[ome-users] Problem loading lambda-scans from .oir files

[Eric Kercher]

I'm trying to load some lambda scans taken with an Olympus microscope (.oir
file) and ran into a potential bug.

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:

plane = r.openBytes(...

    ip.Results.iPlane - 1, ip.Results.x - 1, ip.Results.y - 1, ...

    ip.Results.width, ip.Results.height);


r.openBytes loads identical vectors for 'plane' through each iteration of
the loop in bfopen.m.

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).

This script reproduces the bug:

% Read data

impath = 'path/to/lambda/scan.oir';

data = bfOpen3DVolume(impath);

im = data{1,1}{1,1};

% Compare channels

isequal(im(:,:,1), im(:,:,2))

plot(squeeze(mean(mean(im))));


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.

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.

I've uploaded a sample .oir lambda scan file (
exampleLambdaScan_AF546soln.oir) 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.

Regards,
Eric Kercher
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