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Hi Eric,
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<div class="">Thank you very much for providing the detailed report and sample file.</div>
<div class="">I have been able to reproduce the issue exactly as described and have been able to do some further debugging on the problem.</div>
<div class="">This is a bug in the Bio-Formats OIRReader and I have opened a Trello card on the Bio-Formats inbox with details to track the issue: <a href="https://trello.com/c/D6wZog99/252-oir-duplicate-planes" class="">https://trello.com/c/D6wZog99/252-oir-duplicate-planes</a></div>
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<div class="">With Thanks,</div>
<div class="">David Gault</div>
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<div class="">On 22 Jun 2018, at 18:25, Eric Kercher <<a href="mailto:kercher.e@husky.neu.edu" class="">kercher.e@husky.neu.edu</a>> wrote:</div>
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<div class="gmail_default" style="font-family:"trebuchet ms",sans-serif">I'm trying to load some lambda scans taken with an Olympus microscope (.oir file) and ran into a potential bug.</div>
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<div class="gmail_default" style="font-family:"trebuchet ms",sans-serif">Bio-formats recognizes the correct number of channels, but loads the first channel of the image for each subsequent plane. This occurs in both imageJ and Matlab. In Matlab, I traced the
issue to line 78 in the bfGetPlane.m file:</div>
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plane = r.openBytes(<span class="gmail-m_-9120028544603819777gmail-s1" style="color:rgb(4,51,255)">...</span></div>
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<span class="gmail-m_-9120028544603819777gmail-Apple-converted-space"> </span>
ip.Results.iPlane - 1, ip.Results.x - 1, ip.Results.y - 1, <span class="gmail-m_-9120028544603819777gmail-s1" style="color:rgb(4,51,255)">
...</span></div>
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<span class="gmail-m_-9120028544603819777gmail-Apple-converted-space"> </span>
ip.Results.width, ip.Results.height);</div>
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r.openBytes loads identical vectors for 'plane' through each iteration of the loop in bfopen.m. </div>
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<div class="gmail_default" style="font-family:"trebuchet ms",sans-serif">I've reproduced this problem using the BF matlab toolbox and imageJ plugins on both windows (Windows server 2016) and Mac (macOS High Sierra 10.13.5); each system has the latest versions
of BF (5.8.2) and Java (10.0.1). </div>
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<div class="gmail_default" style="font-family:"trebuchet ms",sans-serif">This script reproduces the bug:</div>
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% Read data</div>
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<span class="gmail-s1" style="">impath = </span>'path/to/lambda/scan.oir'<span class="gmail-s1" style="">;</span></div>
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data = bfOpen3DVolume(impath);</div>
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im = data{1,1}{1,1};</div>
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% Compare channels</div>
<div style="margin: 0px; line-height: normal;" class=""><font face="Courier New" class=""><span style="font-size:11px" class="">isequal(im(:,:,1), im(:,:,2))</span></font><br class="">
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<div style="margin: 0px; line-height: normal;" class=""><font face="Courier New" class=""><span style="font-size:11px" class="">plot(squeeze(mean(mean(im))));</span><br class="">
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<div class="gmail_default" style="font-family:"trebuchet ms",sans-serif">isequal returns true for any 2 channels you pick; the plot displays the full z-axis profile which is a flat line. In ImageJ, Image>Stacks>Plot Z-axis Profile also produces the same flat
line. I also tried loading the image using each stack configuration option (XYCTZ, XYZCT, etc...) with no luck.</div>
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<div class="gmail_default" style="font-family:"trebuchet ms",sans-serif">The OlympusViewer plugin for ImageJ (not the BF one) loads the lambda scans correctly on the Mac & Windows systems described above. I also downloaded the three z-stacks from the OME repository
and those load correctly as well. I searched through the metadata (comparing z-scan and lambda-scan) but found nothing out of the ordinary; so I don't know if its an issue with my data files or if its an actual bug. </div>
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<div class="gmail_default" style="font-family:"trebuchet ms",sans-serif">I've uploaded a sample .oir lambda scan file (<span style="color:rgb(85,85,85);font-family:Arial,Verdana,Lucida,Helvetica,sans-serif;text-align:left;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline" class="">exampleLambdaScan_AF546soln.oir)</span>
for reproduction through the OME QA uploader. In the meantime, please let me know if I missed anything. Thank you and happy to provide more information as needed.</div>
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<div class="gmail_default" style="font-family:"trebuchet ms",sans-serif">Regards,</div>
<div class="gmail_default" style="font-family:"trebuchet ms",sans-serif">Eric Kercher </div>
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