<div dir="ltr"><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><div class="gmail_default" style="font-family:"trebuchet ms",sans-serif"><br></div><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><div class="gmail_default" style="font-family:"trebuchet ms",sans-serif"><br></div><div class="gmail_default" style="font-family:"trebuchet ms",sans-serif">
<span></span>
<p class="gmail-m_-9120028544603819777gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-weight:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:"Courier New"">plane = r.openBytes(<span class="gmail-m_-9120028544603819777gmail-s1" style="color:rgb(4,51,255)">...</span></p>
<p class="gmail-m_-9120028544603819777gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-weight:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:"Courier New""><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></p>
<p class="gmail-m_-9120028544603819777gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-weight:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:"Courier New""><span class="gmail-m_-9120028544603819777gmail-Apple-converted-space"> </span>ip.Results.width, ip.Results.height);</p>
<p class="gmail-m_-9120028544603819777gmail-p2" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-weight:normal;font-stretch:normal;font-size:12px;line-height:normal;font-family:"Courier New";min-height:14px"><br></p>
r.openBytes loads identical vectors for 'plane' through each iteration of the loop in bfopen.m. </div><div class="gmail_default" style="font-family:"trebuchet ms",sans-serif"><br></div><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><div class="gmail_default" style="font-family:"trebuchet ms",sans-serif"><br></div><div class="gmail_default" style="font-family:"trebuchet ms",sans-serif">This script reproduces the bug:</div><div class="gmail_default" style="font-family:"trebuchet ms",sans-serif"><br></div><div class="gmail_default">
<font face="trebuchet ms, sans-serif"><span></span></font>
<p class="gmail-p1" style="font-family:"Courier New";margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-weight:normal;font-stretch:normal;font-size:11px;line-height:normal;color:rgb(37,153,45)">% Read data</p>
<p class="gmail-p2" style="font-family:"Courier New";margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-weight:normal;font-stretch:normal;font-size:11px;line-height:normal;color:rgb(178,69,243)"><span class="gmail-s1" style="color:rgb(0,0,0)">impath = </span>'path/to/lambda/scan.oir'<span class="gmail-s1" style="color:rgb(0,0,0)">;</span></p>
<p class="gmail-p3" style="font-family:"Courier New";margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-weight:normal;font-stretch:normal;font-size:11px;line-height:normal">data = bfOpen3DVolume(impath);</p>
<p class="gmail-p3" style="font-family:"Courier New";margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-weight:normal;font-stretch:normal;font-size:11px;line-height:normal">im = data{1,1}{1,1};</p>
<p class="gmail-p1" style="font-family:"Courier New";margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-weight:normal;font-stretch:normal;font-size:11px;line-height:normal;color:rgb(37,153,45)">% Compare channels</p>
<p class="gmail-p3" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;line-height:normal"><font face="Courier New"><span style="font-size:11px">isequal(im(:,:,1), im(:,:,2))</span></font><br></p><p class="gmail-p3" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;line-height:normal"><font face="Courier New"><span style="font-size:11px">plot(squeeze(mean(mean(im))));</span><br></font></p><p class="gmail-p3" style="font-family:"Courier New";margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-weight:normal;font-stretch:normal;font-size:11px;line-height:normal"><br></p>
</div><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><div class="gmail_default" style="font-family:"trebuchet ms",sans-serif"><br></div><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><div class="gmail_default" style="font-family:"trebuchet ms",sans-serif"><br></div><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">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><div class="gmail_default" style="font-family:"trebuchet ms",sans-serif"><br></div><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></div>