<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=us-ascii">
<meta name="Generator" content="Microsoft Word 12 (filtered medium)">
<style><!--
/* Font Definitions */
@font-face
{font-family:"Cambria Math";
panose-1:2 4 5 3 5 4 6 3 2 4;}
@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
@font-face
{font-family:Tahoma;
panose-1:2 11 6 4 3 5 4 4 2 4;}
@font-face
{font-family:"Book Antiqua";
panose-1:2 4 6 2 5 3 5 3 3 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0cm;
margin-bottom:.0001pt;
font-size:12.0pt;
font-family:"Times New Roman","serif";}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:blue;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{mso-style-priority:99;
color:purple;
text-decoration:underline;}
span.EmailStyle17
{mso-style-type:personal-reply;
font-family:"Book Antiqua","serif";
color:#1F497D;}
.MsoChpDefault
{mso-style-type:export-only;}
@page WordSection1
{size:612.0pt 792.0pt;
margin:72.0pt 72.0pt 72.0pt 72.0pt;}
div.WordSection1
{page:WordSection1;}
--></style><!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext="edit">
<o:idmap v:ext="edit" data="1" />
</o:shapelayout></xml><![endif]-->
</head>
<body lang="EN-GB" link="blue" vlink="purple">
<div class="WordSection1">
<p class="MsoNormal"><font size="2" color="#1f497d" face="Book Antiqua"><span style="font-size:11.0pt;font-family:"Book Antiqua","serif";color:#1F497D">Hi Curtis,<o:p></o:p></span></font></p>
<p class="MsoNormal"><font size="2" color="#1f497d" face="Book Antiqua"><span style="font-size:11.0pt;font-family:"Book Antiqua","serif";color:#1F497D"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font size="2" color="#1f497d" face="Book Antiqua"><span style="font-size:11.0pt;font-family:"Book Antiqua","serif";color:#1F497D">Thanks. In addition, I should also thank the team for including support for ImSpectorPro (*.msr) files. I’ve
had no problems (yet!) opening these files since upgrading to Bioformats 5.<o:p></o:p></span></font></p>
<p class="MsoNormal"><font size="2" color="#1f497d" face="Book Antiqua"><span style="font-size:11.0pt;font-family:"Book Antiqua","serif";color:#1F497D"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font size="2" color="#1f497d" face="Book Antiqua"><span style="font-size:11.0pt;font-family:"Book Antiqua","serif";color:#1F497D">Paul.<o:p></o:p></span></font></p>
<p class="MsoNormal"><font size="2" color="#1f497d" face="Calibri"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">____________________<o:p></o:p></span></font></p>
<p class="MsoNormal"><font size="2" color="#1f497d" face="Calibri"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Dr. Paul Thomas, Manager,<o:p></o:p></span></font></p>
<p class="MsoNormal"><font size="2" color="#1f497d" face="Calibri"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">The Henry Wellcome Laboratory for Cell Imaging,<o:p></o:p></span></font></p>
<p class="MsoNormal"><font size="2" color="#1f497d" face="Calibri"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Faculty of Science,<o:p></o:p></span></font></p>
<p class="MsoNormal"><font size="2" color="#1f497d" face="Calibri"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">University of East Anglia,<o:p></o:p></span></font></p>
<p class="MsoNormal"><font size="2" color="#1f497d" face="Calibri"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Norwich Research Park,<o:p></o:p></span></font></p>
<p class="MsoNormal"><font size="2" color="#1f497d" face="Calibri"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Norwich,<o:p></o:p></span></font></p>
<p class="MsoNormal"><font size="2" color="#1f497d" face="Calibri"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">NR4 7TJ,<o:p></o:p></span></font></p>
<p class="MsoNormal"><font size="2" color="#1f497d" face="Calibri"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">United Kingdom.<o:p></o:p></span></font></p>
<p class="MsoNormal"><font size="2" color="#1f497d" face="Calibri"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font size="2" color="#1f497d" face="Calibri"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">e-mail: p.thomas@uea.ac.uk<o:p></o:p></span></font></p>
<p class="MsoNormal"><font size="2" color="#1f497d" face="Calibri"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Tel: +44-1603-592196<o:p></o:p></span></font></p>
<p class="MsoNormal"><font size="2" color="#1f497d" face="Calibri"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Fax: +44-1603-592250<o:p></o:p></span></font></p>
<p class="MsoNormal"><font size="2" color="#1f497d" face="Calibri"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Imaging web-site: https://www.uea.ac.uk/biological-sciences/research/facilities/henry-wellcome-lab<o:p></o:p></span></font></p>
<p class="MsoNormal"><font size="2" color="#1f497d" face="Calibri"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Personal web-page: https://www.uea.ac.uk/biological-sciences/research/facilities/henry-wellcome-lab/people<o:p></o:p></span></font></p>
<p class="MsoNormal"><font size="2" color="#1f497d" face="Book Antiqua"><span style="font-size:11.0pt;font-family:"Book Antiqua","serif";color:#1F497D"><o:p> </o:p></span></font></p>
<div style="border:none;border-left:solid blue 1.5pt;padding:0cm 0cm 0cm 4.0pt">
<div>
<div style="border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm 0cm">
<p class="MsoNormal"><b><font size="2" face="Tahoma"><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";font-weight:bold">From:</span></font></b><font size="2" face="Tahoma"><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">
ctrueden.wisc@gmail.com [mailto:ctrueden.wisc@gmail.com] <b><span style="font-weight:bold">On Behalf Of
</span></b>Curtis Rueden<br>
<b><span style="font-weight:bold">Sent:</span></b> 05 March 2014 20:08<br>
<b><span style="font-weight:bold">To:</span></b> Paul Thomas (SCI)<br>
<b><span style="font-weight:bold">Cc:</span></b> melissa@glencoesoftware.com; vbindokas; ome-users@lists.openmicroscopy.org.uk<br>
<b><span style="font-weight:bold">Subject:</span></b> Re: [ome-users] CZI dimension<o:p></o:p></span></font></p>
</div>
</div>
<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:12.0pt"><o:p> </o:p></span></font></p>
<div>
<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:12.0pt">Hi Paul,<o:p></o:p></span></font></p>
<div>
<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:12.0pt"><o:p> </o:p></span></font></p>
</div>
<div>
<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:12.0pt">> </span></font><font size="2" face="Arial"><span style="font-size:10.0pt;font-family:"Arial","sans-serif"">I had to do a complete reinstallation of Fiji to update Bioformats
to version 5.</span></font><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:12.0pt"><o:p> </o:p></span></font></p>
</div>
<div>
<p class="MsoNormal"><font size="2" face="Arial"><span style="font-size:10.0pt;font-family:"Arial","sans-serif"">I completed the update of Fiji to use Bio-Formats 5 earlier today. Simply updating Fiji should now give you a working Bio-Formats 5.0.0. And enabling
the Bio-Formats update site (</span></font><font face="Arial"><span style="font-family:"Arial","sans-serif""><a href="http://fiji.sc/Bio-Formats#Daily_builds">http://fiji.sc/Bio-Formats#Daily_builds</a>) should give you the latest development builds.</span></font><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:12.0pt"><o:p> </o:p></span></font></p>
</div>
<div>
<p class="MsoNormal"><font size="3" face="Arial"><span style="font-size:12.0pt;font-family:"Arial","sans-serif"">Regards,</span></font><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><font size="3" face="Arial"><span style="font-size:12.0pt;font-family:"Arial","sans-serif"">Curtis</span></font><o:p></o:p></p>
</div>
</div>
<div>
<p class="MsoNormal" style="margin-bottom:12.0pt"><font size="3" face="Times New Roman"><span style="font-size:12.0pt"><o:p> </o:p></span></font></p>
<div>
<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:12.0pt">On Thu, Feb 27, 2014 at 10:11 AM, Paul Thomas (SCI) <<a href="mailto:P.Thomas@uea.ac.uk" target="_blank">P.Thomas@uea.ac.uk</a>> wrote:<o:p></o:p></span></font></p>
<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:12.0pt">This didn't work for me, I had to do a complete reinstallation of Fiji to update Bioformats to version 5.<br>
Paul.<br>
<br>
____________________<br>
Dr. Paul Thomas, Manager,<br>
The Henry Wellcome Laboratory for Cell Imaging,<br>
Faculty of Science,<br>
University of East Anglia,<br>
Norwich Research Park,<br>
Norwich,<br>
NR4 7TJ,<br>
United Kingdom.<br>
<br>
e-mail: <a href="mailto:p.thomas@uea.ac.uk">p.thomas@uea.ac.uk</a><br>
Tel: <a href="tel:%2B44-1603-592196">+44-1603-592196</a><br>
Fax: <a href="tel:%2B44-1603-592250">+44-1603-592250</a><br>
Imaging web-site: <a href="https://www.uea.ac.uk/biological-sciences/research/facilities/henry-wellcome-lab" target="_blank">
https://www.uea.ac.uk/biological-sciences/research/facilities/henry-wellcome-lab</a><br>
Personal web-page: <a href="https://www.uea.ac.uk/biological-sciences/research/facilities/henry-wellcome-lab/people" target="_blank">
https://www.uea.ac.uk/biological-sciences/research/facilities/henry-wellcome-lab/people</a><o:p></o:p></span></font></p>
<div>
<div>
<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:12.0pt"><br>
> -----Original Message-----<br>
> From: <a href="mailto:ome-users-bounces@lists.openmicroscopy.org.uk">ome-users-bounces@lists.openmicroscopy.org.uk</a> [mailto:<a href="mailto:ome-users-">ome-users-</a><br>
> <a href="mailto:bounces@lists.openmicroscopy.org.uk">bounces@lists.openmicroscopy.org.uk</a>] On Behalf Of Melissa Linkert<br>
> Sent: 27 February 2014 01:23<br>
> To: vbindokas<br>
> Cc: <a href="mailto:ome-users@lists.openmicroscopy.org.uk">ome-users@lists.openmicroscopy.org.uk</a><br>
> Subject: Re: [ome-users] CZI dimension<br>
><br>
> Hi Vytas,<br>
><br>
> > Might there be instructions on how to install the rc? I did the<br>
> > drag/drop in FIJI with bio-formats and/or loci_plugins jars [one at a<br>
> > time], but when i ask help/about Loci, it still reports vers<br>
> > 4.4.10-DEV. I take it I'm not running 5.0.<br>
> > I've deleted all bio-formats and loci jars I found in fiji, except<br>
> for<br>
> > the installed rc.<br>
> > What am I doing wrong?<br>
><br>
> The best way to use 5.0.0 with Fiji is by following the instructions<br>
> here:<br>
><br>
> <a href="http://fiji.sc/Bio-Formats#Daily_builds" target="_blank">http://fiji.sc/Bio-Formats#Daily_builds</a><br>
><br>
> Downloading the files by hand and copying them into the plugins folder<br>
> is not recommended when using Fiji, as it is very easy to accidentally<br>
> have an older version of the plugin still installed.<br>
><br>
> If "Help > About Plugins > ..." shows something other than 5.0.0 after<br>
> following those instructions, please let us know.<br>
><br>
> Regards,<br>
> -Melissa<br>
><br>
> On Tue, Feb 25, 2014 at 09:27:04AM -0600, vbindokas wrote:<br>
> > Dear Melissa,<br>
> > Thanks for the response.<br>
> > Might there be instructions on how to install the rc? I did the<br>
> > drag/drop in FIJI with bio-formats and/or loci_plugins jars [one at a<br>
> > time], but when i ask help/about Loci, it still reports vers<br>
> > 4.4.10-DEV. I take it I'm not running 5.0.<br>
> > I've deleted all bio-formats and loci jars I found in fiji, except<br>
> for<br>
> > the installed rc.<br>
> > What am I doing wrong?<br>
> > thanks!<br>
> ><br>
> > On 2/24/2014 6:45 PM, Melissa Linkert wrote:<br>
> > >Hi Vytas,<br>
> > ><br>
> > >>>It appears bioformats importer does not recognize the CZI fields<br>
> > >>>created by the recent Lightsheet microscope system. The<br>
> lightsheet<br>
> > >>>stored angular rotation "views" within the structure in addition<br>
> to<br>
> > >>>CH, T, Z. The importer does open the first 'view', but not beyond<br>
> that.<br>
> > >>>Can I request that tag/data be read for CZI?<br>
> > >Which version of Bio-Formats are you currently using? If you<br>
> haven't<br>
> > >already, I would suggest updating to 5.0.0-rc1:<br>
> > ><br>
> > ><a href="http://downloads.openmicroscopy.org/bio-formats/5.0.0-rc1" target="_blank">http://downloads.openmicroscopy.org/bio-formats/5.0.0-rc1</a><br>
> > ><br>
> > >and/or the very, very soon-to-be-released 5.0.0. 5.0.0-rc1 contains<br>
> > >many improvements to .czi support, and I would expect it to open all<br>
> > >rotations in a lightsheet dataset.<br>
> > ><br>
> > >>>The Zeiss software export is not very friendly [outputs views in<br>
> > >>>stacks per Z and time], meaning that output must be then split and<br>
> > >>>resorted to get data suitable for openSPIM processing.<br>
> > >>>These are hugely big.<br>
> > >>>If the czi could be opened as a virtual stack and then written out<br>
> > >>>with the usual sequential tif naming, then it at least saves one<br>
> > >>>step and much time/space.<br>
> > >>>[I can try to upload a smaller czi file (5GBs), if that helps]<br>
> > >A sample dataset would be very helpful if you find that there are<br>
> > >still problems with 5.0.0-rc1/<a href="http://5.0.0." target="_blank">5.0.0.</a> If you are interested in<br>
> > >uploading a file, please let me know and I will send the current FTP<br>
> > >server information off-list.<br>
> > ><br>
> > >Regards,<br>
> > >-Melissa<br>
> > ><br>
> > >On Fri, Feb 21, 2014 at 10:23:43AM -0600, Curtis Rueden wrote:<br>
> > >>Hi Vytas,<br>
> > >><br>
> > >>>It appears bioformats importer does not recognize the CZI fields<br>
> > >>>created by the recent Lightsheet microscope system.<br>
> > >>I am replying with the OME-users mailing list in CC, which is the<br>
> > >>best place to report Bio-Formats issues.<br>
> > >><br>
> > >>Regards,<br>
> > >>Curtis<br>
> > >><br>
> > >><br>
> > >>On Wed, Feb 19, 2014 at 8:45 AM, vbindokas<br>
> <<a href="mailto:vbindoka@bsd.uchicago.edu">vbindoka@bsd.uchicago.edu</a>>wrote:<br>
> > >><br>
> > >>>Dear Curtis,<br>
> > >>>It appears bioformats importer does not recognize the CZI fields<br>
> > >>>created by the recent Lightsheet microscope system. The<br>
> lightsheet<br>
> > >>>stored angular rotation "views" within the structure in addition<br>
> to<br>
> > >>>CH, T, Z. The importer does open the first 'view', but not beyond<br>
> that.<br>
> > >>>Can I request that tag/data be read for CZI?<br>
> > >>>The Zeiss software export is not very friendly [outputs views in<br>
> > >>>stacks per Z and time], meaning that output must be then split and<br>
> > >>>resorted to get data suitable for openSPIM processing.<br>
> > >>>These are hugely big.<br>
> > >>>If the czi could be opened as a virtual stack and then written out<br>
> > >>>with the usual sequential tif naming, then it at least saves one<br>
> > >>>step and much time/space.<br>
> > >>>[I can try to upload a smaller czi file (5GBs), if that helps]<br>
> best<br>
> > >>>regards,<br>
> > >>><br>
> > >>>--<br>
> > >>>__<br>
> > >>><br>
> > >>>Vytas Bindokas, Ph.D.<br>
> > >>>Research Assoc. / Assoc. Prof.,<br>
> > >>>Director, BSD Light Microscopy Core Facility<br>
> > >>>phone: <a href="tel:773-702-4875">773-702-4875</a><br>
> > >>><br>
> > >>> [address for letters ONLY (see shipping addr below):] Dept<br>
> > >>>Pharmacol Physiol Sci MC0926<br>
> > >>>947 E 58th Street<br>
> > >>>The University of Chicago<br>
> > >>>Chicago IL 60637<br>
> > >>>Room Abbott 129<br>
> > >>><br>
> > >>><br>
> > >>>shipping address (main KCBD site):<br>
> > >>>V. Bindokas<br>
> > >>>900 E 57th Street<br>
> > >>>KCBD room 1250, Microscopy Core<br>
> > >>>The University of Chicago<br>
> > >>>Chicago IL 60637<br>
> > >>><br>
> > >>><br>
> > >>>email <a href="mailto:vbindoka@bsd.uchicago.edu">vbindoka@bsd.uchicago.edu</a><br>
> > >>>web site for LMCF:<br>
> > >>><a href="http://digital.uchicago.edu/index.html" target="_blank">http://digital.uchicago.edu/index.html</a><br>
> > >>><br>
> > >>><br>
> > >>_______________________________________________<br>
> > >>ome-users mailing list<br>
> > >><a href="mailto:ome-users@lists.openmicroscopy.org.uk">ome-users@lists.openmicroscopy.org.uk</a><br>
> > >><a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users" target="_blank">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users</a><br>
> ><br>
> > --<br>
> > __<br>
> ><br>
> > Vytas Bindokas, Ph.D.<br>
> > Research Assoc. / Assoc. Prof.,<br>
> > Director, BSD Light Microscopy Core Facility<br>
> > phone: <a href="tel:773-702-4875">773-702-4875</a><br>
> ><br>
> > [address for letters ONLY (see shipping addr below):] Dept<br>
> > Pharmacol Physiol Sci MC0926<br>
> > 947 E 58th Street<br>
> > The University of Chicago<br>
> > Chicago IL 60637<br>
> > Room Abbott 129<br>
> ><br>
> ><br>
> > shipping address (main KCBD site):<br>
> > V. Bindokas<br>
> > 900 E 57th Street<br>
> > KCBD room 1250, Microscopy Core<br>
> > The University of Chicago<br>
> > Chicago IL 60637<br>
> ><br>
> ><br>
> > email <a href="mailto:vbindoka@bsd.uchicago.edu">vbindoka@bsd.uchicago.edu</a><br>
> > web site for LMCF:<br>
> > <a href="http://digital.uchicago.edu/index.html" target="_blank">http://digital.uchicago.edu/index.html</a><br>
> ><br>
> _______________________________________________<br>
> ome-users mailing list<br>
> <a href="mailto:ome-users@lists.openmicroscopy.org.uk">ome-users@lists.openmicroscopy.org.uk</a><br>
> <a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users" target="_blank">
http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users</a><br>
_______________________________________________<br>
ome-users mailing list<br>
<a href="mailto:ome-users@lists.openmicroscopy.org.uk">ome-users@lists.openmicroscopy.org.uk</a><br>
<a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users" target="_blank">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users</a><o:p></o:p></span></font></p>
</div>
</div>
</div>
<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:12.0pt"><o:p> </o:p></span></font></p>
</div>
</div>
</div>
</body>
</html>