieved from CellProfiler for downstream data workflows
              enabled by AEP. Some details on using the component are provided
              <a href=
              "http://d1zymp9ayga15t.cloudfront.net/content/Accelyrs_AEP_CellProfilerOnServer_Usage_tips.pdf">here</a>.
            </td>
          </tr>

          <tr>
            <td align="center">
              <a href=
              "http://www.perkinelmer.com/pages/020/cellularimaging/products/columbus.xhtml"
              style="text-decoration:none"><img src="http://d1zymp9ayga15t.cloudfront.net/images/logo_columbus.png"
              vspace="5" width="200" /><br />
              <b>Columbus</b></a>
            </td>
            <td>
              The Columbus system (Perkin Elmer) is a universal high-volume
              image data storage and analysis system that brings access to
              images from a wide range of sources including all major high
              content screening instruments via the Internet.
            </td>
            <td align="center">
              Using the final building block (Define Results) of a Columbus
              analysis routine, data can be exported in a format that
              CellProfiler Analyst can read. Instructions <a href=
              "http://d1zymp9ayga15t.cloudfront.net/Exporting_images_data_from_Columbus_to_CellProfiler_Analyst.pdf">
              here</a>.
            </td>
          </tr>

          <tr>
            <td align="center">
              <table>
                <tr>
                  <td align="center">
                    <a href="http://office.microsoft.com/en-us/excel/" style=
                    "text-decoration:none"><img hspace="20" src=
                    "http://d1zymp9ayga15t.cloudfront.net/images/logo_excel.png" vspace="5" width="50" /><br />
                    <b>Excel</b></a>
                  </td>
                  <td align="center">
                    <a href="https://www.libreoffice.org/discover/calc/" style=
                    "text-decoration:none"><img hspace="20" src=
                    "http://d1zymp9ayga15t.cloudfront.net/images/logo_openofficecalc.png" vspace="5" width=
                    "50" /><br />
                    <b>Calc</b></a>
                  </td>
                </tr>

                <tr>
                  <td align="center">
                    <a href=
                    "http://www.graphpad.com/scientific-software/prism/" style=
                    "text-decoration:none"><img hspace="20" src=
                    "http://d1zymp9ayga15t.cloudfront.net/images/logo_graphpadprism.png" vspace="5" width=
                    "50" /><br />
                    <b>Prism</b></a>
                  </td>
                </tr>
              </table>
            </td>
            <td>
              Spreadsheet programs like these are useful for plotting small
              amounts of data. Excel (Microsoft) is a general business
              comercial package, whereas Prism (Graphpad) is a commercial
              program tailored towards research scientists for statistical
              analyses. Calc (LibreOffice) is open-source software and
              freely-available.
            </td>
            <td align="center">
              These tools can read comma- or tab-delimited files generated by
              the CellProfiler <a href=
              "http://d1zymp9ayga15t.cloudfront.net/CPmanual/ExportToSpreadsheet.html">ExportToSpreadsheet</a>
              module or data tool.
            </td>
          </tr>

          <tr>
            <td align="center">
              <a href="http://www.denovosoftware.com/" style=
              "text-decoration:none"><img src="http://d1zymp9ayga15t.cloudfront.net/images/logo_fcs_express.jpg"
              vspace="5" width="200" /><br />
              <b>FCS Express Image Cytometry</b></a>
            </td>
            <td>
              FCS Express 4 Image Cytometry (De Novo Software) provides
              population based analytical tools common in flow cytometry. The
              image cytometry version allows the user to review and analyze
              multi-parametric data sets and relate results back to the
              original images.
            </td>
            <td align="center">
              FCS Express 4 software can <a href=
              "http://www.denovosoftware.com/site/manual/index.html?cell_profiler_export.htm">
              import</a> comma-delimited files produced by the CellProfiler
              <a href=
              "http://d1zymp9ayga15t.cloudfront.net/CPmanual/ExportToSpreadsheet.html">ExportToSpreadsheet</a>
              module or data tool.
            </td>
          </tr>

          <tr>
            <td align="center">
              <a href=
              "http://www.broadinstitute.org/cancer/software/genepattern/"
              style="text-decoration:none"><img src=
              "http://d1zymp9ayga15t.cloudfront.net/images/logo_genepattern.jpg" vspace="5" width="200" /><br />
              <b>GenePattern</b></a>
            </td>
            <td>
              GenePattern (Broad Institute) is open source software that gives
              a broad audience access to a growing repository of sophisticated
              analytic tools for genomic data, while an API supports
              computational biologists.
            </td>
            <td align="center">
              CellProfiler can format and export image-based data as a
              GenePattern GCT file (.gct) through the <a href=
              "http://d1zymp9ayga15t.cloudfront.net/CPmanual/ExportToSpreadsheet.html">ExportToSpreadsheet</a>
              module or data tool.
            </td>
          </tr>

          <tr>
            <td align="center">
              <a href=
              "http://www.gelifesciences.com/webapp/wcs/stores/servlet/CategoryDisplay?categoryId=1309574&catalogId=78149&productId=&top=Y&storeId=11787&langId=-1"
              style="text-decoration:none"><img src="http://d1zymp9ayga15t.cloudfront.net/images/GE_logo.png" width=
              "180" /><br />
              <b>IN Cell Analyzer</b></a>
            </td>
            <td>
              IN Cell Analyzer automated cell imaging systems yield
              morphological and molecular data via high content imaging and
              analysis.
            </td>
            <td align="center">
              The IN Cell Analyzer acquisition software from GE Healthcare
              generates customizable CSV reports in a format that allows
              CellProfiler to import images and metadata via the LoadData
              module.
            </td>
          </tr>

          <tr>
            <td align="center">
              <a href="http://www.knime.org/" style=
              "text-decoration:none"><img src="http://d1zymp9ayga15t.cloudfront.net/images/logo_knime.jpg" width=
              "200" /><br />
              <b>KNIME</b></a>
            </td>
            <td>
              KNIME (University of Konstanz) is an open source modular data
              exploration platform that enables the user to visually create
              data flows, selectively execute some or all analysis steps, and
              later investigate the results through interactive views on data
              and models.
            </td>
            <td align="center">
              KNIME includes a Database Reader node that can access
              CellProfiler-produced data. [<a href=
              "https://github.com/CellProfiler/CellProfiler/wiki/Interfacing-with-other-software">more</a>]
            </td>
          </tr>

          <tr>
            <td align="center">
              <a href="http://www.mathworks.com/products/matlab/" style=
              "text-decoration:none"><img src="http://d1zymp9ayga15t.cloudfront.net/images/logo_matlab.png" vspace=
              "5" width="100" /><br />
              <b>MATLAB</b></a>
            </td>
            <td>
              MATLAB (Mathworks) is a high-level language and interactive
              environment for data analysis and visualization.
            </td>
            <td align="center">
              CellProfiler can produce MATLAB (.mat) output files.
            </td>
          </tr>

          <tr>
            <td>
              <table cellpadding="5">
                <tr>
                  <td align="center">
                    <a href="http://www.r-project.org/" style=
                    "text-decoration:none"><img height="50" hspace="20" src=
                    "http://d1zymp9ayga15t.cloudfront.net/images/logo_r.png" vspace="5" /><br />
                    <b>R</b></a>
                  </td>
                  <td align="center">
                    <a href="http://www.python.org/" style=
                    "text-decoration:none"><img height="50" hspace="20" src=
                    "http://d1zymp9ayga15t.cloudfront.net/images/logo_python.png" vspace="5" /><br />
                    <b>Python</b></a>
                  </td>
                </tr>
              </table>
            </td>
            <td>
              Any analysis or visualization tools that can query a database
              (such as R or python+pylab) can be used to analyze data that has
              been deposited into a MySQL database.
            </td>
            <td align="center">
              Databases containing image and/or object data can be produced
              using the CellProfiler <a href=
              "http://d1zymp9ayga15t.cloudfront.net/CPmanual/ExportToDatabase.html">ExportToDatabase</a>
              module or data tool. <a href=
              "http://code.google.com/p/cellprofile-r/">CellProfile-R</a>, an R
              package for CellProfiler database access and analysis, is
              available. Users can write their own CellProfiler modules in
              Python by following the instructions <a href=
              "https://github.com/CellProfiler/CellProfiler/wiki#wiki-What_if_I_want_to_contribute_to_CellProfiler">
              here</a>.
            </td>
          </tr>

          <tr>
            <td align="center">
              <a href="http://www.cambridgesoft.com/ensemble/spotfire/" style=
              "text-decoration:none"><img src="http://d1zymp9ayga15t.cloudfront.net/images/logo_perkinspotfire.png"
              vspace="5" width="200" /><br />
              <b>Spotfire</b></a>
            </td>
            <td>
              Spotfire provides a dynamic, collaborative interface that
              assimilates data from multiple sources— chemical structures,
              text, numbers, images, chemical properties, biological assays,
              and more—and empowers you to perform complex analyses and create
              easy-to-use visual dashboards.
            </td>
            <td align="center">
              SpotFire is able to import data generated by the CellProfiler
              <a href=
              "http://d1zymp9ayga15t.cloudfront.net/CPmanual/ExportToSpreadsheet.html">ExportToSpreadsheet</a>
              (for small data sets) or <a href=
              "http://d1zymp9ayga15t.cloudfront.net/CPmanual/ExportToDatabase.html">ExportToDatabase</a>
              modules or data tools (for large data sets).
            </td>
          </tr>
        </table>

        <h2>
          <a name="partners">Software Partnerships</a>
        </h2>

        <p>
          <a name="partners">CellProfiler has partnered with academic and
          commercial groups to create a variety of software interfaces. These
          efforts not only expand the functionality of CellProfiler and
          CellProfiler Analyst but also leverage the strengths of other
          packages.</a>
        </p>

        <table border="0" cellpadding="15">
          <tr>
            <td align="center">
              <b>Software</b>
            </td>
            <td align="center">
              <b>Description</b>
            </td>
            <td align="center">
              <b>Interface</b>
            </td>
          </tr>

          <tr>
            <td align="center">
              <a href=
              "http://www.openmicroscopy.org/site/support/bio-formats/users/cellprofiler/" style=
              "text-decoration:none"><img src="http://d1zymp9ayga15t.cloudfront.net/images/bioformat.png"
              vspace="5" width="200" /><br />
              <b>BioFormats</b></a>
            </td>
            <td>
              Bio-Formats is an open source Java library for reading and
              writing microscopy file formats. It facilitates the exchange of
              microscopy data by converting proprietary microscopy data into
              the OME data model standard.
            </td>
            <td align="center">
              CellProfiler 2.1.0 is packaged with Bio-Formats and uses it to
              read/write images from disk, as well as write movies. [<a href=
              "http://loci.wisc.edu/bio-formats/cellprofiler">more</a>]
            </td>
          </tr>

          <tr>
            <td align="center">
              <a href="http://www.ilastik.org/" style=
              "text-decoration:none"><img src="http://d1zymp9ayga15t.cloudfront.net/images/logo_ilastik.png" vspace=
              "5" width="75" /><br />
              <b>Ilastik</b></a>
            </td>
            <td>
              Ilastik is an open source tool for pixel-based classification of
              2,3 and 4D images. The user first trains a classifier by
              identifying areas of images that fall into one of several
              classes, such as cell body, nucleus, background or membrane. The
              classifier can then be applied to those and similar images to
              identify areas in those images that correspond to the trained
              classes.
            </td>
            <td align="center">
              CellProfiler can read a classifier file from Ilastik and apply
              its classifiers to an image using the <a href=
              "http://d1zymp9ayga15t.cloudfront.net/CPmanual/ClassifyPixels.html">ClassifyPixels</a>
              module to produce a probability map: an image whose intensity is
              higher for parts of images that are likely to be the chosen
              class. [<a href=
              "http://old.ilastik.org/index.php?cat=20_Documentation&page=03_Cellprofiler">more</a>]
            </td>
          </tr>

          <tr>
            <td align="center">
              <a href="http://imagej.nih.gov/ij/" style=
              "text-decoration:none"><img src="http://d1zymp9ayga15t.cloudfront.net/images/logo_imagej.png" vspace=
              "5" width="75" /><br />
              <b>ImageJ</b></a>
            </td>
            <td>
              ImageJ is an open source image processing program providing
              extensibility via Java plugins and recordable macros. Custom
              acquisition, analysis and processing plugins can be developed
              using a built-in editor and a Java compiler.
            </td>
            <td align="center">
              Via the RunImageJ module, CellProfiler can load images, run an
              ImageJ macro or plugin on them, and retrieve the results for
              downstream analysis via the <a href=
              "http://d1zymp9ayga15t.cloudfront.net/CPmanual/RunImageJ.html">RunImageJ</a>
              module.
            </td>
          </tr>

          <tr>
            <td align="center">
              <a name="OMERO"></a><a href="http://www.openmicroscopy.org/site"
              style="text-decoration:none"><img src="http://d1zymp9ayga15t.cloudfront.net/images/ome-logo-800.png"
              vspace="5" width="200" /><br />
              <b>Open Microscopy Environment (OME)</b></a>
            </td>
            <td>
              OMERO is an open source application for visualization,
              management, and analysis of biological image data. It allows the
              scientists to remotely manage, view, annotate and measure
              multi-dimensional images from anywhere.
            </td>
            <td align="center">
              The 2.1.0 release of CellProfiler has first-class support for
              loading images from OMERO. Details can be found by following
              <a href=
              "https://github.com/CellProfiler/CellProfiler/wiki/OMERO:-Accessing-images-from-CellProfiler">
              this link</a>.
            </td>
          </tr>

          <tr>
            <td>
              <table>
                <tr>
                  <td align="center">
                    <a href=
                    "http://www.imls.uzh.ch/research/pelkmans/softwareprojects/iBRAIN.html"
                    style="text-decoration:none"><img hspace="20" src=
                    "http://d1zymp9ayga15t.cloudfront.net/images/logo_ibrain.png" vspace="5" width="100" /><br />
                    <b>iBrain</b></a>
                  </td>
                  <td align="center">
                    <a href="http://www.cisd.ethz.ch/software/openBIS" style=
                    "text-decoration:none"><img src="http://d1zymp9ayga15t.cloudfront.net/images/logo_openbis.png"
                    vspace="5" width="100" /><br />
                    <b>openBIS</b></a>
                  </td>
                </tr>
              </table>
            </td>
            <td>
              OpenBIS is a data management framework to track and annotate raw
              data for screening, proteomics, FACS and deep sequencing data.
              iBRAIN is a platform for performing image analysis on large
              datasets automatically.
            </td>
            <td align="center">
              The SyBIT project, part of <a href=
              "http://www.SystemsX.ch">SystemsX</a>, delivers integrated
              analysis pipelines that use CellProfiler as a building block.
              SyBIT has developed automated workflows for data exchange and
              analysis based on the openBIS database, CellProfiler, and iBRAIN,
              using cluster infrastructures for data processing. The project
              continues to tailor these workflows to suit the research needs of
              several systems biology projects.
            </td>
          </tr>
        </table>
      </div>