[SCIFIO] Scrambled tiles in czi files with Scifio-Itk bridge

[Roysam, Badri]

Gentlemen, Can anyone help us sooner? I am worried that this project is falling behind.
Thanks,

Badri Roysam, D.Sc.
Hugh Roy and Lillie Cranz Cullen University Professor
Chair, Electrical & Computer Engineering
N325, Engineering Building 1
University of Houston
Houston, Texas 77204-4005
Office: 713-743-1773/4435
Lab (W349): 713-743-0790
Fax:  713-743-4444
Email: broysam at central.uh.edu
ECE Department website: www.ee.uh.edu<http://www.ee.uh.edu>
Laboratory website: www.farsight-toolkit.org


[cid:90E25201-50A2-4ADF-A9CB-F8931F26DA67]

From: Mark Hiner <hinerm at gmail.com<mailto:hinerm at gmail.com>>
Date: Thursday, June 19, 2014 7:34 AM
To: Kedar Grama <gbkedar at gmail.com<mailto:gbkedar at gmail.com>>, "scifio at scif.io<mailto:scifio at scif.io>" <scifio at scif.io<mailto:scifio at scif.io>>
Cc: Dragan Maric <maricd at ninds.nih.gov<mailto:maricd at ninds.nih.gov>>, Matt McCormick <matt.mccormick at kitware.com<mailto:matt.mccormick at kitware.com>>, Curtis Rueden <ctrueden.wisc at gmail.com<mailto:ctrueden.wisc at gmail.com>>, Badri Roysam <broysam at central.uh.edu<mailto:broysam at central.uh.edu>>
Subject: Re: Scrambled tiles in czi files with Scifio-Itk bridge

Hi Kedar,

 Just wanted to let you know that I'll be out of the country for two weeks starting tomorrow, and all of my time right now is being spent on the ImageJ2 release<http://developer.imagej.net/2014/06/04/imagej-200-release-candidate>.

 Would you mind filing this as an issue on the scifio-itk-bridge github site: https://github.com/scifio/scifio-itk-bridge ? That way it won't get lost in my e-mail and I can investigate when I get back.

Thanks!
- Mark


On Wed, Jun 18, 2014 at 2:39 PM, Kedar Grama <gbkedar at gmail.com<mailto:gbkedar at gmail.com>> wrote:
Hi Mark,

I used SCIFIO to write czi as a 3d stack of either nrrd or tiffs. I get tiles that are scrambled and this happens at random. My code to convert the files is here:
https://github.com/gbkedar/farsight/blob/IlluminationGraphCuts/IlluminationCorrection/readCziWriteCorrectedTiles.cpp

I have made montages of the same image in three instances where tiles were scrambled and once when it worked. The czi file is similar to the one I sent you in June or July last year. Please let me know if you need the file that I'm using right now and I'll upload it.

Thanks,

-Kedar

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