source: trunk/loci/visbio/help/measuring.html @ 3069

Revision 3069, 5.1 KB checked in by curtis, 13 years ago (diff)

Clean up tutorial a little.

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1<html>
2<title>VisBio Measurements Tutorial</title>
3<body>
4<h2>Getting started with measuring</h2>
5
6<p><i>Tutorial by Abraham Sorber</i></p>
7
8<hr>
9
10<p>This tutorial is intended to help you start taking measurements as quickly
11as possible in VisBio.</p>
12
13<h2>1) Load images</h2>
14
15<h3>Start VisBio</h3>
16<p>Double click the VisBio icon on the desktop to start the program. The red
17VisBio logo will appear with a progress bar indicating that VisBio is loading.
18Then the main VisBio screen appears:</p>
19
20<p><img src="measuring/main.png"></p>
21
22<h3>Import images</h3>
23<i>For more detail, see
24<a href="import_data.html">Importing a dataset from disk</a>.</i>
25<p>To load images into VisBio, click the "Add &gt;" button and then select
26"Dataset" from the menu. The "Import data" window appears:</p>
27
28<p><img src="measuring/import-data.png"></p>
29
30<p>Click the "Select File" button, then pick the file you want to load. If the
31file you want to load is part of a numbered series, VisBio will try to guess
32the other files in the series and load them all as one dataset.</p>
33
34<p>Click the "Next &gt;" button.</p>
35
36<p><img src="measuring/next.png"></p>
37
38<p>VisBio will read the dimensions of the image in microns if possible from the
39image.</p>
40
41<p><img src="measuring/microns.png"></p>
42
43<p>Click the "Finish" button. VisBio will load the image and offer you
44several display options.</p>
45
46<br>
47<h2>2) Create a display with overlays</h2>
48<i>For more detail, see <a href="overlays.html">Overlays</a>.</i>
49
50<p>Select the option "In 2D with overlays" and click the "Ok" button.</p>
51
52<p><img src="measuring/visualize.png"></p>
53
54<p>Click "OK" in this window to generate the display.</p>
55
56<p><img src="measuring/add2d.png"></p>
57
58<p>VisBio will display two windows: 1) the Display window, containing your
59image and 2) the Tools window, which you will use for drawing measurements.</p>
60
61<p><img src="measuring/display1.png"></p>
62
63<br>
64<h2>2) Take measurements</h2>
65
66<h3>Zoom-in on the area you want to measure</h3>
67
68<p>First, use the display window's controls to zoom, pan, and rotate the image.
69These are located at the top right of this window under "Appearance":</p>
70
71<p><img src="measuring/appearance.png"></p>
72
73<p>You can also click and drag with the right mouse button to pan the image,
74or drag while holding shift to zoom.</p>
75
76<h3>Select a measurement tool</h3>
77
78<p>There are several tools which can be used for measurements. Select the tool
79you want by clicking its icon in the tools window:</p>
80
81<p><img src="measuring/tools.png"></p>
82
83<h3>Line tool</h3>
84
85<p><img src="measuring/line.png"></p>
86
87<p>Use the line tool for measuring straight lines. Click and drag to draw a
88line.</p>
89
90<p><img src="measuring/lineDrawn.png"></p>
91
92<p>The line's length appears in the "Statistics" area of the tools window.</p>
93
94<p><img src="measuring/lineStats.png"></p>
95
96<h3>Freeform tool</h3>
97
98<img src="measuring/freeform.png">
99
100<p>Use the freeform tool for measuring curved lines. Click and drag to draw a
101freeform line.</p>
102
103<p><img src="measuring/freeformDrawn.png"></p>
104
105<p>The freeform's length appears in the "Statistics" area of the tools
106window.</p>
107
108<p><img src="measuring/freeformStats.png"></p>
109
110<h3>Polyline tool</h3>
111
112<p><img src="measuring/polyline.png"></p>
113
114<p>The polyline tool can also be used for measuring curved lines. Click once to
115place a new "node" in the polyline. Double-click to end the polyline.</p>
116
117<p><img src="measuring/polylineDrawn.png"></p>
118
119<br>
120<h2>3) View measurements in a spreadsheet</h2>
121
122<p>To view measurements in a spreadsheet application such as Excel, click
123"Export overlays..." in the tools window.</p>
124
125<p><img src="measuring/exportButton.png"></p>
126
127<p>Before exporting, you may select the statistics you wish to include in the
128Excel file (these are the same statistics that appear in the "Statistics" area
129of the control window).
130By default, all statistics are exported. You may want to "turn off" some
131statistics to make your files easier to read.</p>
132
133<p><img src="measuring/export.png"></p>
134
135<p>The .xls file generated looks like this:</p>
136
137<p><img src="measuring/spreadsheet.png"></p>
138
139<br>
140<h2>4) Save your measurements</h2>
141
142<p><img src="measuring/saveButton.png"></p>
143
144<p>If you want to reload your measurements at a later time, click "Save
145overlays..." in the tools window. As when exporting, you may select which
146statistics to store in the text file. <i>(Note: these statistics are printed in
147the text file for your convenience only—when you reload your measurements
148later, VisBio will recalculate all overlay statistics, whether explicitly saved
149or not.)</i></p>
150
151<p><img src="measuring/save.png"></p>
152
153<p>VisBio will save your overlays to a text file which it can reread. These
154text files contain the same information as the Excel files which VisBio
155generates, and are formatted almost identically:</p>
156
157<p><img src="measuring/text.png"></p>
158
159<br>
160<h2>5) Load your measurements</h2>
161
162<p>Follow this tutorial up to step 2. Then click "Load overlays..." in the
163Controls window.</p>
164
165<p><img src="measuring/loadButton.png"></p>
166
167<p>Select the text file containing the overlays you wish to load and click
168OK.</p>
169
170<p><img src="measuring/load.png"></p>
171
172<p>VisBio will reload your overlays for you to view or modify.</p>
173
174<p>&nbsp;<p></body></html>
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