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Hi Zara,
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<div class="">Thank you for uploading the sample file. I tried loading the file with BigStitcher and although I can see the “<span style="font-family: Menlo; font-size: 11px;" class="">[ERROR] bad version 72 at filePos 94692298</span>” message I was not able
to reproduce the exception you are seeing. </div>
<div class="">Can you provide further step by step instructions on the workflow you used to reproduce the issue?</div>
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<div class="">With Thanks,</div>
<div class="">David Gault</div>
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<div class="">On 28 Mar 2019, at 20:38, Zara Weinberg <<a href="mailto:weinberz@umich.edu" class="">weinberz@umich.edu</a>> wrote:</div>
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<div dir="ltr" class="">Hello,
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<div class="">Andor Technology maintains a software package Fusion that is used to control their Dragonfly microscopy unit. Fusion outputs acquired images in an Imaris-compatible .ims format, but as noted elsewhere (<a href="https://forum.image.sc/t/andor-dragonfly-ims-files-with-z-stack-failing-to-open-with-bioformats-5-9-2/21768" class="">https://forum.image.sc/t/andor-dragonfly-ims-files-with-z-stack-failing-to-open-with-bioformats-5-9-2/21768</a>)
this format is not identical to Imaris's format. As such this can cause issues when using third party plugins (such as BigStitcher) in FIJI to process Fusion IMS files. </div>
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<div class="">I have updated an example file at <a href="https://www.openmicroscopy.org/qa2/qa/feedback/27456/?token=8a29b3c3c9c5596f1402ef4693e45252" class="">https://www.openmicroscopy.org/qa2/qa/feedback/27456/?token=8a29b3c3c9c5596f1402ef4693e45252</a>.
This is properly loaded by Fiji (although the console reports '[ERROR] bad version 72 at filePos 94692298'). However, when attempting to load individual frames (as with BigStitcher's method of loading multiple timepoints from the same file), those file loads
with the follow error and stack trace:</div>
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<div class="">java.lang.IndexOutOfBoundsException: Index: 0, Size: 0</div>
<div class=""><span style="white-space:pre" class=""></span>at java.util.ArrayList.rangeCheck(ArrayList.java:653)</div>
<div class=""><span style="white-space:pre" class=""></span>at java.util.ArrayList.get(ArrayList.java:429)</div>
<div class=""><span style="white-space:pre" class=""></span>at ome.xml.model.Pixels.getPlane(Pixels.java:738)</div>
<div class=""><span style="white-space:pre" class=""></span>at ome.xml.meta.OMEXMLMetadataImpl.getPlanePositionX(OMEXMLMetadataImpl.java:3773)</div>
<div class=""><span style="white-space:pre" class=""></span>at net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyStackImgLoaderLOCI.loadTileLocation(LegacyStackImgLoaderLOCI.java:527)</div>
<div class=""><span style="white-space:pre" class=""></span>at net.preibisch.mvrecon.fiji.datasetmanager.StackListLOCI.loadTileLocationFromMetaData(StackListLOCI.java:95)</div>
<div class=""><span style="white-space:pre" class=""></span>at net.preibisch.mvrecon.fiji.datasetmanager.StackList.loadAllTileLocations(StackList.java:188)</div>
<div class=""><span style="white-space:pre" class=""></span>at net.preibisch.mvrecon.fiji.datasetmanager.StackList.createDataset(StackList.java:308)</div>
<div class=""><span style="white-space:pre" class=""></span>at net.preibisch.mvrecon.fiji.plugin.Define_Multi_View_Dataset.defineDataset(Define_Multi_View_Dataset.java:134)</div>
<div class=""><span style="white-space:pre" class=""></span>at net.preibisch.mvrecon.fiji.plugin.Define_Multi_View_Dataset.run(Define_Multi_View_Dataset.java:78)</div>
<div class=""><span style="white-space:pre" class=""></span>at ij.IJ.runUserPlugIn(IJ.java:229)</div>
<div class=""><span style="white-space:pre" class=""></span>at ij.IJ.runPlugIn(IJ.java:193)</div>
<div class=""><span style="white-space:pre" class=""></span>at ij.Executer.runCommand(Executer.java:137)</div>
<div class=""><span style="white-space:pre" class=""></span>at ij.Executer.run(Executer.java:66)</div>
<div class=""><span style="white-space:pre" class=""></span>at java.lang.Thread.run(Thread.java:745)</div>
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<div class="">It'd be awesome if these could be natively supported in Bio-Formats!</div>
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<div class="">Let me know if you need anything else from me! I have also cc'ed Andor's support alias , in case they might be able to provide more info about how these files differ from Imaris's implementation.</div>
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<div class="">Cheers,</div>
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<div class="">Zara Weinberg, Ph.D</div>
<div class="">Postdoctoral Scholar</div>
<div class="">Puthenveedu Lab</div>
<div class="">University of Michigan</div>
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