[ome-users] missing images reading Nikon nd2 files

[Balaji Ramalingam]

Hi Karsten,

I tried the to read the nd2 file with both bftools and imageJ, and the results matched (series ordering and image dimensions wise).
Here are my settings,

Bio-Formats Plugins for ImageJ, revision db6d5c5, built 29July 2014
Release : 5.0.2-DEV

ImageJ : 1.49b

Java Version :

java version "1.7.0_51"

Java(TM) SE Runtime Environment (build 1.7.0_51-b13)

Java HotSpot(TM) 64-Bit Server VM (build 24.51-b03, mixed mode)


Results from showinf:


Filename = /Volumes/ome/data_repo/from_skyking/nd2/karsten/100720104_TestglasSchott_MM63_C10h.nd2

Series count = 105

Series #0 :

Image count = 3

RGB = false (1)

Interleaved = false

Indexed = false (false color)

Width = 1280

Height = 960

SizeZ = 1

SizeT = 1

SizeC = 3

Thumbnail size = 128 x 96

Endianness = intel (little)

Dimension order = XYCZT (uncertain)

Pixel type = uint8

Valid bits per pixel = 8

Metadata complete = true

Thumbnail series = false

-----

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

Plane #1 <=> Z 0, C 1, T 0

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

.... Series #104:..


Results from ImageJ:


 BitsPerPixel 8

 DimensionOrder XYCZT

 IsInterleaved false

 IsRGB false

 LittleEndian true

 PixelType uint8

 Series 0 Name 100720104_TestglasSchott_MM63_C10h.nd2 (series 1)

 SizeC 3

 SizeT 1

 SizeX 1280

 SizeY 960

 SizeZ 1

 uiSequenceCount 105


Could you please check the bioformats version via the help section of ImageJ,

Clicking on Help->'About Plugins'-> Bio-Formats Plugins...

Should give you the information, and will help us troubleshoot your issue a little better.


Hope that helps.


Best,

Balaji





__________________

Mr Balaji Ramalingam

Software Developer

OME Team

College of Life Sciences

University of Dundee

From: Karsten <karo13de at googlemail.com<mailto:karo13de at googlemail.com>>
Date: Monday, 28 July 2014 15:58
To: Sebastien Besson <seb.besson at gmail.com<mailto:seb.besson at gmail.com>>
Cc: "OME-users ome-users at lists.openmicroscopy.org.uk<mailto:ome-users at lists.openmicroscopy.org.uk>" <ome-users at lists.openmicroscopy.org.uk<mailto:ome-users at lists.openmicroscopy.org.uk>>, Roger Leigh <r.leigh at dundee.ac.uk<mailto:r.leigh at dundee.ac.uk>>
Subject: Re: [ome-users] missing images reading Nikon nd2 files


Merci Sebastien,

I just tried bioformats_package.jar with bftools and loci_tools.jar with ImageJ (1.49e) from that given artifacts folder (Java 1.8). The first reads the expected number of images, the latter not.
I have only one version of loci_tools.jar in my plugins folder! Also still surprising the sorting order of the metadata. The numbered series are not sorted numerically.

Regards
Karsten

Am 28.07.2014 um 14:03 schrieb Sebastien Besson <seb.besson at gmail.com<mailto:seb.besson at gmail.com>>:

Hi Karsten,

if you want to test the latest version of Bio-Formats against your data. You can download the
artifacts produced by our continuous integration infrastructure at:
http://ci.openmicroscopy.org/job/BIOFORMATS-5.0-latest/lastSuccessfulBuild/artifact/artifacts/.
Note these artifacts should not be considered as release-quality although we expect them to be
very close to the final 5.0.3 release.

Best regards,
Sebastien

On 28 Jul 2014, at 10:35, Karsten <karo13de at googlemail.com<mailto:karo13de at googlemail.com>> wrote:


Concerning Final .nd2 fixes for 5.0.3 by melissalinkert · Pull Request #1226 · openmicroscopy/bioformats · GitHub<https://github.com/openmicroscopy/bioformats/pull/1226>

Is it possible to access a release candidate of biodata ? If yes, how?

Regards

Karsten



Karsten
karo13de at googlemail.com<mailto:karo13de at googlemail.com>



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Karsten
karo13de at googlemail.com<mailto:karo13de at googlemail.com>




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