Changeset 3069


Ignore:
Timestamp:
08/09/07 14:41:55 (12 years ago)
Author:
curtis
Message:

Clean up tutorial a little.

File:
1 edited

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  • trunk/loci/visbio/help/measuring.html

    r2906 r3069  
    44<h2>Getting started with measuring</h2> 
    55 
    6 <p>This tutorial is intended to help you start taking measurements as quickly as possible in VisBio.</p> 
     6<p><i>Tutorial by Abraham Sorber</i></p> 
    77 
     8<hr> 
    89 
    9  
     10<p>This tutorial is intended to help you start taking measurements as quickly 
     11as possible in VisBio.</p> 
    1012 
    1113<h2>1) Load images</h2> 
    1214 
    1315<h3>Start VisBio</h3> 
    14 <p>Double click the VisBio icon on the desktop to start the program.  The red VisBio logo will appear with a progress bar indicating that VisBio is loading.  Then the main VisBio screen appears:</p> 
     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> 
    1519 
    16 <p><img src="measuring/main.png" border="0" alt=""></p> 
     20<p><img src="measuring/main.png"></p> 
    1721 
    1822<h3>Import images</h3> 
    19 <i>For more detail, see <a href="import_data.html">Importing a dataset from disk</a>.</i> 
    20 <p>To load images into Visbio, click the "Add >" button and then select "Dataset".  The "Import data" window appears:</p> 
     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> 
    2127 
    22 <p><img src="measuring/import-data.png" border="0" alt=""></p> 
     28<p><img src="measuring/import-data.png"></p> 
    2329 
    24 <p>Click "Select File", then pick the file you want to load.  If the file you want to load is part of a numbered series, VisBio will try to guess the other files in the series and load them all as one dataset.</p> 
     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> 
    2533 
    26 <p>Click "Next >".</p> 
     34<p>Click the "Next &gt;" button.</p> 
    2735 
    28 <p><img src="measuring/next.png" border="0" alt=""></p> 
     36<p><img src="measuring/next.png"></p> 
    2937 
    30 <p>VisBio will read the dimensions of the image in microns if possible from the image. </p>  
     38<p>VisBio will read the dimensions of the image in microns if possible from the 
     39image.</p> 
    3140 
    32 <p><img src="measuring/microns.png" border="0" alt=""></p> 
     41<p><img src="measuring/microns.png"></p> 
    3342 
    34 <p>Click "Finish".  VisBio will load the image and offer you a several display options.</p> 
    35  
    36  
     43<p>Click the "Finish" button. VisBio will load the image and offer you 
     44several display options.</p> 
    3745 
    3846<br> 
     
    4048<i>For more detail, see <a href="overlays.html">Overlays</a>.</i> 
    4149 
     50<p>Select the option "In 2D with overlays" and click the "Ok" button.</p> 
    4251 
    43 <p>Select the option "In 2D with overlays" and click "Ok."</p> 
    44  
    45 <p><img src="measuring/visualize.png" border="0" alt=""></p> 
     52<p><img src="measuring/visualize.png"></p> 
    4653 
    4754<p>Click "OK" in this window to generate the display.</p> 
    4855 
    49 <p><img src="measuring/add2d.png"  border="0" alt=""></p> 
     56<p><img src="measuring/add2d.png"></p> 
    5057 
    51 <p>VisBio will display two windows: 1) the Display window, containing your image and 2) the Tools window, which you will use for drawing measurements.</p> 
     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> 
    5260 
    53 <p><img src="measuring/display1.png"  border="0" alt=""></p> 
    54  
    55  
     61<p><img src="measuring/display1.png"></p> 
    5662 
    5763<br> 
     
    6066<h3>Zoom-in on the area you want to measure</h3> 
    6167 
    62 <p>First, use the display window's controls to zoom, pan, and rotate the image.  These are located at the top right of this window under "Appearance":</p> 
     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> 
    6370 
    64 <p><img src="measuring/appearance.png"  border="0" alt=""></p> 
     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> 
    6575 
    6676<h3>Select a measurement tool</h3> 
    6777 
    68 <p>There are several tools which can be used for measurements.  Select the tool you want by clicking it's icon in the tools window:</p> 
     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> 
    6980 
    70 <p><img src="measuring/tools.png"  border="0" alt=""></p> 
     81<p><img src="measuring/tools.png"></p> 
    7182 
    7283<h3>Line tool</h3> 
    7384 
    74 <p><img src="measuring/line.png"  border="0" alt=""></p> 
     85<p><img src="measuring/line.png"></p> 
    7586 
    76 <p>Use the line tool for measuring straight lines.  Click and drag to draw a line.</p> 
     87<p>Use the line tool for measuring straight lines. Click and drag to draw a 
     88line.</p> 
    7789 
    78 <p><img src="measuring/lineDrawn.png" border="0" alt=""></p> 
     90<p><img src="measuring/lineDrawn.png"></p> 
    7991 
    8092<p>The line's length appears in the "Statistics" area of the tools window.</p> 
    8193 
    82 <p><img src="measuring/lineStats.png"  border="0" alt=""></p> 
     94<p><img src="measuring/lineStats.png"></p> 
    8395 
    8496<h3>Freeform tool</h3> 
    8597 
    86 <img src="measuring/freeform.png"  border="0" alt=""> 
     98<img src="measuring/freeform.png"> 
    8799 
    88 <p>Use the freeform tool for measuring curved lines.  Click and drag to draw a freeform line.</p>   
     100<p>Use the freeform tool for measuring curved lines. Click and drag to draw a 
     101freeform line.</p> 
    89102 
    90 <p><img src="measuring/freeformDrawn.png" border="0" alt=""></p> 
     103<p><img src="measuring/freeformDrawn.png"></p> 
    91104 
    92 <p>The freeform's length appears in the "Statistics" area of the tools window.</p> 
     105<p>The freeform's length appears in the "Statistics" area of the tools 
     106window.</p> 
    93107 
    94 <p><img src="measuring/freeformStats.png"  border="0" alt=""></p> 
     108<p><img src="measuring/freeformStats.png"></p> 
    95109 
    96110<h3>Polyline tool</h3> 
    97111 
    98 <p><img src="measuring/polyline.png"  border="0" alt=""></p> 
     112<p><img src="measuring/polyline.png"></p> 
    99113 
    100 <p>The polyline tool can also be used for measuring curved lines.  Click once to place a new "node" in the polyline.  Double-click to end the polyline.</p> 
     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> 
    101116 
    102 <p><img src="measuring/polylineDrawn.png"  border="0" alt=""></p> 
     117<p><img src="measuring/polylineDrawn.png"></p> 
    103118 
    104119<br> 
    105120<h2>3) View measurements in a spreadsheet</h2> 
    106121 
    107 <p>To view measurements in a spreadsheet application such as Excel, click "Export overlays..." in the tools window.</p> 
     122<p>To view measurements in a spreadsheet application such as Excel, click 
     123"Export overlays..." in the tools window.</p> 
    108124 
    109 <p><img src="measuring/exportButton.png"  border="0" alt="">  </p> 
     125<p><img src="measuring/exportButton.png"></p> 
    110126 
    111 <p>Before exporting, you may select the statistics you wish to include in the Excel file (these are the same statistics that appear in the "Statistics" area of the control window).   
    112 By default, all statistics are exported.  You may want to "turn off" some statistics to make your files easier to read.</p> 
     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> 
    113132 
    114 <p><img src="measuring/export.png" alt=""></p> 
     133<p><img src="measuring/export.png"></p> 
    115134 
    116135<p>The .xls file generated looks like this:</p> 
    117136 
    118 <p><img src="measuring/spreadsheet.png"  border="0" alt=""></p>   
     137<p><img src="measuring/spreadsheet.png"></p> 
    119138 
    120139<br> 
    121140<h2>4) Save your measurements</h2> 
    122141 
    123 <p><img src="measuring/saveButton.png"  border="0" alt="">  </p> 
     142<p><img src="measuring/saveButton.png"></p> 
    124143 
    125 <p>If you want to reload your measurements at a later time, click "Save overlays..." in the tools window.  As when exporting, you may select which statistics to store in the text file.  <i>(Note: these statistics are printed in the text file for your convenience only—when you reload your measurements later, VisBio will recalculate all overlay statistics, whether explicitly saved or not.)</i></p> 
     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> 
    126150 
    127 <p><img src="measuring/save.png"  border="0" alt="">  </p> 
     151<p><img src="measuring/save.png"></p> 
    128152 
    129 <p>VisBio will save your overlays to a text file which it can reread.  These text files contain the same information as the Excel files which VisBio generates, and are formatted almost identically:</p> 
     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> 
    130156 
    131 <p><img src="measuring/text.png"  border="0" alt=""> </p>  
     157<p><img src="measuring/text.png"></p> 
    132158 
    133159<br> 
    134 <h2>5) Load your measurements</h2>  
     160<h2>5) Load your measurements</h2> 
    135161 
    136 <p>Follow this tutorial up to step 2.  Then click "Load overlays..." in the Controls window.</p> 
     162<p>Follow this tutorial up to step 2. Then click "Load overlays..." in the 
     163Controls window.</p> 
    137164 
    138 <p><img src="measuring/loadButton.png"  border="0" alt="">  </p> 
     165<p><img src="measuring/loadButton.png"></p> 
    139166 
    140 <p>Select the text file containing the overlays you wish to load and click OK.</p> 
     167<p>Select the text file containing the overlays you wish to load and click 
     168OK.</p> 
    141169 
    142 <p><img src="measuring/load.png"  border="0" alt="">  </p> 
     170<p><img src="measuring/load.png"></p> 
    143171 
    144172<p>VisBio will reload your overlays for you to view or modify.</p> 
    145 <br> 
    146 <br> 
    147 <br> 
    148 </body></html> 
     173 
     174<p>&nbsp;<p></body></html> 
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