http://measurebiology.org/w/index.php?title=Matlab:_Scalebars&feed=atom&action=history
Matlab: Scalebars - Revision history
2024-03-29T14:39:12Z
Revision history for this page on the wiki
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http://measurebiology.org/w/index.php?title=Matlab:_Scalebars&diff=40412&oldid=prev
MAXINE JONAS at 20:37, 31 January 2019
2019-01-31T20:37:57Z
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<td colspan='2' style="background-color: white; color:black; text-align: center;">Revision as of 20:37, 31 January 2019</td>
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<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>%      imageName            : EITHER an image variable name (e.g. foo)</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>%      imageName            : EITHER an image variable name (e.g. foo)</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>%                              OR a file path and filename (e.g. ~/foo.png)</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>%                              OR a file path and filename (e.g. ~/foo.png)</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>%      pixelSize (float)    : the actual size of a camera pixel (e.g. <del class="diffchange diffchange-inline">7</del>.<del class="diffchange diffchange-inline">4</del>)</div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>%      pixelSize (float)    : the actual size of a camera pixel (e.g. <ins class="diffchange diffchange-inline">6</ins>.<ins class="diffchange diffchange-inline">9</ins>)</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>%      magnification (float) : the microscope magnification (e.g. 40)</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>%      magnification (float) : the microscope magnification (e.g. 40)</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>%      barScale (float)      : bar size in image units (e.g. <del class="diffchange diffchange-inline">100</del>)</div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>%      barScale (float)      : bar size in image units (e.g. <ins class="diffchange diffchange-inline">10</ins>)</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>%      units (string)        : the units of the image (e.g. micron)</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>%      units (string)        : the units of the image (e.g. micron)</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>%  Example, put a 10 micron scalebar onto an image of a cell:</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>%  Example, put a 10 micron scalebar onto an image of a cell:</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>%      scalebar(cellImage, <del class="diffchange diffchange-inline">7</del>.<del class="diffchange diffchange-inline">4</del>, 40, 10, 'microns')</div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>%      scalebar(cellImage, <ins class="diffchange diffchange-inline">6</ins>.<ins class="diffchange diffchange-inline">9</ins>, 40, 10, 'microns')</div></td></tr>
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MAXINE JONAS
http://measurebiology.org/w/index.php?title=Matlab:_Scalebars&diff=38110&oldid=prev
Eliot Frank at 20:49, 4 March 2018
2018-03-04T20:49:05Z
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<td colspan='2' style="background-color: white; color:black; text-align: center;">← Older revision</td>
<td colspan='2' style="background-color: white; color:black; text-align: center;">Revision as of 20:49, 4 March 2018</td>
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<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div><pre></div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div><pre></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>function hImage = scalebar(imageName, pixelSize, magnification, barScale, units, negative)</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>function hImage = scalebar(imageName, pixelSize, magnification, barScale, units, negative)</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>% SCALEBAR(<del class="diffchange diffchange-inline">imageFile</del>, pixelSize, <del class="diffchange diffchange-inline">pixelSize</del>, <del class="diffchange diffchange-inline">magnification</del>, units, negative)</div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>% SCALEBAR(<ins class="diffchange diffchange-inline">imageName</ins>, pixelSize, <ins class="diffchange diffchange-inline">magnification</ins>, <ins class="diffchange diffchange-inline">barScale</ins>, units, negative)</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>%  Adds a scale bar in the lower right-hand corner of an image in the  </div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>%  Adds a scale bar in the lower right-hand corner of an image in the  </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>%  active set of axes. Be sure that your whole scale bar fits within the</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>%  active set of axes. Be sure that your whole scale bar fits within the</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>%  Optional input:</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>%  Optional input:</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>%      negative (int)        : white tone or black (e.g. 1)</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>%      negative (int)        : white tone or black (e.g. 1)</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">%</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">%  Example, put a 10 micron scalebar onto an image of a cell:</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">%      scalebar(cellImage, 7.4, 40, 10, 'microns')</ins></div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>%  SFNagle 2015 v1</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>%  SFNagle 2015 v1</div></td></tr>
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Eliot Frank
http://measurebiology.org/w/index.php?title=Matlab:_Scalebars&diff=9946&oldid=prev
Steven Nagle at 01:02, 1 March 2015
2015-03-01T01:02:25Z
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<td colspan='2' style="background-color: white; color:black; text-align: center;">Revision as of 01:02, 1 March 2015</td>
</tr><tr><td colspan="2" class="diff-lineno">Line 4:</td>
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<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>The code shown below can be used to add a scalebar to any image. Take care to ensure that the left edge of the scale bar is not off the left edge of the image. Otherwise it is up to you to decide how large, and in what units, the scalebar should be. Regarding size, your instructors suggest some modest multiple of the most characteristic object size in the image, such as a cell or bead.</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>The code shown below can be used to add a scalebar to any image. Take care to ensure that the left edge of the scale bar is not off the left edge of the image. Otherwise it is up to you to decide how large, and in what units, the scalebar should be. Regarding size, your instructors suggest some modest multiple of the most characteristic object size in the image, such as a cell or bead.</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">The program returns a handle to the figure containing the image. You can then save that figure or print to a file. This is not ideal because it adds a border, just like in the figure. It would be better to save the image data only, with the scalar overlaid. Unfortunately the getimage command in Matlab does not retain the rectangle or text data, so we (or you) will have to be more clever.</ins></div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div><pre></div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div><pre></div></td></tr>
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Steven Nagle
http://measurebiology.org/w/index.php?title=Matlab:_Scalebars&diff=9936&oldid=prev
Steven Nagle: Created page with "Category:20.309 Category:Matlab {{Template:20.309}} The code shown below can be used to add a scalebar to any image. Take care to ensure that the left edge of the sca..."
2015-02-22T22:58:47Z
<p>Created page with "<a href="/w/index.php?title=Category:20.309&action=edit&redlink=1" class="new" title="Category:20.309 (page does not exist)">Category:20.309</a> <a href="/w/index.php?title=Category:Matlab&action=edit&redlink=1" class="new" title="Category:Matlab (page does not exist)">Category:Matlab</a> {{Template:20.309}} The code shown below can be used to add a scalebar to any image. Take care to ensure that the left edge of the sca..."</p>
<p><b>New page</b></p><div>[[Category:20.309]]<br />
[[Category:Matlab]]<br />
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<br />
The code shown below can be used to add a scalebar to any image. Take care to ensure that the left edge of the scale bar is not off the left edge of the image. Otherwise it is up to you to decide how large, and in what units, the scalebar should be. Regarding size, your instructors suggest some modest multiple of the most characteristic object size in the image, such as a cell or bead.<br />
<br />
<pre><br />
function hImage = scalebar(imageName, pixelSize, magnification, barScale, units, negative)<br />
% SCALEBAR(imageFile, pixelSize, pixelSize, magnification, units, negative)<br />
% Adds a scale bar in the lower right-hand corner of an image in the <br />
% active set of axes. Be sure that your whole scale bar fits within the<br />
% image width (minus 10%). It should not touch the left edge of your<br />
% image.<br />
%<br />
% Required inputs are:<br />
% imageName : EITHER an image variable name (e.g. foo)<br />
% OR a file path and filename (e.g. ~/foo.png)<br />
% pixelSize (float) : the actual size of a camera pixel (e.g. 7.4)<br />
% magnification (float) : the microscope magnification (e.g. 40)<br />
% barScale (float) : bar size in image units (e.g. 100)<br />
% units (string) : the units of the image (e.g. micron)<br />
%<br />
% Optional input:<br />
% negative (int) : white tone or black (e.g. 1)<br />
%<br />
% SFNagle 2015 v1<br />
<br />
if nargin < 6<br />
negative = 1;<br />
end<br />
<br />
% read in the image and display<br />
if ischar(imageName)<br />
image1 = imread(imageName);<br />
else<br />
image1 = imageName;<br />
end<br />
hImage = imshow(image1);<br />
<br />
% plot a scale bar in black first<br />
scaleBarWidth = floor( 1/(pixelSize/magnification) * barScale);<br />
scaleBarHeight = 7;<br />
xPos = size(image1,2)*0.9 - scaleBarWidth;<br />
yPos = size(image1,1)*0.9 - scaleBarHeight;<br />
textCenterX = xPos + floor(scaleBarWidth/2);<br />
textCenterY = yPos + scaleBarHeight*5;<br />
rectPosition = [xPos, yPos, scaleBarWidth, scaleBarHeight];<br />
hRect = rectangle('Position', rectPosition);<br />
<br />
% label the scale bar<br />
str = sprintf(['%4d ' units], barScale);<br />
hText = text(textCenterX,textCenterY,str);<br />
set(hText,'HorizontalAlignment','center');<br />
<br />
% set tone as requested<br />
if negative<br />
set(hRect,'EdgeColor','w');<br />
set(hRect,'FaceColor','w');<br />
set(hText,'Color','w');<br />
else<br />
set(hRect,'EdgeColor','k');<br />
set(hRect,'FaceColor','k');<br />
set(hText,'Color','k');<br />
end<br />
</pre><br />
<br />
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Steven Nagle