forked from ome/ome-help
-
Notifications
You must be signed in to change notification settings - Fork 0
Expand file tree
/
Copy pathimporting-data-5.html
More file actions
268 lines (169 loc) · 9.5 KB
/
importing-data-5.html
File metadata and controls
268 lines (169 loc) · 9.5 KB
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
---
layout: default
title: Importing Data with OMERO.insight v. 5.0.2
menu-id: l1-insight
pdfs:
- importing-data-5.pdf
---
<p>Using the OMERO.insight to import image data onto the OMERO server.</p>
<div class="line-block">
<div class="line"><br /></div> <!-- end #line -->
</div> <!-- end #line-block -->
<ol class="step">
<li><p class="first">Select <span class="bold">Import</span> from the <span class="bold">File</span> menu;</p>
<p>or click on the Import icon in the toolbar;</p>
<p>or select a destination Project or Dataset for the imported data and right click then select <span class="bold">Import</span>.</p>
<div class="line-block">
<div class="line"><br /></div> <!-- end #line -->
</div> <!-- end #line-block -->
<img alt="{{ site.baseurl }}/images/importingDataManager.jpg" class="align-center" src="{{ site.baseurl }}/images/importingDataManager.jpg" style="width: 100%;" />
<div class="line-block">
<div class="line"><br /></div> <!-- end #line -->
</div> <!-- end #line-block -->
</li>
<li><p class="first">Use the <span class="bold">File Finder</span> to locate data to be imported on local or networked drives.</p>
<p>Select files for importing and click the top arrow to add them to the import queue.</p>
<div class="line-block">
<div class="line"><br /></div> <!-- end #line -->
</div> <!-- end #line-block -->
<img alt="{{ site.baseurl }}/images/importingData5Importer.jpg" class="align-center" src="{{ site.baseurl }}/images/importingData5Importer.jpg" style="width: 100%;" />
<div class="line-block">
<div class="line"><br /></div> <!-- end #line -->
</div> <!-- end #line-block -->
</li>
<li><p class="first">Use the <span class="bold">Location Selection</span> window to determine the destination of the imported data.</p>
<p>Choose an existing project or dataset using the drop-down menus;</p>
<p>or click <span class="bold">New</span> to create a new project or dataset;</p>
<p>When import location has been set, click <span class="bold">Add to the Queue</span>.</p>
<div class="line-block">
<div class="line"><br /></div> <!-- end #line -->
</div> <!-- end #line-block -->
<img alt="{{ site.baseurl }}/images/importingDataProjectDataset.jpg" class="align-center" src="{{ site.baseurl }}/images/importingDataProjectDataset.jpg" style="width: 100%;" />
<div class="line-block">
<div class="line"><br /></div> <!-- end #line -->
</div> <!-- end #line-block -->
</li>
<li><p class="first">When ready, click <span class="bold">Import</span> to start importing queued data.</p>
<p>The progress of imports is shown in the <span class="bold">Import</span> tab.</p>
<p>A green tick indicates when the queue is successfully imported.</p>
<div class="line-block">
<div class="line"><br /></div> <!-- end #line -->
</div> <!-- end #line-block -->
<img alt="{{ site.baseurl }}/images/importingData5Start.jpg" class="align-center" src="{{ site.baseurl }}/images/importingData5Start.jpg" style="width: 100%;" />
<div class="line-block">
<div class="line"><br /></div> <!-- end #line -->
</div> <!-- end #line-block -->
</li>
<li><p class="first">Mouse-over the thumbnails of successfully imported images to see a preview.</p>
<p>Click on the <span class="bold">View</span> menu to view the image in the <span class="bold">Viewer</span> or <span class="bold">Data Manager</span>, or view the <span class="bold">Import Log</span> and the data <span class="bold">Checksum</span> verification.</p>
<p>or close the <span class="bold">Import</span> window to view the data in the <span class="bold">Data Manager</span>.</p>
<div class="line-block">
<div class="line"><br /></div> <!-- end #line -->
</div> <!-- end #line-block -->
<img alt="{{ site.baseurl }}/images/importingData5End.jpg" class="align-center" src="{{ site.baseurl }}/images/importingData5End.jpg" style="width: 82%;" />
<div class="line-block">
<div class="line"><br /></div> <!-- end #line -->
</div> <!-- end #line-block -->
<div class="line-block">
<div class="line"><br /></div> <!-- end #line -->
</div> <!-- end #line-block -->
<div class="note">
<p class="note-title">Note</p>
<p class="note-text">From Version 5, OMERO imports and stores image files unchanged, in their original format. Therefore there is no longer any need to archive files on import.</p>
</div>
<div class="line-block">
<div class="line"><br /></div> <!-- end #line -->
</div> <!-- end #line-block -->
<div class="line-block">
<div class="line"><br /></div> <!-- end #line -->
</div> <!-- end #line-block -->
</li>
<li><p class="first">Select an image and click on the green <span class="bold">File Path</span> button to see the file path of the imported data in the OMERO data repository.</p>
<div class="line-block">
<div class="line"><br /></div> <!-- end #line -->
</div> <!-- end #line-block -->
<img alt="{{ site.baseurl }}/images/importingData5FilePath.jpg" class="align-center" src="{{ site.baseurl }}/images/importingData5FilePath.jpg" style="width: 82%;" />
<div class="line-block">
<div class="line"><br /></div> <!-- end #line -->
</div> <!-- end #line-block -->
</li>
</ol>
<div class="section" id="importing-options">
<h2>Importing Options</h2>
<p>The following points illustrate how to set some of the options that can be used when importing.</p>
<div class="line-block">
<div class="line"><br /></div> <!-- end #line -->
</div> <!-- end #line-block -->
<h3>Adding tags at import</h3>
<ol class="step">
<li><p class="first">Click the Options tab then <span class="bold">Add Tags</span> to batch-add tags to the data as it is imported.</p>
<div class="line-block">
<div class="line"><br /></div> <!-- end #line -->
</div> <!-- end #line-block -->
<img alt="{{ site.baseurl }}/images/importingData5AddTag1.jpg" class="align-center" src="{{ site.baseurl }}/images/importingData5AddTag1.jpg" style="width: 100%;" />
<div class="line-block">
<div class="line"><br /></div> <!-- end #line -->
</div> <!-- end #line-block -->
</li>
<li><p class="first">Select an existing tag in the left hand pane and click the right arrow;</p>
<p>or enter the name of a new tag and click <span class="bold">Add</span>.</p>
<p>Click <span class="bold">Save</span> to add these tags to the data at import.</p>
<div class="line-block">
<div class="line"><br /></div> <!-- end #line -->
</div> <!-- end #line-block -->
<img alt="{{ site.baseurl }}/images/importingDataAddTag2.jpg" class="align-center" src="{{ site.baseurl }}/images/importingDataAddTag2.jpg" style="width: 75%;" />
<div class="line-block">
<div class="line"><br /></div> <!-- end #line -->
</div> <!-- end #line-block -->
</li>
<li><p class="first">After saving, added tags can be seen in the <span class="bold">Options</span> tab and can be removed by clicking the <span class="bold">-</span> button.</p>
<div class="line-block">
<div class="line"><br /></div> <!-- end #line -->
</div> <!-- end #line-block -->
<img alt="{{ site.baseurl }}/images/importingData5RemoveTag.jpg" class="align-center" src="{{ site.baseurl }}/images/importingData5RemoveTag.jpg" style="width: 75%;" />
<div class="line-block">
<div class="line"><br /></div> <!-- end #line -->
</div> <!-- end #line-block -->
</li>
</ol>
<h3>Selecting group for import</h3>
<p>If you are a member of more than one group, use the <span class="bold">Group</span> drop down box to select which group to import the data into.</p>
<div class="line-block">
<div class="line"><br /></div> <!-- end #line -->
</div> <!-- end #line-block -->
<img alt="{{ site.baseurl }}/images/importingDataSelectGroup.jpg" class="align-center" src="{{ site.baseurl }}/images/importingDataSelectGroup.jpg" style="width: 100%;" />
<div class="line-block">
<div class="line"><br /></div> <!-- end #line -->
</div> <!-- end #line-block -->
<h3>Toggle between project and screen</h3>
<p>Click the <span class="bold">Project - Screen</span> tabs to change between image and screen data.</p>
<p>The File Finder window changes to reflect available file types, according to the selection.</p>
<div class="line-block">
<div class="line"><br /></div> <!-- end #line -->
</div> <!-- end #line-block -->
<img alt="{{ site.baseurl }}/images/importingDataProjectScreen.jpg" class="align-center" src="{{ site.baseurl }}/images/importingDataProjectScreen.jpg" style="width: 100%;" />
<div class="line-block">
<div class="line"><br /></div> <!-- end #line -->
</div> <!-- end #line-block -->
<div class="line-block">
<div class="line"><br /></div> <!-- end #line -->
</div> <!-- end #line-block -->
<p><span class="bold">Import for Another User</span></p>
<p>If you are an Administrator user, use the <span class="bold">Import For</span> drop down box to select another user to import the data as.</p>
<p>The chosen user will then own this data.</p>
<p>The projects and datasets shown in the drop-down boxes as available to import into, is determined by the permission status of the group.</p>
<div class="line-block">
<div class="line"><br /></div> <!-- end #line -->
</div> <!-- end #line-block -->
<img alt="{{ site.baseurl }}/images/importingDataImportFor.jpg" class="align-center" src="{{ site.baseurl }}/images/importingDataImportFor.jpg" style="width: 100%;" />
<div class="line-block">
<div class="line"><br /></div> <!-- end #line -->
</div> <!-- end #line-block -->
<div class="line-block">
<div class="line"><br /></div> <!-- end #line -->
</div> <!-- end #line-block -->
<div class="page-end">
<p>All Tutorial Material is available on line at: <a href="http://help.openmicroscopy.org">www.help.openmicroscopy.org</a></p>
<p>The Main OME website is at: <a href="http://www.openmicroscopy.org">www.openmicroscopy.org</a></p>
</div> <!-- end page-end -->
</div><!-- end section -->