<commit_before><html>
<title>VisBio Measurements Tutorial</title>
<body>
<h2>Getting started with measuring</h2>

<p>This tutorial is intended to help you start taking measurements as quickly as possible in VisBio.</p>




<h2>1) Load images</h2>

<h3>Start VisBio</h3>
<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>

<p><img src="measuring/main.png" border="0" alt=""></p>

<h3>Import images</h3>
<i>For more detail, see <a href="import_data.html">Importing a dataset from disk</a>.</i>
<p>To load images into Visbio, click the "Add >" button and then select "Dataset".  The "Import data" window appears:</p>

<p><img src="measuring/import-data.png" border="0" alt=""></p>

<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>

<p>Click "Next >".</p>

<p><img src="measuring/next.png" border="0" alt=""></p>

<p>VisBio will read the dimensions of the image in microns if possible from the image. </p> 

<p><img src="measuring/microns.png" border="0" alt=""></p>

<p>Click "Finish".  VisBio will load the image and offer you a several display options.</p>



<br>
<h2>2) Create a display with overlays</h2>
<i>For more detail, see <a href="overlays.html">Overlays</a>.</i>


<p>Select the option "In 2D with overlays" and click "Ok."</p>

<p><img src="measuring/visualize.png" border="0" alt=""></p>

<p>Click "OK" in this window to generate the display.</p>

<p><img src="measuring/add2d.png"  border="0" alt=""></p>

<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>

<p><img src="measuring/display1.png"  border="0" alt=""></p>



<br>
<h2>2) Take measurements</h2>

<h3>Zoom-in on the area you want to measure</h3>

<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>

<p><img src="measuring/appearance.png"  border="0" alt=""></p>

<h3>Select a measurement tool</h3>

<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>

<p><img src="measuring/tools.png"  border="0" alt=""></p>

<h3>Line tool</h3>

<p><img src="measuring/line.png"  border="0" alt=""></p>

<p>Use the line tool for measuring straight lines.  Click and drag to draw a line.</p>

<p><img src="measuring/lineDrawn.png" border="0" alt=""></p>

<p>The line's length appears in the "Statistics" area of the tools window.</p>

<p><img src="measuring/lineStats.png"  border="0" alt=""></p>

<h3>Freeform tool</h3>

<img src="measuring/freeform.png"  border="0" alt="">

<p>Use the freeform tool for measuring curved lines.  Click and drag to draw a freeform line.</p>  

<p><img src="measuring/freeformDrawn.png" border="0" alt=""></p>

<p>The freeform's length appears in the "Statistics" area of the tools window.</p>

<p><img src="measuring/freeformStats.png"  border="0" alt=""></p>

<h3>Polyline tool</h3>

<p><img src="measuring/polyline.png"  border="0" alt=""></p>

<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>

<p><img src="measuring/polylineDrawn.png"  border="0" alt=""></p>

<br>
<h2>3) View measurements in a spreadsheet</h2>

<p>To view measurements in a spreadsheet application such as Excel, click "Export overlays..." in the tools window.</p>

<p><img src="measuring/exportButton.png"  border="0" alt="">  </p>

<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).  
By default, all statistics are exported.  You may want to "turn off" some statistics to make your files easier to read.</p>

<p><img src="measuring/export.png" alt=""></p>

<p>The .xls file generated looks like this:</p>

<p><img src="measuring/spreadsheet.png"  border="0" alt=""></p>  

<br>
<h2>4) Save your measurements</h2>

<p><img src="measuring/saveButton.png"  border="0" alt="">  </p>

<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>

<p><img src="measuring/save.png"  border="0" alt="">  </p>

<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>

<p><img src="measuring/text.png"  border="0" alt=""> </p> 

<br>
<h2>5) Load your measurements</h2> 

<p>Follow this tutorial up to step 2.  Then click "Load overlays..." in the Controls window.</p>

<p><img src="measuring/loadButton.png"  border="0" alt="">  </p>

<p>Select the text file containing the overlays you wish to load and click OK.</p>

<p><img src="measuring/load.png"  border="0" alt="">  </p>

<p>VisBio will reload your overlays for you to view or modify.</p>
<br>
<br>
<br>
</body></html><commit_msg>Clean up tutorial a little.<commit_after><html>
<title>VisBio Measurements Tutorial</title>
<body>
<h2>Getting started with measuring</h2>

<p><i>Tutorial by <NAME></i></p>

<hr>

<p>This tutorial is intended to help you start taking measurements as quickly
as possible in VisBio.</p>

<h2>1) Load images</h2>

<h3>Start VisBio</h3>
<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>

<p><img src="measuring/main.png"></p>

<h3>Import images</h3>
<i>For more detail, see
<a href="import_data.html">Importing a dataset from disk</a>.</i>
<p>To load images into VisBio, click the "Add &gt;" button and then select
"Dataset" from the menu. The "Import data" window appears:</p>

<p><img src="measuring/import-data.png"></p>

<p>Click the "Select File" button, 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>

<p>Click the "Next &gt;" button.</p>

<p><img src="measuring/next.png"></p>

<p>VisBio will read the dimensions of the image in microns if possible from the
image.</p>

<p><img src="measuring/microns.png"></p>

<p>Click the "Finish" button. VisBio will load the image and offer you
several display options.</p>

<br>
<h2>2) Create a display with overlays</h2>
<i>For more detail, see <a href="overlays.html">Overlays</a>.</i>

<p>Select the option "In 2D with overlays" and click the "Ok" button.</p>

<p><img src="measuring/visualize.png"></p>

<p>Click "OK" in this window to generate the display.</p>

<p><img src="measuring/add2d.png"></p>

<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>

<p><img src="measuring/display1.png"></p>

<br>
<h2>2) Take measurements</h2>

<h3>Zoom-in on the area you want to measure</h3>

<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>

<p><img src="measuring/appearance.png"></p>

<p>You can also click and drag with the right mouse button to pan the image,
or drag while holding shift to zoom.</p>

<h3>Select a measurement tool</h3>

<p>There are several tools which can be used for measurements. Select the tool
you want by clicking its icon in the tools window:</p>

<p><img src="measuring/tools.png"></p>

<h3>Line tool</h3>

<p><img src="measuring/line.png"></p>

<p>Use the line tool for measuring straight lines. Click and drag to draw a
line.</p>

<p><img src="measuring/lineDrawn.png"></p>

<p>The line's length appears in the "Statistics" area of the tools window.</p>

<p><img src="measuring/lineStats.png"></p>

<h3>Freeform tool</h3>

<img src="measuring/freeform.png">

<p>Use the freeform tool for measuring curved lines. Click and drag to draw a
freeform line.</p>

<p><img src="measuring/freeformDrawn.png"></p>

<p>The freeform's length appears in the "Statistics" area of the tools
window.</p>

<p><img src="measuring/freeformStats.png"></p>

<h3>Polyline tool</h3>

<p><img src="measuring/polyline.png"></p>

<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>

<p><img src="measuring/polylineDrawn.png"></p>

<br>
<h2>3) View measurements in a spreadsheet</h2>

<p>To view measurements in a spreadsheet application such as Excel, click
"Export overlays..." in the tools window.</p>

<p><img src="measuring/exportButton.png"></p>

<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).
By default, all statistics are exported. You may want to "turn off" some
statistics to make your files easier to read.</p>

<p><img src="measuring/export.png"></p>

<p>The .xls file generated looks like this:</p>

<p><img src="measuring/spreadsheet.png"></p>

<br>
<h2>4) Save your measurements</h2>

<p><img src="measuring/saveButton.png"></p>

<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>

<p><img src="measuring/save.png"></p>

<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>

<p><img src="measuring/text.png"></p>

<br>
<h2>5) Load your measurements</h2>

<p>Follow this tutorial up to step 2. Then click "Load overlays..." in the
Controls window.</p>

<p><img src="measuring/loadButton.png"></p>

<p>Select the text file containing the overlays you wish to load and click
OK.</p>

<p><img src="measuring/load.png"></p>

<p>VisBio will reload your overlays for you to view or modify.</p>

<p>&nbsp;<p></body></html>
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