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

[Pavel Tomancak]

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



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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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