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Dear Peter,
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<div>I am replying cc'd to our users list which is the proper place to ask Bio-Formats related questions.</div>
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<div>The information on what formats Bio-Formats supports is on</div>
<div><a href="http://www.openmicroscopy.org/site/support/bio-formats5/supported-formats.html">http://www.openmicroscopy.org/site/support/bio-formats5/supported-formats.html</a></div>
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<div>If you click on the format type you have in this table, you will find more information about how well each format is supported which should answer your question about the transformation.</div>
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<div>We are hoping to release an updated version of the Bio-Formats plugin early next week but in the meantime, you can download the 'loci-tools.jar' from <a href="http://downloads.openmicroscopy.org/bio-formats/5.0.0-rc1/">http://downloads.openmicroscopy.org/bio-formats/5.0.0-rc1/</a> </div>
<div>and use the documentation on <a href="http://www.openmicroscopy.org/site/support/bio-formats5/users/imagej/installing.html">http://www.openmicroscopy.org/site/support/bio-formats5/users/imagej/installing.html</a> and <a href="http://www.openmicroscopy.org/site/support/bio-formats5/users/imagej/load-images.html">http://www.openmicroscopy.org/site/support/bio-formats5/users/imagej/load-images.html</a>
to guide you through getting it installed and loading your images.</div>
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<div>If you need any further help, please reply to the mailing list and someone will get back to you next week,</div>
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<div>Thanks,</div>
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<div>Helen</div>
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<div>On 21 Feb 2014, at 17:53, Peter Gerondelis <<a href="mailto:peter.z.gerondelis@gsk.com">peter.z.gerondelis@gsk.com</a>> wrote:</div>
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<span style="font-family: Calibri, sans-serif; ">Thank you for contacting us.</span><span class="Apple-converted-space"> </span><br>
<span style="font-family: Calibri, sans-serif; ">Please provide as much information as possible so we can deal with your enquiry efficiently.</span><o:p></o:p></p>
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<o:p> </o:p></p>
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Hi, I am looking to use<span class="Apple-converted-space"> </span><span class="SpellE">ImageJ</span><span class="Apple-converted-space"> </span>to analyze<span class="Apple-converted-space"> </span><span class="SpellE">phosphorimaging</span><span class="Apple-converted-space"> </span>files
from my Typhoon and Storm.<span> <span class="Apple-converted-space"> </span></span>I can no longer use the software provided by the manufacturer (formerly Molecular Dynamics, then<span class="Apple-converted-space"> </span><span class="SpellE">Amersham</span><span class="Apple-converted-space"> </span>and
now GE).<span> <span class="Apple-converted-space"> </span></span>My understanding is that these are not ordinary TIFF files.<span> <span class="Apple-converted-space"> </span></span>They are transformed by the instrument and/or software.<span> </span>Someone
from the<span class="Apple-converted-space"> </span><span class="SpellE">ImageJ</span><span class="Apple-converted-space"> </span>list serve suggested that I try Bio Formats<span class="Apple-converted-space"> </span><span class="SpellE">plugin</span>.<span> <span class="Apple-converted-space"> </span></span>I
thought I would try it but can’t figure out how to install.<span> <span class="Apple-converted-space"> </span></span>Before I put any additional energy to getting this<span class="Apple-converted-space"> </span><span class="SpellE">plugin</span><span class="Apple-converted-space"> </span>and
installing it, I would like to confirm that the<span class="Apple-converted-space"> </span><span class="SpellE">plugin</span><span class="Apple-converted-space"> </span>does more than just open the file, but does it handle the transformation correctly?<span> <span class="Apple-converted-space"> </span></span>If
so, can you explain to me which file I need to download from the website, how to get it properly installed into<span class="Apple-converted-space"> </span><span class="SpellE">ImageJ</span><span class="Apple-converted-space"> </span>and how to use it????<span> </span><o:p></o:p></p>
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Please note the following related post from the<span class="Apple-converted-space"> </span><span class="SpellE">ImageJ</span><span class="Apple-converted-space"> </span>list serve:<o:p></o:p></p>
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<b>Subject:</b><o:p></o:p></p>
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<a href="https://list.nih.gov/cgi-bin/wa.exe?A2=IMAGEJ;9ad542ec.0512" style="color: purple; text-decoration: underline; "><span class="SpellE">Amersham</span><span class="Apple-converted-space"> </span>.gel file warning</a><o:p></o:p></p>
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<b>From:</b><o:p></o:p></p>
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<span class="SpellE">Morri</span><span class="Apple-converted-space"> </span>Feldman <<a href="https://list.nih.gov/cgi-bin/wa.exe?LOGON=A2%3Dind0512%26L%3DIMAGEJ%26P%3DR16807%261%3DIMAGEJ%269%3DA%26I%3D-3%26J%3Don%26d%3DNo%2BMatch%253BMatch%253BMatches%26z%3D4" target="_parent" style="color: purple; text-decoration: underline; ">[log
in to unmask]</a>><o:p></o:p></p>
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<b>Reply-To:</b><o:p></o:p></p>
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<span class="SpellE">ImageJ</span><span class="Apple-converted-space"> </span>Interest Group <<a href="https://list.nih.gov/cgi-bin/wa.exe?LOGON=A2%3Dind0512%26L%3DIMAGEJ%26P%3DR16807%261%3DIMAGEJ%269%3DA%26I%3D-3%26J%3Don%26d%3DNo%2BMatch%253BMatch%253BMatches%26z%3D4" target="_parent" style="color: purple; text-decoration: underline; ">[log
in to unmask]</a>><o:p></o:p></p>
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<b>Date:</b><o:p></o:p></p>
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Tue, 20 Dec 2005 11:54:00 -0800<o:p></o:p></p>
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<pre style="margin: 0in 0in 0.0001pt; font-size: 7pt; font-family: 'Courier New'; "><span style="">The <span class="SpellE">Amersham</span> .gel file format is based on the tiff standard.<span> </span><span class="SpellE">ImageJ</span><o:p></o:p></span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 7pt; font-family: 'Courier New'; "><span style="">will read .gel files because they are tiff files.<span> </span>Unfortunately<o:p></o:p></span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 7pt; font-family: 'Courier New'; "><span class="SpellE">Amersham</span><span style=""> scanners (e.g. Typhoon and Storm) transform the original<o:p></o:p></span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 7pt; font-family: 'Courier New'; "><span style="">pixel values by taking their square root and scaling them before<o:p></o:p></span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 7pt; font-family: 'Courier New'; "><span style="">saving them to a .gel file.<span> </span>When <span class="SpellE">imagej</span> opens a .gel file, it doesn't<o:p></o:p></span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 7pt; font-family: 'Courier New'; "><span style="">reverse this transformation making the images appear muted and<o:p></o:p></span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 7pt; font-family: 'Courier New'; "><span style="">unsuitable for quantification.<o:p></o:p></span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 7pt; font-family: 'Courier New'; "><span style=""> </span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 7pt; font-family: 'Courier New'; "><span style="">Here are some links.<o:p></o:p></span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 7pt; font-family: 'Courier New'; "><span style=""> </span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 7pt; font-family: 'Courier New'; "><span style="">A short note about <span class="SpellE">Amersham's</span> .gel file format:<o:p></o:p></span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 7pt; font-family: 'Courier New'; "><span style=""><a href="http://www4.amershambiosciences.com/aptrix/upp00919.nsf/content/1F801602120AE332C1256EB400484111?OpenDocument&querytitle=&hometitle=search" target="_blank" style="color: purple; text-decoration: underline; ">http://www4.amershambiosciences.com/aptrix/upp00919.nsf/content/1F801602120AE332C1256EB400484111?OpenDocument&querytitle=&hometitle=search</a><o:p></o:p></span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 7pt; font-family: 'Courier New'; "><span style=""> </span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 7pt; font-family: 'Courier New'; "><span style="">A <span class="SpellE">pdf</span> document from when Molecular Dynamics owned the .gel file format:<o:p></o:p></span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 7pt; font-family: 'Courier New'; "><span style=""><a href="http://research.stowers-institute.org/efg/ScientificSoftware/Utility/TiffTags/GEL-FileFormat.pdf" target="_blank" style="color: purple; text-decoration: underline; ">http://research.stowers-institute.org/efg/ScientificSoftware/Utility/TiffTags/GEL-FileFormat.pdf</a><o:p></o:p></span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 7pt; font-family: 'Courier New'; "><span style=""> </span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 7pt; font-family: 'Courier New'; "><span style="">If the information in the <span class="SpellE">pdf</span> is current, it should be possible to<o:p></o:p></span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 7pt; font-family: 'Courier New'; "><span style="">read a few private tiff tags from the .gel file and use their values<o:p></o:p></span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 7pt; font-family: 'Courier New'; "><span style="">to reverse the image transformation.<span> </span>Barring this solution, be wary<o:p></o:p></span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 7pt; font-family: 'Courier New'; "><span style="">of quantifying data directly from .gel files.<o:p></o:p></span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 7pt; font-family: 'Courier New'; "><span style=""> </span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 7pt; font-family: 'Courier New'; "><span style="">Best,<o:p></o:p></span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 7pt; font-family: 'Courier New'; "><span class="SpellE">Morri</span><span style=""><o:p></o:p></span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 7pt; font-family: 'Courier New'; "><span style=""> </span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 7pt; font-family: 'Courier New'; "><span style="">--<o:p></o:p></span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 7pt; font-family: 'Courier New'; "><span class="SpellE">Morri</span><span style=""> Feldman<o:p></o:p></span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 7pt; font-family: 'Courier New'; "><span style="">(415) 514-0575<o:p></o:p></span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 7pt; font-family: 'Courier New'; "><span class="SpellE">Shokat</span><span style=""> Lab<o:p></o:p></span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 7pt; font-family: 'Courier New'; "><span style="">UCSF Biophysics Program<o:p></o:p></span></pre>
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Best, Pete<o:p></o:p></p>
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<span style="font-family: Calibri, sans-serif; "> </span></div>
<div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; ">
<b><span style="font-size: 10pt; font-family: Arial, sans-serif; ">Peter Gerondelis, Ph.D.<o:p></o:p></span></b></div>
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<span style="font-size:10pt;">The University of Dundee is a registered Scottish Charity, No: SC015096</span>
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