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<body><span class="vcard"><a class="email" href="mailto:wsr@nih.gov" title="Wayne Rasband <wsr@nih.gov>"> <span class="fn">Wayne Rasband</span></a>
</span> changed
<a class="bz_bug_link
bz_status_RESOLVED bz_closed"
title="RESOLVED FIXED - "Analyse particles" - potential bug if applied to 4-dimensional stack"
href="http://fiji.sc/bugzilla/show_bug.cgi?id=969">bug 969</a>
<br>
<table border="1" cellspacing="0" cellpadding="8">
<tr>
<th>What</th>
<th>Removed</th>
<th>Added</th>
</tr>
<tr>
<td style="text-align:right;">Status</td>
<td>NEW
</td>
<td>RESOLVED
</td>
</tr>
<tr>
<td style="text-align:right;">CC</td>
<td>
</td>
<td>wsr@nih.gov
</td>
</tr>
<tr>
<td style="text-align:right;">Resolution</td>
<td>---
</td>
<td>FIXED
</td>
</tr></table>
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<b><a class="bz_bug_link
bz_status_RESOLVED bz_closed"
title="RESOLVED FIXED - "Analyse particles" - potential bug if applied to 4-dimensional stack"
href="http://fiji.sc/bugzilla/show_bug.cgi?id=969#c2">Comment # 2</a>
on <a class="bz_bug_link
bz_status_RESOLVED bz_closed"
title="RESOLVED FIXED - "Analyse particles" - potential bug if applied to 4-dimensional stack"
href="http://fiji.sc/bugzilla/show_bug.cgi?id=969">bug 969</a>
from <span class="vcard"><a class="email" href="mailto:wsr@nih.gov" title="Wayne Rasband <wsr@nih.gov>"> <span class="fn">Wayne Rasband</span></a>
</span></b>
<pre>This bug is fixed in the latest ImageJ daily build (1.49n13). The following is
a modified version of the test macro that displays the position and size of all
objects found by the particle analyzer. it omits the
run("Convert to Mask", "method=Triangle background=Dark black stack");
statement because it is only needed when using the "Convert to Mask" command's
"Calculate threshold for each image"option.
run("Mitosis (26MB, 5D stack)");
run("Duplicate...", "duplicate channels=1");
setAutoThreshold("Triangle dark");
roiManager("reset");
run("Analyze Particles...", "size=1-Infinity add stack");
run("Clear Results");
n = roiManager("count");
for (i=0; i<n; i++) {
roiManager("Select", i);
Stack.getPosition(c, z, t);
getStatistics(area, mean);
setResult("z",i,z);
setResult("t",i,t);
setResult("area",i,area);
setResult("mean",i,mean);
}
updateResults;
run("Select None");
And here is a version of the macro that uses an overlay instead of the ROI
Manager:
run("Mitosis (26MB, 5D stack)");
run("Duplicate...", "duplicate channels=1");
setAutoThreshold("Triangle dark");
run("Analyze Particles...", "size=1-Infinity show=[Overlay Outlines] stack");
run("Clear Results");
n = Overlay.size
for (i=0; i<n; i++) {
Overlay.activateSelection(i)
Stack.getPosition(c, z, t);
getStatistics(area, mean);
setResult("z",i,z);
setResult("t",i,t);
setResult("area",i,area);
setResult("mean",i,mean);
}
updateResults;
run("Select None");</pre>
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