Open Microscopy Environment

Posted: **Thu Oct 30, 2014 5:43 pm**

Hi again

(topic looks inexhaustible)

We have now a custom OME.tiff saving procedure that satisfies our speed/metadata and flexibility needs.

However, when I tried, after Ian's suggestion, the bftools' "showinf" utility on generated file, it showed the following message

Image ID 'Image:0' : missing plane #0. Using TiffReader to determine the number of planes.

Reading core metadata
...
Series count = 1
Series #0 :
Image count = 5
RGB = false (1)
Interleaved = false
Indexed = false (false color)
Width = 2559
Height = 1191
SizeZ = 5 (1 null x 5 angle)
SizeT = 1
SizeC = 1
Thumbnail size = 128 x 59
Endianness = motorola (big)
Dimension order = XYZCT (certain)
Pixel type = uint16
Valid bits per pixel = 16
Metadata complete = true
Thumbnail series = fasle
-----
Plane #0 <=> Z 0, C 0, T 0
Plane #2 <=> Z 2, C 0, T 0
Plane #4 <=> Z 4, C 0, T 0

Reading pixel data (0-4)
Read 5/5 plaqes (100%)
[done]

The file looks and behaves normally in ImageJ, Omero, Metadata Viewer, the only worry is the first line in this output - what could cause it, and which potential problem might it indicate?

Best,
Y.

Posted: **Fri Oct 31, 2014 9:27 am**

Actually I was just as concerned by
this section

Plane #0 <=> Z 0, C 0, T 0
Plane #2 <=> Z 2, C 0, T 0
Plane #4 <=> Z 4, C 0, T 0

Which looks as if planes are missing ?

Posted: **Fri Oct 31, 2014 10:42 am**

Hi Ian,

In the image, metadata shows SizeZ = 5, all 5 Planes are present and different, as expected.
It looks like showinf just dispalys info for even Plane #.

Best,
Y.

Posted: **Fri Oct 31, 2014 10:57 am**

Hi Yuriy and Ian,

without the code and/or a sample file, discussing this issue in an efficient manner is extremely difficult. Could you point us to a revision of your source code allowing us to reproduce?

Sebastien

Posted: **Fri Oct 31, 2014 11:03 am**

Hi Sebastien,

Test file is generated by the procedure here

https://github.com/yalexand/Imperial-OMEkit/blob/master/OMEkitFrontEnd/test_add_plane_to_OMEtiff.m

it calls this proc in a loop -

https://github.com/yalexand/Imperial-OMEkit/blob/master/OMEkitFrontEnd/ICUtilities/add_plane_to_OMEtiff_with_metadata.m

Best,
Y.

Posted: **Tue Nov 04, 2014 2:27 pm**

Hi Yuriy,

the problem comes from https://github.com/yalexand/Imperial-OM ... ata.m#L100 where the index variable which defines the index of the plane to be written is updated by an annotation index. This likely causes the showinf error you received.
I would assume fixing this variable naming should be sufficient to solve your issue.

Best,
Sebastien

Posted: **Wed Nov 05, 2014 11:31 am**

Thanks Sebastien - I'll try to fix it & let know, maybe first via internal team communication tools, to keep this thread observable.

Best,
Y.

Posted: **Thu Dec 04, 2014 4:51 pm**

To conclude this - the bug was eventually spotted in this function.
Basically, the value of plane index was erroneously changed from inside its loop.

After fixing, it looks OK, "showinf" doesn't report any missing planes.

Thanks,
Y.

Posted: **Fri Dec 05, 2014 9:20 am**

Glad to hear about it Yuriy,

for future reference https://github.com/yalexand/Imperial-OM ... 13f897d036 contains the commit which fixes the issue described in this thread.

Best,
Sebastien

Open Microscopy Environment

possible issue with OME.tiff generation

possible issue with OME.tiff generation

Re: possible issue with OME.tiff generation

Re: possible issue with OME.tiff generation

Re: possible issue with OME.tiff generation

Re: possible issue with OME.tiff generation

Re: possible issue with OME.tiff generation

Re: possible issue with OME.tiff generation

Re: possible issue with OME.tiff generation

Re: possible issue with OME.tiff generation