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<div style="direction: ltr;font-family: Tahoma;color: #000000;font-size: 10pt;">Hi Curtis,<br>
<br>
We appreciate all your work. Just as some clarification, the SamplesPerPixel field in our metadata corresponds to the number of samples (off of our acquisition hardware) that were already binned together to form the pixel value. We do not provide the ability
to write out each individual sample in the Tiff data, so it would make sense that the Bio-Formats Prairie TIFF reader would always set the SamplesPerPixel field in the OME metadata to 1, regardless of the value of SamplesPerPixels field in the Prairie metadata.
<br>
<br>
For example, with our resonant scanner, we often average 3 raw samples together to form 1 pixel value, and only write the single pixel value to Tiff. We would like our Prairie XML file to still reflect SamplesPerPixel = 3 so users could go back and reference
that value.<br>
<br>
Thanks again and let me know if I'm just interpreting your email incorrectly.<br>
<br>
Regards,<br>
Jimmy<br>
<div><br>
<div style="font-size:13px; font-family:Tahoma">
<div class="WordSection1">
<p class="MsoNormal"><b><span style="font-size:8pt; font-family:'Arial','sans-serif'">Jimmy Fong</span></b></p>
<p class="MsoNormal"><b><span style="font-size:8pt; font-family:'Arial','sans-serif'"></span></b><span style="font-size:8pt; font-family:'Arial','sans-serif'">Software Engineer</span></p>
<p class="MsoNormal"><span style="font-size:8pt; font-family:'Arial','sans-serif'"></span> </p>
<p class="MsoNormal"><span style="font-size:8pt; font-family:'Arial','sans-serif'">Bruker Nano Surfaces Division
</span><a href="mailto:Jimmy.Fong@bruker-nano.com"><span style="font-size:8pt; font-family:'Arial','sans-serif'"><font color="#0000ff">Jimmy.Fong@bruker-nano.com</font></span></a><span style="font-size:8pt; font-family:'Arial','sans-serif'"></span></p>
<p class="MsoNormal"><span style="font-size:8pt; font-family:'Arial','sans-serif'">3030 Laura Lane, Suite 140
</span><a href="https://remote.bruker-nano.com/itweb/www.bruker.com/nano"><span style="font-size:8pt; font-family:'Arial','sans-serif'"><font color="#0000ff">www.bruker.com/nano</font></span></a><span style="font-size:8pt; font-family:'Arial','sans-serif'"></span></p>
<p class="MsoNormal"><span style="font-size:8pt; font-family:'Arial','sans-serif'">Middleton, WI 53562-0677</span></p>
<p class="MsoNormal"><span style="font-size:8pt; font-family:'Arial','sans-serif'">Phone: +1 608-662-0022 x163</span></p>
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<hr tabindex="-1">
<div style="direction: ltr;" id="divRpF387279"><font size="2" color="#000000" face="Tahoma"><b>From:</b> ctrueden.wisc@gmail.com [ctrueden.wisc@gmail.com] on behalf of Curtis Rueden [ctrueden@wisc.edu]<br>
<b>Sent:</b> Thursday, October 09, 2014 5:21 PM<br>
<b>To:</b> Wussow, Mike; Fong, Jimmy<br>
<b>Cc:</b> j.r.swedlow@dundee.ac.uk; ome-devel@lists.openmicroscopy.org.uk; Staniszewski, Kevin<br>
<b>Subject:</b> Re: [ome-devel] Prairie View XML changes for upcoming v5.2 Release<br>
</font><br>
</div>
<div></div>
<div>
<div dir="ltr">Hi Mike, Jimmy, Kevin and everyone,
<div><br>
</div>
<div>
<div>> We'll test the reader when it's released and keep you posted about</div>
<div>> what we find.</div>
</div>
<div><br>
</div>
<div>Thanks for getting back to me (via private mail) with your findings regarding the new PrairieView 5.2 file format reader. I am replying to the public thread to keep others in the loop regarding this work.</div>
<div><br>
</div>
<div><br>
</div>
<div>
<div>== Reading the files as a PrairieView dataset ==</div>
<div><br>
</div>
<div>It is important to note that if you select the .xml or .env file, the dataset will be detected as "Prairie TIFF" format, whereas if you select one of the .ome.tif files, it will be detected as "OME-TIFF" format. Completely separate reader code is used
in each case. The recent changes I made to the PrairieReader [3] only affect the former case.</div>
<div><br>
</div>
<div>In short: please select the .xml or .env file if you wish to use the Bio-Formats Prairie TIFF reader, rather than the OME-TIFF reader.<br>
</div>
<div><br>
</div>
</div>
<div><br>
</div>
<div>== SamplesPerPixel issue when reading as OME-TIFF ==</div>
<div><br>
</div>
<div>Kevin Staniszewski wrote:</div>
<div>
<div>> 1. The "SizeC" attribute is incorrect for all but the first frame.</div>
<div>> This acquisition only contained one channel, but every frame after the</div>
<div>> first reports 5 channels. It appears that the number 5 is coming from</div>
<div>> the "SamplesPerPixel" attribute, as in a separate data set, both</div>
<div>> values reported 6 (using a slightly longer dwell time).</div>
<div>></div>
<div>
<div>
<div>> 2. The "SamplesPerPixel" attribute is incorrect for only the first</div>
<div>> frame. The correct value for this acquisition is 5, but the first</div>
<div>> frame reports a value of 1. The value of 1 may be coming from the</div>
<div>> number of channels in the acquisition.</div>
</div>
</div>
<div><br>
</div>
<div>Actually, SamplesPerPixel needs to be set to 1 for the dataset you sent. From the OME-XML schema documentation [1]:</div>
<div><br>
</div>
<div>
<div> The number of samples the detector takes to form each pixel value.</div>
<div> [units:none] Note: This is not the same as "Frame Averaging" - see</div>
<div> Integration in DetectorSettings</div>
</div>
<div><br>
</div>
<div>SamplesPerPixel is the actual number of recorded sample values per pixel. If you use the "showinf" Bio-Formats command line tool on the dataset, the following warning is shown:</div>
<div><br>
</div>
<div> SamplesPerPixel mismatch: OME=5, TIFF=1</div>
<div><br>
</div>
<div>This indicates that the OME-XML indicates SamplesPerPixel=5, but the TIFF file only contains 1 sample value per pixel (as indicated by the IFD's SamplesPerPixel directory entry—which in this case is absent and hence defaults to 1 according to page 39 of
the TIFF specification [2]).</div>
</div>
<div><br>
</div>
<div>All of that said: I think it is indeed a bug in the Bio-Formats OME-TIFF reader that the first series is marked with "SizeC=1" but subsequent ones are "SizeC=5 (effectively 1)". I will investigate if/how we can fix that on our end.</div>
<div><br>
</div>
<div><br>
</div>
<div>== Failure to extract (X, Y, Z) stage positions ==<br>
</div>
<div><br>
</div>
<div>
<div>Kevin Staniszewski wrote:</div>
<div></div>
</div>
<div>
<div>> The experiment that generated this data was a T series that took one</div>
<div>> image at all XY locations. If I use the bio-formats importer to look</div>
<div>> at the OME data, it shows up in a way such that each frame looks like</div>
<div>> a different time point, instead of a different XY position.</div>
</div>
<div><br>
</div>
<div>Yes, there was a bug! Fixed now:</div>
<div><br>
</div>
<div><a href="https://github.com/ctrueden/bioformats/commit/ffa5e3071b2083cc0385032b6fdbcf40b3157271" target="_blank">https://github.com/ctrueden/bioformats/commit/ffa5e3071b2083cc0385032b6fdbcf40b3157271</a><br>
</div>
<div><br>
</div>
<div><br>
</div>
<div>== Spectral datasets ==</div>
<div><br>
</div>
<div>Next on my list is to finish adding support for spectral datasets. Will keep everyone posted, and file a PR as soon as it is ready.</div>
<div><br>
</div>
<div>Regards,<br>
</div>
<div>Curtis</div>
<div class="gmail_extra"><br>
</div>
<div class="gmail_extra">[1] <a href="https://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2013-06/ome_xsd.html#Channel_SamplesPerPixel" target="_blank">https://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2013-06/ome_xsd.html#Channel_SamplesPerPixel</a></div>
<div class="gmail_extra"><br>
</div>
<div class="gmail_extra">[2] <a href="http://partners.adobe.com/public/developer/en/tiff/TIFF6.pdf" target="_blank">http://partners.adobe.com/public/developer/en/tiff/TIFF6.pdf</a></div>
<div class="gmail_extra"><br>
</div>
<div class="gmail_extra">[3] <a href="https://github.com/openmicroscopy/bioformats/pull/1306" target="_blank">https://github.com/openmicroscopy/bioformats/pull/1306</a></div>
<div class="gmail_extra"><br>
</div>
<div class="gmail_extra"><br>
</div>
<div class="gmail_extra"><br>
</div>
<div class="gmail_extra">
<div class="gmail_quote">On Fri, Aug 29, 2014 at 2:34 PM, Jimmy Fong <span dir="ltr">
<<a href="mailto:Jimmy.Fong@bruker-nano.com" target="_blank">Jimmy.Fong@bruker-nano.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex; border-left-width:1px; border-left-color:rgb(204,204,204); border-left-style:solid; padding-left:1ex">
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We appreciate all your work, Curtis. We'll test the reader when it's released and keep you posted about what we find.<br>
<br>
Thanks again,<br>
Jimmy<br>
<br>
<div>
<div style="font-size:13px; font-family:Tahoma">
<div>
<p class="MsoNormal"><b><span style="font-size:8pt; font-family:Arial,sans-serif">Jimmy Fong</span></b></p>
<p class="MsoNormal"><b><span style="font-size:8pt; font-family:Arial,sans-serif"></span></b><span style="font-size:8pt; font-family:Arial,sans-serif">Software Engineer</span></p>
<p class="MsoNormal"><span style="font-size:8pt; font-family:Arial,sans-serif"></span> </p>
<p class="MsoNormal"><span style="font-size:8pt; font-family:Arial,sans-serif">Bruker Nano Surfaces Division
</span><a href="mailto:Jimmy.Fong@bruker-nano.com" target="_blank"><span style="font-size:8pt; font-family:Arial,sans-serif"><font color="#0000ff">Jimmy.Fong@bruker-nano.com</font></span></a><span style="font-size:8pt; font-family:Arial,sans-serif"></span></p>
<p class="MsoNormal"><span style="font-size:8pt; font-family:Arial,sans-serif">3030 Laura Lane, Suite 140
</span><a href="https://remote.bruker-nano.com/itweb/www.bruker.com/nano" target="_blank"><span style="font-size:8pt; font-family:Arial,sans-serif"><font color="#0000ff">www.bruker.com/nano</font></span></a><span style="font-size:8pt; font-family:Arial,sans-serif"></span></p>
<p class="MsoNormal"><span style="font-size:8pt; font-family:Arial,sans-serif">Middleton, WI 53562-0677</span></p>
<p class="MsoNormal"><span style="font-size:8pt; font-family:Arial,sans-serif">Phone:
<a href="tel:%2B1%20608-662-0022%20x163" value="+16086620022" target="_blank">+1 608-662-0022 x163</a></span></p>
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<p class="MsoNormal"><b><i><span style="font-family:Arial,sans-serif; color:rgb(31,73,125)">We are now Bruker!</span></i></b></p>
<p class="MsoNormal"><span><b><i><span style="font-family:Arial,sans-serif; color:rgb(31,73,125)">Same great products.</span></i></b></span><b><i><span style="font-family:Arial,sans-serif; color:rgb(31,73,125)">
<span>Same great technology.</span></span></i></b></p>
<p class="MsoNormal"><span><b><i><span style="font-family:Arial,sans-serif; color:rgb(31,73,125)">Same great people.</span></i></b></span><b><i><span style="font-family:Arial,sans-serif; color:rgb(31,73,125)">
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<div style="font-family:'Times New Roman'; color:rgb(0,0,0); font-size:16px">
<hr>
<div style="direction:ltr"><font color="#000000" face="Tahoma"><b>From:</b> Jimmy Fong [<a href="mailto:fong@wisc.edu" target="_blank">fong@wisc.edu</a>]<br>
<b>Sent:</b> Friday, August 29, 2014 2:30 PM<br>
<b>To:</b> Jimmy Fong<br>
<b>Subject:</b> Fwd: Re: [ome-devel] Prairie View XML changes for upcoming v5.2 Release<br>
</font><br>
</div>
<div></div>
<div><br>
<div><br>
<br>
-------- Original Message --------
<table border="0" cellpadding="0" cellspacing="0">
<tbody>
<tr>
<th align="RIGHT" nowrap="" valign="BASELINE">Subject: </th>
<td>Re: [ome-devel] Prairie View XML changes for upcoming v5.2 Release</td>
</tr>
<tr>
<th align="RIGHT" nowrap="" valign="BASELINE">Date: </th>
<td>Fri, 29 Aug 2014 14:22:28 -0500</td>
</tr>
<tr>
<th align="RIGHT" nowrap="" valign="BASELINE">From: </th>
<td>Curtis Rueden <a href="mailto:ctrueden@wisc.edu" target="_blank"><ctrueden@wisc.edu></a></td>
</tr>
<tr>
<th align="RIGHT" nowrap="" valign="BASELINE">To: </th>
<td>Mike Wussow <a href="mailto:Mike.Wussow@bruker-nano.com" target="_blank"><Mike.Wussow@bruker-nano.com></a></td>
</tr>
<tr>
<th align="RIGHT" nowrap="" valign="BASELINE">CC: </th>
<td>Jason Swedlow <a href="mailto:j.r.swedlow@dundee.ac.uk" target="_blank"><j.r.swedlow@dundee.ac.uk></a>, OME Development
<a href="mailto:ome-devel@lists.openmicroscopy.org.uk" target="_blank"><ome-devel@lists.openmicroscopy.org.uk></a>, Jimmy Fong
<a href="mailto:fong@wisc.edu" target="_blank"><fong@wisc.edu></a></td>
</tr>
</tbody>
</table>
<div>
<div><br>
<br>
<div dir="ltr">Hi Mike,
<div><br>
</div>
<div>
<div>> We noticed that the latest release of the Bioformats reader did not</div>
<div>> contain an update for the Prairie View Files.</div>
</div>
<div><br>
</div>
<div>Thanks for following up. I have updated the Bio-Formats Prairie file format reader to include support for PrairieView version 5.2 datasets. This work will be merged into the Bio-Formats mainline pending review, and can be browsed here:</div>
<div><br>
</div>
<div><a href="https://github.com/openmicroscopy/bioformats/pull/1305" target="_blank">https://github.com/openmicroscopy/bioformats/pull/1305</a><br>
</div>
<div><br>
</div>
<div>Thanks again for sending details about the new format, and for your continued patience.</div>
<div><br>
</div>
<div>Best regards,</div>
<div>Curtis</div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">On Mon, Aug 18, 2014 at 7:41 AM, Mike Wussow <span dir="ltr">
<<a href="mailto:Mike.Wussow@bruker-nano.com" target="_blank">Mike.Wussow@bruker-nano.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex; border-left-width:1px; border-left-color:rgb(204,204,204); border-left-style:solid; padding-left:1ex">
<div lang="EN-US">
<div>
<p class="MsoNormal"><span style="color:rgb(31,73,125)">Hi Jason and the OME Development Team,</span></p>
<p class="MsoNormal"><span style="color:rgb(31,73,125)"> </span></p>
<p class="MsoNormal"><span style="color:rgb(31,73,125)"> We noticed that the latest release of the Bioformats reader did not contain an update for the Prairie View Files. We are wondering if there is anything we can do to offer further support
so that the capabilities are updated for the next release. Please let me know if we can help in some way.</span></p>
<p class="MsoNormal"><span style="color:rgb(31,73,125)"> </span></p>
<p class="MsoNormal"><span style="color:rgb(31,73,125)">Best,</span></p>
<p class="MsoNormal"><span style="color:rgb(31,73,125)"> </span></p>
<p class="MsoNormal"><span style="color:rgb(31,73,125)">Mike</span></p>
<div>
<p class="MsoNormal"><span style="color:rgb(31,73,125)"> </span></p>
<div>
<p class="MsoNormal"><b><span style="font-size:8pt; font-family:Arial,sans-serif; color:black">Michael C. Wussow</span></b><span></span></p>
<p class="MsoNormal"><span style="font-size:8pt; font-family:Arial,sans-serif; color:black">Director Product Line Management</span></p>
<p class="MsoNormal"><span> </span></p>
<p class="MsoNormal"><span style="font-size:8pt; font-family:Arial,sans-serif; color:black">Bruker Nano Surfaces Division
</span><u><span style="font-size:8pt; font-family:Arial,sans-serif; color:blue"><a href="mailto:mike.wussow@bruker-nano.com" target="_blank"><span style="color:blue">mike.wussow@bruker-nano.com</span></a></span></u><span></span></p>
<p class="MsoNormal"><span style="font-size:8pt; font-family:Arial,sans-serif; color:black">3030 Laura Lane, Suite 140
<a href="http://www.bruker.com/nano" target="_blank">http://www.bruker.com/nano</a></span><span></span></p>
<p class="MsoNormal"><span style="font-size:8pt; font-family:Arial,sans-serif; color:black">Middleton, WI 53562-0677</span><span></span></p>
<p class="MsoNormal"><span style="font-size:8pt; font-family:Arial,sans-serif; color:black">Phone:
<a href="tel:%2B1%20608-662-0022%20x167" value="+16086620022" target="_blank">+1 608-662-0022 x167</a></span></p>
<p class="MsoNormal"><span style="font-size:8pt; font-family:Arial,sans-serif; color:black">Cell:
</span><span style="font-size:8pt; font-family:Arial,sans-serif; color:black">+1 </span>
<span style="font-size:8pt; font-family:Arial,sans-serif; color:black"><a href="tel:608-381-8252" value="+16083818252" target="_blank">608-381-8252</a></span><span></span></p>
<div>
<div>
<div>
<div>
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<hr style="width:6.25in" align="left" noshade="" size="8" width="600">
</span></div>
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<p class="MsoNormal"><span style="color:rgb(31,73,125)"> </span></p>
</div>
<div>
<div style="border-style:solid none none; border-top-color:rgb(181,196,223); border-top-width:1pt; padding:3pt 0in 0in">
<p class="MsoNormal"><b><span style="font-size:10pt; font-family:Tahoma,sans-serif">From:</span></b><span style="font-size:10pt; font-family:Tahoma,sans-serif"> Jason Swedlow [mailto:<a href="mailto:j.r.swedlow@dundee.ac.uk" target="_blank">j.r.swedlow@dundee.ac.uk</a>]
<br>
<b>Sent:</b> Tuesday, June 10, 2014 4:59 AM<br>
<b>To:</b> Mike Wussow<br>
<b>Cc:</b> OME Development<br>
<b>Subject:</b> Re: [ome-devel] Prairie View XML changes for upcoming v5.2 Release</span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"> </p>
<p>Hi Mike</p>
<p>Thanks for this info. It's great to have this spec and the example data. We'll look at this and let you know if we have any questions or issues.</p>
<p>I don't know if we can get this into our upcoming release, as we already have a lot of work scheduled for that. We'll definitely cc you on the relevant tickets so you can follow our progress.</p>
<p>Thanks again for this contribution. We welcome all info and sample data from the commercial imaging community. Thanks to all at Bruker for their support of Bio-Formats.</p>
<p>Cheers,</p>
<p>Jason</p>
<p>Centre for Gene Regulation & Expression | Open Microscopy Environment | University of Dundee</p>
<div>
<p class="MsoNormal"><span>On 9 Jun 2014 15:54, Mike Wussow <<a href="mailto:Mike.Wussow@bruker-nano.com" target="_blank">Mike.Wussow@bruker-nano.com</a>> wrote:</span></p>
</div>
<div>
<div>
<p class="MsoNormal">Dear Bio-formats Community,</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">Prairie View version 5.2 will be released the first week in July 2014. With this release we have found it necessary to make changes to our XML files. We realize that these changes will likely break the Bio-formats reader for our files
but were necessary changes that should serve our customers well moving forward. Therefore we are providing information on the changes and example data sets in advance of our release in the hopes that this community can update the Bio-formats reader to accommodate
these changes.</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">A summary of the changes that have occurred to our XML files can be found here:
<a href="https://www.dropbox.com/s/sf2e634tpuv6ffh/Prairie%20View%20XML%20Evolution.docx" target="_blank">
https://www.dropbox.com/s/sf2e634tpuv6ffh/Prairie%20View%20XML%20Evolution.docx</a> as well as in the text below.</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">Example data sets can be downloaded here: <a href="https://www.dropbox.com/sh/rtd73wcu4oboqt4/AABKM1rdhYLWjFVrw-YA5__Sa" target="_blank">
https://www.dropbox.com/sh/rtd73wcu4oboqt4/AABKM1rdhYLWjFVrw-YA5__Sa</a></p>
<p class="MsoNormal"> </p>
<p class="MsoNormal"><b><span style="font-size:8pt; font-family:Arial,sans-serif; color:black">Michael C. Wussow</span></b></p>
<p class="MsoNormal"><span style="font-size:8pt; font-family:Arial,sans-serif; color:black">Director Product Line Management</span></p>
<p class="MsoNormal"><span> </span></p>
<p class="MsoNormal"><span style="font-size:8pt; font-family:Arial,sans-serif; color:black">Bruker Nano Surfaces Division
</span><u><span style="font-size:8pt; font-family:Arial,sans-serif; color:blue"><a href="mailto:mike.wussow@bruker-nano.com" target="_blank">mike.wussow@bruker-nano.com</a></span></u></p>
<p class="MsoNormal"><span style="font-size:8pt; font-family:Arial,sans-serif; color:black">3030 Laura Lane, Suite 140
<a href="http://www.bruker.com/nano" target="_blank">http://www.bruker.com/nano</a></span></p>
<p class="MsoNormal"><span style="font-size:8pt; font-family:Arial,sans-serif; color:black">Middleton, WI 53562-0677</span></p>
<p class="MsoNormal"><span style="font-size:8pt; font-family:Arial,sans-serif; color:black">Phone:
<a href="tel:%2B1%20608-662-0022%20x167" value="+16086620022" target="_blank">+1 608-662-0022 x167</a></span></p>
<p class="MsoNormal"><span style="font-size:8pt; font-family:Arial,sans-serif; color:black">Cell:
<a href="tel:%2B1%20608-381-8252" value="+16083818252" target="_blank">+1 608-381-8252</a></span></p>
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