<div dir="ltr"><div>Hi,</div><div><br></div><div>Below is a Bio-Formats bug report from Vytas Bindokas (CCed).</div><div><br></div><div>I also uploaded the sample image ('AbI 1-200 1to4_Caption.tif') to the OME QA system on his behalf.</div><div><br></div><div>Regards,</div><div>Curtis</div><div><br></div><div><div class="gmail-m_5713317768945510061gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><span style="font-size:12.8px">--</span></div><div><span style="font-size:12.8px">Curtis Rueden</span><br></div><div><span style="font-size:12.8px">LOCI software architect - <a href="https://loci.wisc.edu/software" target="_blank">https://loci.wisc.edu/software</a></span></div><div>ImageJ2 lead, Fiji maintainer - <span style="font-size:12.8px"><a href="https://imagej.net/User:Rueden" target="_blank">https://imagej.net/User:<wbr>Rueden</a></span></div><div>Did you know ImageJ has a forum? <a href="http://forum.imagej.net/" target="_blank">http://forum.imagej.net/</a></div><div><br></div></div></div></div></div></div></div></div></div></div>
<br><div class="gmail_quote">---------- Forwarded message ----------<br>From: <b class="gmail_sendername">vbindokas</b> <span dir="ltr"><<a href="mailto:vbindoka@bsd.uchicago.edu" target="_blank">vbindoka@bsd.uchicago.edu</a>></span><br>Date: Mon, Jul 17, 2017 at 2:30 PM<br>Subject: bio-formats importer bug<br>To: Curtis Rueden <<a href="mailto:ctrueden@wisc.edu" target="_blank">ctrueden@wisc.edu</a>><br><br><br>
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<p>Hello Curtis,</p>
<p>I'm sure you're busy, so can you please forward to LOCI dev team?
[GUI reporter tool still not working]<br>
</p>
<p>Back in March we were able to open automated scanner TIF exports
using bio-formats, however recent attempts result in red ink:</p>
<p>(Fiji Is Just) ImageJ 2.0.0-rc-61/1.51n; Java 1.8.0_66 [64-bit];
Windows 7 6.1; 1130MB of 15000MB (7%)<br>
java.lang.NullPointerException<br>
at loci.common.Location.<init>(Lo<wbr>cation.java:104)<br>
at loci.common.Location.getParent<wbr>File(Location.java:623)<br>
at
<a href="http://loci.formats.in" target="_blank">loci.formats.in</a>.CellVoyagerRea<wbr>der.isThisType(CellVoyagerRead<wbr>er.java:256)<br>
at loci.formats.ImageReader.getRe<wbr>ader(ImageReader.java:185)<br>
at
loci.plugins.in.ImportProcess.<wbr>createBaseReader(ImportProcess<wbr>.java:618)<br>
at
loci.plugins.in.ImportProcess.<wbr>initializeReader(ImportProcess<wbr>.java:484)<br>
at
loci.plugins.in.ImportProcess.<wbr>execute(ImportProcess.java:137<wbr>)<br>
at loci.plugins.in.Importer.showD<wbr>ialogs(Importer.java:140)<br>
at loci.plugins.in.Importer.run(I<wbr>mporter.java:76)<br>
at loci.plugins.LociImporter.run(<wbr>LociImporter.java:78)<br>
at ij.IJ.runUserPlugIn(IJ.java:21<wbr>7)<br>
at ij.IJ.runPlugIn(IJ.java:181)<br>
at ij.Executer.runCommand(Execute<wbr>r.java:137)<br>
at ij.Executer.run(Executer.java:<wbr>66)<br>
at java.lang.Thread.run(Thread.ja<wbr>va:745)<br>
</p>
<p>I've uploaded a sample via the Help UI; <br>
</p>
<p><!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML 2.0//EN"><br>
<html><head><br>
<title>201 Created</title><br>
</head><body><br>
<h1>Created</h1><br>
<p>Resource /<b>AbI%201-200%201to4_Caption.ti<wbr>f </b>has been
created.</p><br>
<hr /><br>
<address>Apache/2.4.18 (Ubuntu) Server at <a href="http://upload.imagej.net" target="_blank">upload.imagej.net</a>
Port 80</address><br>
</body></html><br>
</p>
<p>I can open this file in IrafanView and resave it there-- that
resave opens normally in fiji. It's a work-around, but time and
space consuming.</p>
<p>BEST REGARDS!~</p>
<p>Vytas<br>
</p>
<pre class="gmail-m_5713317768945510061gmail-m_-4617302372585742484moz-signature" cols="72">--
__
Vytas Bindokas, Ph.D.
Research Assoc. Prof.,
Director, BSD Light Microscopy Core Facility
phone: <a href="tel:(773)%20702-4875" value="+17737024875" target="_blank">773-702-4875</a> [alt's: <a href="tel:(773)%20834-9040" value="+17738349040" target="_blank">773-834-9040</a> or <a href="tel:(773)%20834-2639" value="+17738342639" target="_blank">773-834-2639</a>]
[address for letters ONLY (see shipping addr below):]
Dept Pharmacol Physiol Sci MC0926
947 E 58th Street
The University of Chicago
Chicago IL 60637
Room Abbott 129
shipping address (main KCBD site):
V. Bindokas
900 E 57th Street
KCBD room 1250, Microscopy Core
The University of Chicago
Chicago IL 60637
email <a class="gmail-m_5713317768945510061gmail-m_-4617302372585742484moz-txt-link-abbreviated" href="mailto:vbindoka@bsd.uchicago.edu" target="_blank">vbindoka@bsd.uchicago.edu</a>
web site for LMCF:
<a class="gmail-m_5713317768945510061gmail-m_-4617302372585742484moz-txt-link-freetext" href="http://digital.uchicago.edu" target="_blank">http://digital.uchicago.edu</a></pre>
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