[ome-users] ND2 position meta data with bioformats 5.1.1

[Enno R. Oldewurtel]

Dear Balaji and Melissa,

firstly thanks for your great effort regarding bioformats! Following is a
problem, which I believe could be another bug:

last year I submitted a problem about wrong indexing of x,y data of nd2
files (#12569: BUG: ND2 files - x,y position of the different multi points
returned in the wrong order).

I still use matlab for loading nd2 files and retrieve metadata with
commands like:

r = loci.formats.ChannelFiller();
r = loci.formats.ChannelSeparator(r);
r.setMetadataStore(loci.formats.MetadataTools.createOMEXMLMetadata());
r.setId( FileName);
metadata=r.getMetadataStore();
i=positionIndex;
j=loci.formats.FormatTools.getIndex(r, z, channel, time)
x=double(metadata.getPlanePositionX(i,j).value)
t=double(metadata.getPlaneDeltaT(i,j).value)

Position data for x,y,z retrieved with 5.1.1 for the nd2 file I submitted
with my previous problem, are correct now. However, time-points retrieved
with metadata.getPlaneDeltaT(i,j) in the same manner are in the wrong order.

Furthermore the position data for nd2 files acquired with several z-slices
is wrongly indexed. I have an example nd2 files with T(1) x XY(8) x Z(4)
dimensions. Version 5.0.3 shows the correct order of 4 z-steps at the first
XY position, which is then repeated at the remaining 7 positions. Version
5.1.1 shows the x,y,z values jumping about in the wrong order.

As an aside: I noted that with 5.1.1 the number of the dimensions of nd2
files with all four T, XY, Z and lambda dimensions are correctly
identified. Previously I could only use bioformats with 3 different types
of dimensions. However, as soon as an nd2 files is modified and saved in
NIS elements, the numbers of the dimensions are not correct anymore.

I can supply example nd2 files if needed, but will need to upload them via
the qa system.

Hope this helps, and again many thanks for maintaining and developing such
a great product!

Best,
Enno
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