<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; color: rgb(0, 0, 0); font-size: 14px; font-family: Calibri, sans-serif; "><div>Gentlemen, Can anyone help us sooner? I am worried that this project is falling behind.</div><div>Thanks,</div><div><div><div style="font-family: Calibri, sans-serif; "><div><br></div><div><!--StartFragment--><font face="Calibri,Verdana,Helvetica,Arial"><span style="font-size:11pt">Badri Roysam, D.Sc.<br>
Hugh Roy and Lillie Cranz Cullen University Professor<br>
Chair, Electrical & Computer Engineering<br>
N325, Engineering Building 1<br>
University of Houston<br>
Houston, Texas 77204-4005<br>
Office: 713-743-1773/4435</span></font></div><div><font face="Calibri,Verdana,Helvetica,Arial"><span style="font-size:11pt">Lab (W349): 713-743-0790<br>
Fax: 713-743-4444<br>
Email: <a href="broysam@central.uh.edu">broysam@central.uh.edu</a></span></font><!--EndFragment--></div></div><div style="font-family: Calibri, sans-serif; "><font face="Calibri,Verdana,Helvetica,Arial"><font class="Apple-style-span" size="4"><span class="Apple-style-span" style="font-size: 15px; ">ECE Department website: </span><span class="Apple-style-span" style="font-size: 15px; "><a href="http://www.ee.uh.edu">www.ee.uh.edu</a></span></font></font></div><div style="font-family: Calibri, sans-serif; "><font face="Calibri,Verdana,Helvetica,Arial"><font class="Apple-style-span" size="4"><span class="Apple-style-span" style="font-size: 15px;">Laboratory website: www.farsight-toolkit.org</span></font></font></div><div style="font-family: Calibri, sans-serif; "><font face="Calibri,Verdana,Helvetica,Arial"><font class="Apple-style-span" size="4"><span class="Apple-style-span" style="font-size: 15px;"><br></span></font></font></div><div><font class="Apple-style-span" face="Calibri,Verdana,Helvetica,Arial"><p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 12.0px Helvetica"><img src="cid:90E25201-50A2-4ADF-A9CB-F8931F26DA67" alt="ece.gif" type="image/png"></p></font></div></div></div><div><br></div><span id="OLK_SRC_BODY_SECTION"><div style="font-family:Calibri; font-size:11pt; text-align:left; color:black; BORDER-BOTTOM: medium none; BORDER-LEFT: medium none; PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; PADDING-RIGHT: 0in; BORDER-TOP: #b5c4df 1pt solid; BORDER-RIGHT: medium none; PADDING-TOP: 3pt"><span style="font-weight:bold">From: </span> Mark Hiner <<a href="mailto:hinerm@gmail.com">hinerm@gmail.com</a>><br><span style="font-weight:bold">Date: </span> Thursday, June 19, 2014 7:34 AM<br><span style="font-weight:bold">To: </span> Kedar Grama <<a href="mailto:gbkedar@gmail.com">gbkedar@gmail.com</a>>, "<a href="mailto:scifio@scif.io">scifio@scif.io</a>" <<a href="mailto:scifio@scif.io">scifio@scif.io</a>><br><span style="font-weight:bold">Cc: </span> Dragan Maric <<a href="mailto:maricd@ninds.nih.gov">maricd@ninds.nih.gov</a>>, Matt McCormick <<a href="mailto:matt.mccormick@kitware.com">matt.mccormick@kitware.com</a>>, Curtis Rueden <<a href="mailto:ctrueden.wisc@gmail.com">ctrueden.wisc@gmail.com</a>>, Badri Roysam <<a href="mailto:broysam@central.uh.edu">broysam@central.uh.edu</a>><br><span style="font-weight:bold">Subject: </span> Re: Scrambled tiles in czi files with Scifio-Itk bridge<br></div><div><br></div><div dir="ltr"><div><div>Hi Kedar,<br><br> Just wanted to let you know that I'll be out of the country for two weeks starting tomorrow, and all of my time right now is being spent on the <a href="http://developer.imagej.net/2014/06/04/imagej-200-release-candidate">ImageJ2 release</a>.<br><br></div> Would you mind filing this as an issue on the scifio-itk-bridge github site: <a href="https://github.com/scifio/scifio-itk-bridge">https://github.com/scifio/scifio-itk-bridge</a> ? That way it won't get lost in my e-mail and I can investigate when I get back.<br><br>Thanks!<br></div>- Mark<br><div><br><br><div><div class="gmail_extra"><div class="gmail_quote">On Wed, Jun 18, 2014 at 2:39 PM, Kedar Grama <span dir="ltr"><<a href="mailto:gbkedar@gmail.com" target="_blank">gbkedar@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr">Hi Mark,<br><br>I used SCIFIO to write czi as a 3d stack of either nrrd or tiffs. I get tiles that are scrambled and this happens at random. My code to convert the files is here:<br><a href="https://github.com/gbkedar/farsight/blob/IlluminationGraphCuts/IlluminationCorrection/readCziWriteCorrectedTiles.cpp" target="_blank">https://github.com/gbkedar/farsight/blob/IlluminationGraphCuts/IlluminationCorrection/readCziWriteCorrectedTiles.cpp</a><br><div><br></div><div>I have made montages of the same image in three instances where tiles were scrambled and once when it worked. The czi file is similar to the one I sent you in June or July last year. Please let me know if you need the file that I'm using right now and I'll upload it.</div><div><br></div><div>Thanks,</div><div><br></div><div>-Kedar</div></div></blockquote></div><br></div></div></div></div></span></body></html>