<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
</head>
<body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">
Hi Jacqueline,
<div class=""><br class="">
</div>
<div class="">Thank you for submitting the QA files. I was able to reproduce the issue as you described. From debugging the problem it appears that some of the embedded XML metadata within the file is not valid. We will contact the developers responsible for
the format to try and resolve the issue. I have opened a Trello card on the Bio-Formats inbox to track the issue <a href="https://trello.com/c/GHhVlBxM/229-obfreader-invalid-ome-xml" class="">https://trello.com/c/GHhVlBxM/229-obfreader-invalid-ome-xml</a>.</div>
<div class=""><br class="">
</div>
<div class="">Can you confirm if the sample files provided can be published under a CC-BY license (<a href="http://downloads.openmicroscopy.org/images/" class="">http://downloads.openmicroscopy.org/images/</a>)?</div>
<div class=""><br class="">
</div>
<div class="">With Thanks,</div>
<div class="">David Gault</div>
<div class=""><br class="">
<div>
<blockquote type="cite" class="">
<div class="">On 7 Mar 2018, at 23:43, Jacqueline Ross <<a href="mailto:jacqui.ross@AUCKLAND.AC.NZ" class="">jacqui.ross@AUCKLAND.AC.NZ</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div class="WordSection1" style="page: WordSection1; font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;">
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span style="color: rgb(31, 73, 125);" class="">Hi everyone,<o:p class=""></o:p></span></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span style="color: rgb(31, 73, 125);" class=""> </span></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span style="color: rgb(31, 73, 125);" class="">Further to my previous email, I have now uploaded 2 x datasets. The one that I can open is called #12.msr. The one I can’t open is called Brain_01.msr<o:p class=""></o:p></span></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span style="color: rgb(31, 73, 125);" class=""> </span></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span style="color: rgb(31, 73, 125);" class="">Kind regards,<o:p class=""></o:p></span></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span style="color: rgb(31, 73, 125);" class=""> </span></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span style="color: rgb(31, 73, 125);" class="">Jacqui<o:p class=""></o:p></span></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span style="color: rgb(31, 73, 125);" class=""> </span></div>
<div class="">
<div style="border-style: solid none none; border-top-color: rgb(225, 225, 225); border-top-width: 1pt; padding: 3pt 0cm 0cm;" class="">
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<b class=""><span lang="EN-US" class="">From:</span></b><span lang="EN-US" class=""><span class="Apple-converted-space"> </span>Jacqueline Ross<span class="Apple-converted-space"> </span><br class="">
<b class="">Sent:</b><span class="Apple-converted-space"> </span>Thursday, 8 March 2018 12:29 p.m.<br class="">
<b class="">To:</b><span class="Apple-converted-space"> </span>'<a href="mailto:ome-users@lists.openmicroscopy.org.uk" style="color: rgb(149, 79, 114); text-decoration: underline;" class="">ome-users@lists.openmicroscopy.org.uk</a>' <<a href="mailto:ome-users@lists.openmicroscopy.org.uk" style="color: rgb(149, 79, 114); text-decoration: underline;" class="">ome-users@lists.openmicroscopy.org.uk</a>><br class="">
<b class="">Subject:</b><span class="Apple-converted-space"> </span>Abberior MSR files - having trouble opening them with Fiji and ImageJ<o:p class=""></o:p></span></div>
</div>
</div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<o:p class=""> </o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; font-weight: bold;" class="">
Hi everyone,<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; font-weight: bold;" class="">
<o:p class=""> </o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; font-weight: bold;" class="">
I'm having trouble opening some MSR files acquired on an Abberior STED system. Some are opening but others aren't and I get the error shown below in those cases. I updated my Fiji version and also tried putting the latest version of Bioformats in ImageJ to
no avail. Some of these will be z stacks but not all.<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; font-weight: bold;" class="">
<o:p class=""> </o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; font-weight: bold;" class="">
Interestingly, it is all of the files we acquired later that we can’t open. The first ones were fine. I’m not sure if the first one we can’t open is a z-stack and if that somehow has caused a problem with the rest. We don’t have the Abberior system here so
don’t have the original software available to open the files. I will upload some files but can’t provide metadata or screenshots for the problem files as I can’t open them with Fiji and don’t have the original data. I will upload one file that I can open together
with its metadata.<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; font-weight: bold;" class="">
<o:p class=""> </o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; font-weight: bold;" class="">
I am running the latest Fiji version (ImageJ 1.51u) with Bio-Formats Release 5.8.1 – see attached screenshots. I also couldn’t open these files with an older compilation or on our Mac so I don’t think it’s platform-specific. I am using a 64bit Windows computer
with Java 1.8.<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; font-weight: bold;" class="">
<o:p class=""> </o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; font-weight: bold;" class="">
Can anyone help? It would be very much appreciated.<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; font-weight: bold;" class="">
<o:p class=""> </o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; font-weight: bold;" class="">
(Fiji Is Just) ImageJ 2.0.0-rc-65/1.51u; Java 1.8.0_66 [64-bit]; Windows 7 6.1; 66MB of 100000MB (<1%)<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; font-weight: bold;" class="">
java.lang.IllegalArgumentException: 0 must not be null and positive.<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; font-weight: bold;" class="">
at ome.xml.model.primitives.PositiveInteger.<init>(<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; font-weight: bold;" class="">
PositiveInteger.java:48)<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; font-weight: bold;" class="">
at loci.formats.MetadataTools.populatePixelsOnly(<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; font-weight: bold;" class="">
MetadataTools.java:288)<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; font-weight: bold;" class="">
at loci.formats.MetadataTools.populateMetadata(<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; font-weight: bold;" class="">
MetadataTools.java:251)<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; font-weight: bold;" class="">
at loci.formats.MetadataTools.<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; font-weight: bold;" class="">
populatePixels(MetadataTools.java:151)<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; font-weight: bold;" class="">
at loci.formats.MetadataTools.<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; font-weight: bold;" class="">
populatePixels(MetadataTools.java:97)<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; font-weight: bold;" class="">
at loci.formats.in.OBFReader.initFile(OBFReader.java:217)<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; font-weight: bold;" class="">
at loci.formats.FormatReader.setId(FormatReader.java:1397)<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; font-weight: bold;" class="">
at loci.plugins.in.ImportProcess.<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; font-weight: bold;" class="">
initializeFile(ImportProcess.java:499)<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; font-weight: bold;" class="">
at loci.plugins.in.ImportProcess.<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; font-weight: bold;" class="">
execute(ImportProcess.java:142)<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; font-weight: bold;" class="">
at loci.plugins.in.Importer.showDialogs(Importer.java:140)<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; font-weight: bold;" class="">
at loci.plugins.in.Importer.run(Importer.java:76)<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; font-weight: bold;" class="">
at loci.plugins.LociImporter.run(LociImporter.java:78)<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; font-weight: bold;" class="">
at ij.IJ.runUserPlugIn(IJ.java:221)<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; font-weight: bold;" class="">
at ij.IJ.runPlugIn(IJ.java:185)<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; font-weight: bold;" class="">
at ij.IJ.runPlugIn(IJ.java:174)<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; font-weight: bold;" class="">
at HandleExtraFileTypes.openImage(<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; font-weight: bold;" class="">
HandleExtraFileTypes.java:499)<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; font-weight: bold;" class="">
at HandleExtraFileTypes.run(HandleExtraFileTypes.java:72)<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; font-weight: bold;" class="">
at ij.IJ.runUserPlugIn(IJ.java:221)<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; font-weight: bold;" class="">
at ij.IJ.runPlugIn(IJ.java:185)<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; font-weight: bold;" class="">
at ij.IJ.runPlugIn(IJ.java:174)<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; font-weight: bold;" class="">
at ij.io.Opener.openWithHandleExtraFileTypes(<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; font-weight: bold;" class="">
Opener.java:515)<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; font-weight: bold;" class="">
at ij.io.Opener.openImage(Opener.java:369)<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; font-weight: bold;" class="">
at ij.io.Opener.openImage(Opener.java:242)<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; font-weight: bold;" class="">
at ij.io.Opener.open(Opener.java:109)<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; font-weight: bold;" class="">
at ij.io.Opener.openAndAddToRecent(Opener.java:291)<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; font-weight: bold;" class="">
at ij.plugin.DragAndDrop.openFile(DragAndDrop.java:192)<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; font-weight: bold;" class="">
at ij.plugin.DragAndDrop.run(DragAndDrop.java:159)<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; font-weight: bold;" class="">
at java.lang.Thread.run(Thread.java:745)<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; font-weight: bold;" class="">
<o:p class=""> </o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; font-weight: bold;" class="">
Kind regards,<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; font-weight: bold;" class="">
<o:p class=""> </o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; font-weight: bold;" class="">
Jacqui<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<o:p class=""> </o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<o:p class=""> </o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<b class=""><span style="font-size: 10pt; font-family: Verdana, sans-serif; color: rgb(31, 73, 125);" class="">Jacqueline Ross<o:p class=""></o:p></span></b></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span style="font-size: 10pt; font-family: Verdana, sans-serif; color: rgb(31, 73, 125);" class="">Biomedical Imaging Microscopist<br class="">
Biomedical Imaging Research Unit (BIRU)<br class="">
School of Medical Sciences <br class="">
Faculty of Medical & Health Sciences<span class="Apple-converted-space"> </span><br class="">
The University of Auckland<span class="Apple-converted-space"> </span><br class="">
Private Bag 92019<span class="Apple-converted-space"> </span><br class="">
Auckland 1142, NEW ZEALAND<span class="Apple-converted-space"> </span><br class="">
<br class="">
Telephone: Ext 87438; DDI: +64 9 923 7438<span class="Apple-converted-space"> </span><br class="">
<br class="">
Website: <span class="Apple-converted-space"> </span><a href="http://www.auckland.ac.nz/biru" style="color: rgb(149, 79, 114); text-decoration: underline;" class=""><span style="color: blue;" class="">http://www.auckland.ac.nz/biru</span></a><o:p class=""></o:p></span></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span style="font-size: 10pt; font-family: Verdana, sans-serif; color: rgb(31, 73, 125);" class=""> </span></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span style="font-size: 10pt; font-family: Verdana, sans-serif; color: rgb(31, 73, 125);" class=""> </span></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<o:p class=""> </o:p></div>
</div>
<span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">_______________________________________________</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">ome-users
mailing list</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<a href="mailto:ome-users@lists.openmicroscopy.org.uk" style="color: rgb(149, 79, 114); text-decoration: underline; font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">ome-users@lists.openmicroscopy.org.uk</a><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users" style="color: rgb(149, 79, 114); text-decoration: underline; font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users</a></div>
</blockquote>
</div>
<br class="">
</div>
<br>
<span style="font-size:10pt;">The University of Dundee is a registered Scottish Charity, No: SC015096</span>
</body>
</html>