source: trunk/doc/src/docbook/userdoc/scans_images.xml @ 3318

<?xml version="1.0" encoding="UTF-8"?>
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<sect1 id="experiments_analysis.scans">
  <title>Scans and images</title>
  <para>
    When you have done your hybridization and scanned it,
    you can register information about the scanning process
    as a <guilabel>Scan</guilabel> item in BASE. A scan
    item holds information about the scanning process,
    such as which scanner and what settings you have 
    used. It can also hold information about the images
    that was produced as well as the actual image files.
  </para>
  
  <note>
    A scan doesn't have information about the spots or
    raw data. The process of analysing the images is
    considered a separate step. This information is held
    by raw bioassays.
  </note>
  
  <sect2 id="experiment_analysis.scans.properties">
    <title>Scan properties</title>
    
    <para>
      A scan has the following properties:
    </para>
    
    <helptext external_id="scan.edit" title="Edit scan">
    <variablelist>
      <varlistentry>
        <term><guilabel>Name</guilabel></term>
        <listitem>
          <para>
            The name of the scan.
          </para>
        </listitem>
      </varlistentry>
      <varlistentry>
        <term><guilabel>Hybridization</guilabel></term>
        <listitem>
          <para>
            The hybridization this scan comes from.
          </para>
        </listitem>
      </varlistentry>
      <varlistentry>
        <term><guilabel>Scanner</guilabel></term>
        <listitem>
          <para>
            The scanner that was used (optional).
          </para>
        </listitem>
      </varlistentry>
      <varlistentry>
        <term><guilabel>Protocol</guilabel></term>
        <listitem>
          <para>
            The protocol used for scanning (optional). Scanning
            parameters may be registered as part of
            the protocol.
          </para>
        </listitem>
      </varlistentry>
      <varlistentry>
        <term><guilabel>Description</guilabel></term>
        <listitem>
          <para>
            A decription of the scan (optional).
          </para>
        </listitem>
      </varlistentry>
    </variablelist>
    
    <seeother>
      <other external_id="annotations.edit">Annotations</other>
      <other external_id="annotations.edit.inerited">Inherit annotations</other>
    </seeother>
    
    </helptext>
    
    <para>
      A scan can have annotations. Read more about this in
      <xref linkend="annotations"/>.
    </para>
    
  </sect2>
  
  <sect2 id="experiment_analysis.scans.images">
    <title>Images</title>
    
    <para>
      If you want you can upload the images from the scan
      to BASE. This is optional, but the images
      are needed if you want to create spot images later 
      on.
    </para>
    
    <para>
      To upload images for a scan you must first go to
      the single-item view for the scan. On this page
      you will find the <guilabel>Images</guilabel>
      tab which will take you to a list view 
      of the images from this scan. New images are created
      in the same way as any other item in BASE,
      by clicking the <guilabel>New&hellip;</guilabel> button.
      You may add as many images as you like.
    </para>
    
    <para>
      An image has the following properties:
    </para>

    <helptext external_id="image.edit" title="Edit image">
    
    <variablelist>
      <varlistentry>
        <term><guilabel>Name</guilabel></term>
        <listitem>
          <para>
            The name of the image. The name is automatically
            generated from the name of the scan, but you may
            enter a different name.
          </para>
        </listitem>
      </varlistentry>
      <varlistentry>
        <term><guilabel>File</guilabel></term>
        <listitem>
          <para>
            The file containing the actual
            image data (optional). Use the <guibutton>Select</guibutton>
            button to select an existing file or upload a new
            one.
          </para>
        </listitem>
      </varlistentry>
      <varlistentry>
        <term><guilabel>Format</guilabel></term>
        <listitem>
          <para>
            The image format (optional). You can select between
            <emphasis>TIFF</emphasis>, <emphasis>JPEG</emphasis> 
            and <emphasis>Unknown</emphasis>.
          </para>
        </listitem>
      </varlistentry>
      <varlistentry>
        <term><guilabel>Preview</guilabel></term>
        <listitem>
          <para>
            If the image is a preview image or the full
            scan.
          </para>
        </listitem>
      </varlistentry>
      <varlistentry>
        <term><guilabel>Description</guilabel></term>
        <listitem>
          <para>
            A description of the image (optional).
          </para>
        </listitem>
      </varlistentry>
    </variablelist>
    </helptext>       
    
  </sect2>
  
</sect1>