[ome-users] BioFormats Bug report: MetaMoprh .nd files parsing incorrectly

[Wendy Salmon]

Hi, 
I just found a bug related component parsing when importing files from a MetaMorph .nd file. When we try to open one of our files by loading the .nd file into Fiji, it shows the right parameters (number of channels, number of time points and positions) and shows a thumbnail image for each position, but the images that appear are not parsed into the correct parameters. In this case, a time series with 4 channels, multiple positions and no z series opens as a single stack with only three of the channels interlaced--the forth channel is missing. 


I eventually figured out that the individual channel Z stack designations is the root cause. The .nd file for this dataset shows "WaveDoZ1" "WaveDoZ2" and "WaveDoZ3" set to TRUE, WaveDoZ4 set to FALSE and "DoZSeries" set to FALSE. The images that open correspond to the wavelengths that have a TRUE value, indicating that the "WaveDoZ#" value is over-ruling the "DoZSeries" value. And indeed, c hanging the "WaveDoZ#" values all to FALSE restores proper image parsing. 



I uploaded the original .nd file (B+T.nd), the 4 images from the first position and time point (B+T_w1...tif, etc), and a version of the .nd file that has the "TRUE" values reset to "FALSE" (B+T_adjusted). 


Please let me know if you need any more information! 



Thank you, 
Wendy 

~~~~~~~~~~~~~~~~~~~~~~~ 
Wendy Salmon 
Light Microscopy Specialist 
Whitehead Institute for Biomedical Research 
W.M. Keck Imaging Facility 
9 Cambridge Center, Rm 447 
Cambridge, MA 02142 
c: 617-429-0158 
e: wsalmon at wi.mit.edu 
w: http://staffa.wi.mit.edu/microscopy/ 

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