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

Last change on this file since 3318 was 3318, checked in by Nicklas Nordborg, 14 years ago

Split 'Experiments and analysis' into several files.
Wrote 'Scans and images' section and part of 'Raw bioassays' section.

File size: 5.4 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: experiments_analysis.xml 3308 2007-05-08 12:34:07Z nicklas $
7
8  Copyright (C) Authors contributing to this file.
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 2
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 this program; if not, write to the Free Software
25  Foundation, Inc., 59 Temple Place - Suite 330,
26  Boston, MA  02111-1307, USA.
27-->
28<sect1 id="experiments_analysis.scans">
29  <title>Scans and images</title>
30  <para>
31    When you have done your hybridization and scanned it,
32    you can register information about the scanning process
33    as a <guilabel>Scan</guilabel> item in BASE. A scan
34    item holds information about the scanning process,
35    such as which scanner and what settings you have
36    used. It can also hold information about the images
37    that was produced as well as the actual image files.
38  </para>
39 
40  <note>
41    A scan doesn't have information about the spots or
42    raw data. The process of analysing the images is
43    considered a separate step. This information is held
44    by raw bioassays.
45  </note>
46 
47  <sect2 id="experiment_analysis.scans.properties">
48    <title>Scan properties</title>
49   
50    <para>
51      A scan has the following properties:
52    </para>
53   
54    <helptext external_id="scan.edit" title="Edit scan">
55    <variablelist>
56      <varlistentry>
57        <term><guilabel>Name</guilabel></term>
58        <listitem>
59          <para>
60            The name of the scan.
61          </para>
62        </listitem>
63      </varlistentry>
64      <varlistentry>
65        <term><guilabel>Hybridization</guilabel></term>
66        <listitem>
67          <para>
68            The hybridization this scan comes from.
69          </para>
70        </listitem>
71      </varlistentry>
72      <varlistentry>
73        <term><guilabel>Scanner</guilabel></term>
74        <listitem>
75          <para>
76            The scanner that was used (optional).
77          </para>
78        </listitem>
79      </varlistentry>
80      <varlistentry>
81        <term><guilabel>Protocol</guilabel></term>
82        <listitem>
83          <para>
84            The protocol used for scanning (optional). Scanning
85            parameters may be registered as part of
86            the protocol.
87          </para>
88        </listitem>
89      </varlistentry>
90      <varlistentry>
91        <term><guilabel>Description</guilabel></term>
92        <listitem>
93          <para>
94            A decription of the scan (optional).
95          </para>
96        </listitem>
97      </varlistentry>
98    </variablelist>
99   
100    <seeother>
101      <other external_id="annotations.edit">Annotations</other>
102      <other external_id="annotations.edit.inerited">Inherit annotations</other>
103    </seeother>
104   
105    </helptext>
106   
107    <para>
108      A scan can have annotations. Read more about this in
109      <xref linkend="annotations"/>.
110    </para>
111   
112  </sect2>
113 
114  <sect2 id="experiment_analysis.scans.images">
115    <title>Images</title>
116   
117    <para>
118      If you want you can upload the images from the scan
119      to BASE. This is optional, but the images
120      are needed if you want to create spot images later
121      on.
122    </para>
123   
124    <para>
125      To upload images for a scan you must first go to
126      the single-item view for the scan. On this page
127      you will find the <guilabel>Images</guilabel>
128      tab which will take you to a list view
129      of the images from this scan. New images are created
130      in the same way as any other item in BASE,
131      by clicking the <guilabel>New&hellip;</guilabel> button.
132      You may add as many images as you like.
133    </para>
134   
135    <para>
136      An image has the following properties:
137    </para>
138
139    <helptext external_id="image.edit" title="Edit image">
140   
141    <variablelist>
142      <varlistentry>
143        <term><guilabel>Name</guilabel></term>
144        <listitem>
145          <para>
146            The name of the image. The name is automatically
147            generated from the name of the scan, but you may
148            enter a different name.
149          </para>
150        </listitem>
151      </varlistentry>
152      <varlistentry>
153        <term><guilabel>File</guilabel></term>
154        <listitem>
155          <para>
156            The file containing the actual
157            image data (optional). Use the <guibutton>Select</guibutton>
158            button to select an existing file or upload a new
159            one.
160          </para>
161        </listitem>
162      </varlistentry>
163      <varlistentry>
164        <term><guilabel>Format</guilabel></term>
165        <listitem>
166          <para>
167            The image format (optional). You can select between
168            <emphasis>TIFF</emphasis>, <emphasis>JPEG</emphasis> 
169            and <emphasis>Unknown</emphasis>.
170          </para>
171        </listitem>
172      </varlistentry>
173      <varlistentry>
174        <term><guilabel>Preview</guilabel></term>
175        <listitem>
176          <para>
177            If the image is a preview image or the full
178            scan.
179          </para>
180        </listitem>
181      </varlistentry>
182      <varlistentry>
183        <term><guilabel>Description</guilabel></term>
184        <listitem>
185          <para>
186            A description of the image (optional).
187          </para>
188        </listitem>
189      </varlistentry>
190    </variablelist>
191    </helptext>       
192   
193  </sect2>
194 
195</sect1>
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