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<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Arial","sans-serif";
color:black'>Frans,<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Arial","sans-serif";
color:black'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Arial","sans-serif";
color:black'>Actually what would be even more powerful would be to be able to
embed the bitmaps as ROIs. I believe ROI (polygons) are supported by OME-Tiff/OME-XML
as an SVG map. The question is how can bitmaps be converted as such. I am not
sure what format imageJ uses to male its ROI using the particle detector.
Perhaps someone has an easy way to do this?<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Arial","sans-serif";
color:black'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Arial","sans-serif";
color:black'>Best,<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Arial","sans-serif";
color:black'><o:p> </o:p></span></p>
<div>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:11.0pt;
font-family:"Arial","sans-serif";color:black'>Ghislain Bonamy, PhD<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:11.0pt;
font-family:"Arial","sans-serif";color:black'>__________________________________________<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:11.0pt;
font-family:"Arial","sans-serif";color:black'>Research Investigator I<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:11.0pt;
font-family:"Arial","sans-serif";color:black'><o:p> </o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:11.0pt;
font-family:"Arial","sans-serif";color:black'>Genomic Institute of the<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:11.0pt;
font-family:"Arial","sans-serif";color:black'>Novartis Research<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:11.0pt;
font-family:"Arial","sans-serif";color:black'>Foundation<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:11.0pt;
font-family:"Arial","sans-serif";color:black'>Department of Molecular &
Cell Biology, room G214<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:11.0pt;
font-family:"Arial","sans-serif";color:black'>10675 John Jay Hopkins Drive<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:11.0pt;
font-family:"Arial","sans-serif";color:black'>San Diego CA 92121<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:11.0pt;
font-family:"Arial","sans-serif";color:black'>USA<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:11.0pt;
font-family:"Arial","sans-serif";color:black'><o:p> </o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:11.0pt;
font-family:"Arial","sans-serif";color:black'>+1 (858) 812-1534 (W & F)<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:11.0pt;
font-family:"Arial","sans-serif";color:black'>+1 (757) 941-4194 (H)<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:11.0pt;
font-family:"Arial","sans-serif";color:black'>+1 (858) 354-7388 (M)<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:11.0pt;
font-family:"Arial","sans-serif";color:black'><a href="www.gnf.org"><span
style='color:blue'>www.gnf.org</span></a><o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:11.0pt;
font-family:"Arial","sans-serif";color:black'><o:p> </o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:11.0pt;
font-family:"Arial","sans-serif";color:black'>Hudson-Alpha Institute for
Biotechnology<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:11.0pt;
font-family:"Arial","sans-serif";color:black'><a href="www.haib.org"><span
style='color:blue'>www.hudsonalpha.org</span></a><o:p></o:p></span></p>
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<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Arial","sans-serif";
color:black'><o:p> </o:p></span></p>
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<p class=MsoNormal><b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span
style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'> ome-users-bounces@lists.openmicroscopy.org.uk
[mailto:ome-users-bounces@lists.openmicroscopy.org.uk] <b>On Behalf Of </b>Cornelissen,
Frans [PRDBE]<br>
<b>Sent:</b> Monday, January 05, 2009 6:50 AM<br>
<b>To:</b> ome-users@lists.openmicroscopy.org.uk<br>
<b>Subject:</b> [ome-users] Can I convert 1-bit PNG files to 1-bit OME.TIFF
files?<o:p></o:p></span></p>
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<p class=MsoNormal><o:p> </o:p></p>
<p style='margin-left:144.0pt'><span lang=EN-AU style='font-size:10.0pt;
font-family:"Arial","sans-serif";color:navy'>All, </span><o:p></o:p></p>
<p style='margin-left:144.0pt'><span lang=EN-AU style='font-size:10.0pt;
font-family:"Arial","sans-serif";color:navy'>best wishes for 2009</span><o:p></o:p></p>
<p><span style='font-size:10.0pt;font-family:"Arial","sans-serif";color:navy'>Is</span>
<span style='font-size:10.0pt;font-family:"Arial","sans-serif";color:navy'>it
possible to convert 1-bit PNG files (cell-boundaries as a binay image) to 1-bit
OME.Tiff files?</span><o:p></o:p></p>
<p><span style='font-size:10.0pt;font-family:"Arial","sans-serif";color:navy'>If
I use the bfconvert command line tool, it ends up as a</span> <span
style='font-size:10.0pt;font-family:"Arial","sans-serif";color:navy'>UINT8
image…</span><o:p></o:p></p>
<p><span style='font-size:10.0pt;font-family:"Arial","sans-serif";color:navy'>The
(compressed) PNG file is only 4 K, the Tiff becomes 3900 K.</span><o:p></o:p></p>
<p><span style='font-size:10.0pt;font-family:"Arial","sans-serif";color:navy'>I
have individual overlay files for the CellBodies, the Nuclei and the
Neurites.</span><o:p></o:p></p>
<p><span style='font-size:10.0pt;font-family:"Arial","sans-serif";color:navy'>Ultimately,
I want to import these PNG files as</span> <span style='font-size:10.0pt;
font-family:"Arial","sans-serif";color:navy'>new</span> <span style='font-size:
10.0pt;font-family:"Arial","sans-serif";color:navy'>“Channels”</span> <span
style='font-size:10.0pt;font-family:"Arial","sans-serif";color:navy'>of an
existing file (with already 2 channels)</span> <span style='font-size:10.0pt;
font-family:"Arial","sans-serif";color:navy'>to show it as an</span> <span
style='font-size:10.0pt;font-family:"Arial","sans-serif";color:navy'>“overlay”
in the Insight Viewer.</span><o:p></o:p></p>
<p><span style='font-size:10.0pt;font-family:"Arial","sans-serif";color:navy'>Are
there easier ways to do this ?</span><o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p><span style='font-size:10.0pt;font-family:"Arial","sans-serif";color:navy'>Thanks,</span><o:p></o:p></p>
<p><span style='font-size:10.0pt;font-family:"Arial","sans-serif";color:navy'>Best
regads, frans</span><o:p></o:p></p>
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