<html dir="ltr">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
<style type="text/css" id="owaParaStyle"></style>
</head>
<body fpstyle="1" ocsi="0">
<div style="direction: ltr;font-family: Courier New;color: #000000;font-size: 10pt;">
Dear List,
<div><br>
</div>
<div>I have been trying to convert some files in the proprietary jpeg2000 format used by PICTools medical into tiffs--is there some utility that can do this in batch method (all files in directory x)? These files are readable by fiji but not plain imagej, and
I wrote a macro in fiji but which keeps prompting me with a dialog for every image. Here is the macro:</div>
<div><br>
</div>
<div><br style="color: rgb(34, 34, 34); font-family: arial, sans-serif; background-color: rgb(255, 255, 255);">
<span style="color: rgb(34, 34, 34); font-family: arial, sans-serif; background-color: rgb(255, 255, 255);"> for (i=0; i<10; i++) {</span><br style="color: rgb(34, 34, 34); font-family: arial, sans-serif; background-color: rgb(255, 255, 255);">
<span style="color: rgb(34, 34, 34); font-family: arial, sans-serif; background-color: rgb(255, 255, 255);"> for (j=0; j<10; j++) {</span><br style="color: rgb(34, 34, 34); font-family: arial, sans-serif; background-color: rgb(255, 255, 255);">
<span style="color: rgb(34, 34, 34); font-family: arial, sans-serif; background-color: rgb(255, 255, 255);"> for (k=0; k<10; k++) {</span><br style="color: rgb(34, 34, 34); font-family: arial, sans-serif; background-color: rgb(255, 255, 255);">
<span style="color: rgb(34, 34, 34); font-family: arial, sans-serif; background-color: rgb(255, 255, 255);">one = d2s(i, 0);</span><br style="color: rgb(34, 34, 34); font-family: arial, sans-serif; background-color: rgb(255, 255, 255);">
<span style="color: rgb(34, 34, 34); font-family: arial, sans-serif; background-color: rgb(255, 255, 255);">two = d2s(j, 0);</span><br style="color: rgb(34, 34, 34); font-family: arial, sans-serif; background-color: rgb(255, 255, 255);">
<span style="color: rgb(34, 34, 34); font-family: arial, sans-serif; background-color: rgb(255, 255, 255);">thr = d2s(k, 0);</span><br style="color: rgb(34, 34, 34); font-family: arial, sans-serif; background-color: rgb(255, 255, 255);">
<span style="color: rgb(34, 34, 34); font-family: arial, sans-serif; background-color: rgb(255, 255, 255);">setBatchMode(true);</span><br style="color: rgb(34, 34, 34); font-family: arial, sans-serif; background-color: rgb(255, 255, 255);">
<span style="color: rgb(34, 34, 34); font-family: arial, sans-serif; background-color: rgb(255, 255, 255);">filename = "C:\\Users\\Jacob\\Desktop\\</span><wbr style="color: rgb(34, 34, 34); font-family: arial, sans-serif; background-color: rgb(255, 255, 255);"><span style="color: rgb(34, 34, 34); font-family: arial, sans-serif; background-color: rgb(255, 255, 255);">ZfishBrains\\SPC00_TM00"+one+</span><wbr style="color: rgb(34, 34, 34); font-family: arial, sans-serif; background-color: rgb(255, 255, 255);"><span style="color: rgb(34, 34, 34); font-family: arial, sans-serif; background-color: rgb(255, 255, 255);">two+thr+"_ANG000_CM0_CHN00_</span><wbr style="color: rgb(34, 34, 34); font-family: arial, sans-serif; background-color: rgb(255, 255, 255);"><span style="color: rgb(34, 34, 34); font-family: arial, sans-serif; background-color: rgb(255, 255, 255);">PH0.jp2";</span><br style="color: rgb(34, 34, 34); font-family: arial, sans-serif; background-color: rgb(255, 255, 255);">
<span style="color: rgb(34, 34, 34); font-family: arial, sans-serif; background-color: rgb(255, 255, 255);">print(filename);</span><br style="color: rgb(34, 34, 34); font-family: arial, sans-serif; background-color: rgb(255, 255, 255);">
<span style="color: rgb(34, 34, 34); font-family: arial, sans-serif; background-color: rgb(255, 255, 255);">open(filename);</span><br style="color: rgb(34, 34, 34); font-family: arial, sans-serif; background-color: rgb(255, 255, 255);">
<span style="color: rgb(34, 34, 34); font-family: arial, sans-serif; background-color: rgb(255, 255, 255);">saveAs("Tiff", "X:\\Zebrafish_Brain_Images\\</span><wbr style="color: rgb(34, 34, 34); font-family: arial, sans-serif; background-color: rgb(255, 255, 255);"><span style="color: rgb(34, 34, 34); font-family: arial, sans-serif; background-color: rgb(255, 255, 255);">tifs\\SPC00_TM00"+one+two+thr+</span><wbr style="color: rgb(34, 34, 34); font-family: arial, sans-serif; background-color: rgb(255, 255, 255);"><span style="color: rgb(34, 34, 34); font-family: arial, sans-serif; background-color: rgb(255, 255, 255);">"_ANG000_CM0_CHN00_PH0x.tif");</span><br style="color: rgb(34, 34, 34); font-family: arial, sans-serif; background-color: rgb(255, 255, 255);">
<span style="color: rgb(34, 34, 34); font-family: arial, sans-serif; background-color: rgb(255, 255, 255);">close();</span></div>
<div><br>
</div>
<div><br>
</div>
<div>Jacob<br>
<div><br>
<div style="font-family:Tahoma; font-size:13px">
<div><font face="Courier New">*******************************************</font></div>
<div><font face="Courier New">Jacob Pearson Keller, PhD</font></div>
<div><font face="Courier New">Postdoctoral Associate</font></div>
<div><font face="Courier New">HHMI Janelia Farms Research Campus</font></div>
<div><font face="Courier New">email: j-keller2@northwestern.edu</font></div>
<div><font face="Courier New">*******************************************</font></div>
</div>
</div>
</div>
</div>
</body>
</html>