source: trunk/doc/src/docbook/userdoc/scans_images.xml @ 4509

Last change on this file since 4509 was 4509, checked in by Jari Häkkinen, 13 years ago

Addresses #1106. Missed to change reference wherefrom retrive GPLv3 license text. And some other changes.

  • Property svn:eol-style set to native
  • Property svn:keywords set to Date Id
File size: 5.2 KB
Line 
1<?xml version="1.0" encoding="UTF-8"?>
2<!DOCTYPE sect1 PUBLIC
3    "-//Dawid Weiss//DTD DocBook V3.1-Based Extension for XML and graphics inclusion//EN"
4    "../../../../lib/docbook/preprocess/dweiss-docbook-extensions.dtd">
5<!--
6  $Id: scans_images.xml 4509 2008-09-11 20:01:44Z jari $
7
8  Copyright (C) 2007 Peter Johansson, Nicklas Nordborg
9
10  This file is part of BASE - BioArray Software Environment.
11  Available at http://base.thep.lu.se/
12
13  BASE is free software; you can redistribute it and/or
14  modify it under the terms of the GNU General Public License
15  as published by the Free Software Foundation; either version 3
16  of the License, or (at your option) any later version.
17
18  BASE is distributed in the hope that it will be useful,
19  but WITHOUT ANY WARRANTY; without even the implied warranty of
20  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
21  GNU General Public License for more details.
22
23  You should have received a copy of the GNU General Public License
24  along with BASE. If not, see <http://www.gnu.org/licenses/>.
25-->
26<sect1 id="experiments_analysis.scans">
27  <title>Scans and images</title>
28  <para>
29    When you have done your hybridization and scanned it,
30    you can register information about the scanning process
31    as a <guilabel>Scan</guilabel> item in BASE. A scan
32    item holds information about the scanning process,
33    such as which scanner and what settings you have
34    used. It can also hold information about the images
35    that was produced as well as the actual image files.
36  </para>
37 
38  <note>
39    A scan does not have information about the spots or
40    raw data. The process of analysing the images is
41    considered a separate step. This information is held
42    by raw bioassays.
43  </note>
44 
45  <sect2 id="experiment_analysis.scans.properties">
46    <title>Scan properties</title>
47   
48    <para>
49      A scan has the following properties:
50    </para>
51   
52    <helptext external_id="scan.edit" title="Edit scan">
53    <variablelist>
54      <varlistentry>
55        <term><guilabel>Name</guilabel></term>
56        <listitem>
57          <para>
58            The name of the scan.
59          </para>
60        </listitem>
61      </varlistentry>
62      <varlistentry>
63        <term><guilabel>Hybridization</guilabel></term>
64        <listitem>
65          <para>
66            The hybridization this scan comes from.
67          </para>
68        </listitem>
69      </varlistentry>
70      <varlistentry>
71        <term><guilabel>Scanner</guilabel></term>
72        <listitem>
73          <para>
74            The scanner that was used (optional).
75          </para>
76        </listitem>
77      </varlistentry>
78      <varlistentry>
79        <term><guilabel>Protocol</guilabel></term>
80        <listitem>
81          <para>
82            The protocol used for scanning (optional). Scanning
83            parameters may be registered as part of
84            the protocol.
85          </para>
86        </listitem>
87      </varlistentry>
88      <varlistentry>
89        <term><guilabel>Description</guilabel></term>
90        <listitem>
91          <para>
92            A decription of the scan (optional).
93          </para>
94        </listitem>
95      </varlistentry>
96    </variablelist>
97   
98    <seeother>
99      <other external_id="annotations.edit">Annotations</other>
100      <other external_id="annotations.edit.inerited">Inherit annotations</other>
101    </seeother>
102   
103    </helptext>
104   
105    <para>
106      A scan can have annotations. Read more about this in
107      <xref linkend="annotations"/>.
108    </para>
109   
110  </sect2>
111 
112  <sect2 id="experiment_analysis.scans.images">
113    <title>Images</title>
114   
115    <para>
116      If you want you can upload the images from the scan
117      to BASE. This is optional, but the images
118      are needed if you want to create spot images later
119      on.
120    </para>
121   
122    <para>
123      To upload images for a scan you must first go to
124      the single-item view for the scan. On this page
125      you will find the <guilabel>Images</guilabel>
126      tab which will take you to a list view
127      of the images from this scan. New images are created
128      in the same way as any other item in BASE,
129      by clicking the <guilabel>New&hellip;</guilabel> button.
130      You may add as many images as you like.
131    </para>
132   
133    <para>
134      An image has the following properties:
135    </para>
136
137    <helptext external_id="image.edit" title="Edit image">
138   
139    <variablelist>
140      <varlistentry>
141        <term><guilabel>Name</guilabel></term>
142        <listitem>
143          <para>
144            The name of the image. The name is automatically
145            generated from the name of the scan, but you may
146            enter a different name.
147          </para>
148        </listitem>
149      </varlistentry>
150      <varlistentry>
151        <term><guilabel>File</guilabel></term>
152        <listitem>
153          <para>
154            The file containing the actual
155            image data (optional). Use the <guibutton>Select</guibutton>
156            button to select an existing file or upload a new
157            one.
158          </para>
159        </listitem>
160      </varlistentry>
161      <varlistentry>
162        <term><guilabel>Format</guilabel></term>
163        <listitem>
164          <para>
165            The image format (optional). You can select between
166            <emphasis>TIFF</emphasis>, <emphasis>JPEG</emphasis> 
167            and <emphasis>Unknown</emphasis>.
168          </para>
169        </listitem>
170      </varlistentry>
171      <varlistentry>
172        <term><guilabel>Preview</guilabel></term>
173        <listitem>
174          <para>
175            If the image is a preview image or the full
176            scan.
177          </para>
178        </listitem>
179      </varlistentry>
180      <varlistentry>
181        <term><guilabel>Description</guilabel></term>
182        <listitem>
183          <para>
184            A description of the image (optional).
185          </para>
186        </listitem>
187      </varlistentry>
188    </variablelist>
189    </helptext>       
190   
191  </sect2>
192 
193</sect1>
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