<div dir="ltr">Hi Paul,<div><br></div><div><div>> Further to your update, I just started Fiji and was prompted to</div><div>> update. I did so, restarted and then discovered Bioformats had been</div><div>> completely removed!</div>
</div><div><br></div><div>There are a couple of bugs [1, 2] that might have caused this.</div><div><br></div><div>Please run Help > Update Fiji, click Advanced Mode. Click "Manage update sites" and ensure that both "ImageJ" and "Fiji" are checked. ("Bio-Formats" can be checked too if you want the Bio-Formats developer builds; that is up to you.)</div>
<div><br></div><div>Next, click "Advanced mode" and change the View Options to "View uninstalled files only". If you see any JARs there, especially anything with "bio-formats" in the path, then mark it for installation (right-click and "Install it"). Finally click "Apply changes" and then restart Fiji.</div>
<div><br></div><div>Please let us know if this does not fix the problem for you.</div><div><br></div><div>HTH,</div><div>Curtis</div><div><br></div><div>[1] <a href="https://github.com/imagej/imagej/issues/43">https://github.com/imagej/imagej/issues/43</a></div>
<div>[2] <a href="https://github.com/imagej/imagej/issues/44">https://github.com/imagej/imagej/issues/44</a></div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Thu, Mar 6, 2014 at 7:24 AM, Paul Thomas (SCI) <span dir="ltr"><<a href="mailto:P.Thomas@uea.ac.uk" target="_blank">P.Thomas@uea.ac.uk</a>></span> wrote:<br>
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<p class="MsoNormal"><font face="Book Antiqua"><span style="font-size:11.0pt;font-family:"Book Antiqua","serif"">Hi Curtis,<u></u><u></u></span></font></p>
<p class="MsoNormal"><font face="Book Antiqua"><span style="font-size:11.0pt;font-family:"Book Antiqua","serif""><u></u> <u></u></span></font></p>
<p class="MsoNormal"><font face="Book Antiqua"><span style="font-size:11.0pt;font-family:"Book Antiqua","serif"">Further to your update, I just started Fiji and was prompted to update. I did so, restarted and then discovered Bioformats had been completely
removed! I tried to update again; using “Manage sites” I checked Bioformats, but “Apply changes” is greyed-out so I cannot update to restore Bioformats.<u></u><u></u></span></font></p>
<p class="MsoNormal"><font face="Book Antiqua"><span style="font-size:11.0pt;font-family:"Book Antiqua","serif""><u></u> <u></u></span></font></p>
<p class="MsoNormal"><font face="Book Antiqua"><span style="font-size:11.0pt;font-family:"Book Antiqua","serif"">Fortunately, I have a back-up of my installation and can just copy the folder back, but there is clearly a problem here.<u></u><u></u></span></font></p>
<p class="MsoNormal"><font face="Book Antiqua"><span style="font-size:11.0pt;font-family:"Book Antiqua","serif""><u></u> <u></u></span></font></p>
<p class="MsoNormal"><font face="Book Antiqua"><span style="font-size:11.0pt;font-family:"Book Antiqua","serif"">Paul.<u></u><u></u></span></font></p>
<p class="MsoNormal"><font face="Calibri"><span style="font-size:11.0pt">____________________<u></u><u></u></span></font></p>
<p class="MsoNormal"><font face="Calibri"><span style="font-size:11.0pt">Dr. Paul Thomas, Manager,<u></u><u></u></span></font></p>
<p class="MsoNormal"><font face="Calibri"><span style="font-size:11.0pt">The Henry Wellcome Laboratory for Cell Imaging,<u></u><u></u></span></font></p>
<p class="MsoNormal"><font face="Calibri"><span style="font-size:11.0pt">Faculty of Science,<u></u><u></u></span></font></p>
<p class="MsoNormal"><font face="Calibri"><span style="font-size:11.0pt">University of East Anglia,<u></u><u></u></span></font></p>
<p class="MsoNormal"><font face="Calibri"><span style="font-size:11.0pt">Norwich Research Park,<u></u><u></u></span></font></p>
<p class="MsoNormal"><font face="Calibri"><span style="font-size:11.0pt">Norwich,<u></u><u></u></span></font></p>
<p class="MsoNormal"><font face="Calibri"><span style="font-size:11.0pt">NR4 7TJ,<u></u><u></u></span></font></p>
<p class="MsoNormal"><font face="Calibri"><span style="font-size:11.0pt">United Kingdom.<u></u><u></u></span></font></p>
<p class="MsoNormal"><font face="Calibri"><span style="font-size:11.0pt"><u></u> <u></u></span></font></p>
<p class="MsoNormal"><font face="Calibri"><span style="font-size:11.0pt">e-mail: <a href="mailto:p.thomas@uea.ac.uk" target="_blank">p.thomas@uea.ac.uk</a><u></u><u></u></span></font></p>
<p class="MsoNormal"><font face="Calibri"><span style="font-size:11.0pt">Tel: <a href="tel:%2B44-1603-592196" value="+441603592196" target="_blank">+44-1603-592196</a><u></u><u></u></span></font></p>
<p class="MsoNormal"><font face="Calibri"><span style="font-size:11.0pt">Fax: <a href="tel:%2B44-1603-592250" value="+441603592250" target="_blank">+44-1603-592250</a><u></u><u></u></span></font></p>
<p class="MsoNormal"><font face="Calibri"><span style="font-size:11.0pt">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><u></u><u></u></span></font></p>
<p class="MsoNormal"><font face="Calibri"><span style="font-size:11.0pt">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><u></u><u></u></span></font></p>
<p class="MsoNormal"><font face="Calibri"><span style="font-size:11.0pt"><u></u> <u></u></span></font></p>
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