[ome-devel] [fiji-devel] problems with opening .czi Lightsheet Z1 files

Thu May 15 02:18:33 BST 2014

Hi Pavel,

> After a while I came back to working hands on with the multi-view SPIM data from Lightsheet Z1 saved in .czi files. I completely understand that this new format is creating problems. We have always been pragmatic and tried to identify a way that works for us. i.e. saving the files in a way that can be opened. Now however even the established workarounds do not work anymore.
> 
> I have a long series of .czi files, saved at LZ1 as a single file per angle. 5 angles per time point, meaning that the first two time points are represented by the following 10 files

*snip*

> When I simply try to import them using the Bioformats Fiji import pluign without changing any parameters and using the fix http://curtis.imagej.net/fiji-bug-744/formats-gpl.jar that Curtis Rueden provided (see "[fiji-devel] [Bug 744] problem opening .czi" files thread), I get the following results
> 
> spim_TL1_Angel1.czi -> bioformats detects two series, only the second one contains data, when I click on the second series I get the stack with the correct image data (as you will see this is hard to script because it does not ALWAYS happen).
> spim_TL1_Angel2.czi -> no series dialog appears, image opens fine
> spim_TL1_Angel3.czi -> series dialog with FOUR series, last one contains data
> spim_TL1_Angel4.czi -> series dialog with FIVE series, last one contains data
> spim_TL1_Angel5.czi -> no series dialog appears, image opens fine
> spim_TL2_Angel6.czi -> no series dialog appears, image opens fine
> spim_TL2_Angel7.czi -> series dialog with TWO series, last one contains data, the resulting image opens as time series, first time point is empty, second contains data (this can be fixed by setting the t_begin=1000 BTW) 
> spim_TL2_Angel8.czi -> no series dialog appears, the resulting image opens as time series, first time point is empty, second contains data 
> spim_TL2_Angel9.czi -> series dialog with FOUR series, the resulting image opens as time series, first time point is empty, second contains data 
> spim_TL2_Angel10.czi -> series dialog with FIVE series, the resulting image opens as time series, first time point is empty, second contains data 
> 
> I am at my wits end. I cannot understand the pattern here, I cannot script it and thus I cannot use it.

My understanding is that the patched jar that you have does not contain
most of the (many, many) proposed fixes we are reviewing for Zeiss .czi
files:

https://github.com/openmicroscopy/bioformats/pull/1078

The symptoms listed above are identical to what has been reported by
others on and off the mailing list, so I would expect that pull request
to fix this problem as well.  We are intending to merge that pull
request in the next couple of days, as soon as testing is finished and
we're confident that all outstanding Zeiss .czi issues are resolved.  It
will be in the upcoming 5.0.2 release of Bio-Formats; a development
build will also be available shortly after the pull request is merged
("Latest build" column of
http://downloads.openmicroscopy.org/bio-formats/5.0.1).

> I am happy to share the files if you tell me where to upload them, they are big.

I will send FTP information privately for how to send large files;
again, I strongly suspect that the above pull request will fix this, but
we can certainly double check any data that you send prior to 5.0.2
being released.

Regards,
-Melissa

On Thu, May 15, 2014 at 04:00:20PM +0200, Pavel Tomancak wrote:
> Dear OME Team,
> 
> After a while I came back to working hands on with the multi-view SPIM data from Lightsheet Z1 saved in .czi files. I completely understand that this new format is creating problems. We have always been pragmatic and tried to identify a way that works for us. i.e. saving the files in a way that can be opened. Now however even the established workarounds do not work anymore.
> 
> I have a long series of .czi files, saved at LZ1 as a single file per angle. 5 angles per time point, meaning that the first two time points are represented by the following 10 files
> 
> spim_TL1_Angel1.czi
> spim_TL1_Angel2.czi
> spim_TL1_Angel3.czi
> spim_TL1_Angel4.czi
> spim_TL1_Angel5.czi
> spim_TL2_Angel6.czi
> spim_TL2_Angel7.czi
> spim_TL2_Angel8.czi
> spim_TL2_Angel9.czi
> spim_TL2_Angel10.czi
> 
> When I simply try to import them using the Bioformats Fiji import pluign without changing any parameters and using the fix http://curtis.imagej.net/fiji-bug-744/formats-gpl.jar that Curtis Rueden provided (see "[fiji-devel] [Bug 744] problem opening .czi" files thread), I get the following results
> 
> spim_TL1_Angel1.czi -> bioformats detects two series, only the second one contains data, when I click on the second series I get the stack with the correct image data (as you will see this is hard to script because it does not ALWAYS happen).
> spim_TL1_Angel2.czi -> no series dialog appears, image opens fine
> spim_TL1_Angel3.czi -> series dialog with FOUR series, last one contains data
> spim_TL1_Angel4.czi -> series dialog with FIVE series, last one contains data
> spim_TL1_Angel5.czi -> no series dialog appears, image opens fine
> spim_TL2_Angel6.czi -> no series dialog appears, image opens fine
> spim_TL2_Angel7.czi -> series dialog with TWO series, last one contains data, the resulting image opens as time series, first time point is empty, second contains data (this can be fixed by setting the t_begin=1000 BTW) 
> spim_TL2_Angel8.czi -> no series dialog appears, the resulting image opens as time series, first time point is empty, second contains data 
> spim_TL2_Angel9.czi -> series dialog with FOUR series, the resulting image opens as time series, first time point is empty, second contains data 
> spim_TL2_Angel10.czi -> series dialog with FIVE series, the resulting image opens as time series, first time point is empty, second contains data 
> 
> I am at my wits end. I cannot understand the pattern here, I cannot script it and thus I cannot use it.
> 
> I am happy to share the files if you tell me where to upload them, they are big.
> 
> Please help.
> 
> All the best
> 
> PAvle
> 
> 
> 
> --------------------------------------------------------------------------------------------------
> Pavel Tomancak, Ph.D.
> 
> Research Group Leader
> Max Planck Institute of Molecular Cell Biology and Genetics in Dresden
> Pfotenhauerstr. 108
> D-01307 Dresden							Tel.: +49 351 210 2670
> Germany									Fax: +49 351 210 2020
> 
> tomancak at mpi-cbg.de
> http://www.mpi-cbg.de/research/research-groups/pavel-tomancak.html
> twitter: @PavelTomancak
> --------------------------------------------------------------------------------------------------
> 
> 
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