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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 - batch mode not working"
href="http://fiji.sc/bugzilla/show_bug.cgi?id=1171">bug 1171</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>NEEDSINFO
</td>
<td>RESOLVED
</td>
</tr>
<tr>
<td style="text-align:right;">Resolution</td>
<td>---
</td>
<td>FIXED
</td>
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<b><a class="bz_bug_link
bz_status_RESOLVED bz_closed"
title="RESOLVED FIXED - batch mode not working"
href="http://fiji.sc/bugzilla/show_bug.cgi?id=1171#c7">Comment # 7</a>
on <a class="bz_bug_link
bz_status_RESOLVED bz_closed"
title="RESOLVED FIXED - batch mode not working"
href="http://fiji.sc/bugzilla/show_bug.cgi?id=1171">bug 1171</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>Here is a version of your macro that should work better. I marked the changes
with "//**".
dir = getDirectory("Choose Sorce Directory"); //with slash at the end
dir2 = getDirectory("Choose Destination Directory");
acq = getFileList(dir);
setBatchMode(true);
for (i=0; i<acq.length; i++) {
if (endsWith(acq[i], "tif")) {
open(dir+acq[i]);
run("Make Composite");
run("Split Channels");
close("C3-"+acq[i]);
imageCalculator("Subtract stack", "C2-"+acq[i], "C1-"+acq[i]);
//Save Z-projection of 169
selectWindow("C2-"+acq[i]);
run("Despeckle", "stack"); //**
run("Z Project...", "projection=[Average Intensity]");
selectWindow("AVG_C2-"+acq[i]);
path = dir2+"Zproj-169-BGsubtr-"+acq[i]; //**
run("Save", "save=&path"); //**
close("AVG_C2-"+acq[i]);
//Save Z-projection of SHG
selectWindow("C4-"+acq[i]);
run("Despeckle", "stack"); //**
run("Z Project...", "projection=[Average Intensity]");
selectWindow("AVG_C4-"+acq[i]);
path = dir2+"Zproj-SHG-BGsubtr-"+acq[i]; //**
run("Save", "save=&path"); //**
close("*");
}
}</pre>
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