[ome-users] Potential Bug in BioFormats 5.0.5 with CZI

[Melissa Linkert]

Hi Sebi,

> I have acquired a 2.6 GB Timelapse CZI file with 3 Channel and 300 Frames.
> 
> When I open this via BioFormats in Fiji the images itself is "assembled"
> wrong (i found no better term to put) --> see the screenshot attached.
> 
> When I export the CZI from ZEN as OME-TIFF (is them 1.92 GB) it works fine
> with Fiji.
> 
> When I cut out the first 3 TimePoints in ZEN, save the CZI again and open
> the short version og the CZI in Fiji via BioFormats it looks fine. This CZI
> can be found here:
> 
> https://dl.dropboxusercontent.com/u/623476/ADD_Ute_TL_GFP_mCherry_3frames_10s.czi
> 
> 
> Do you have any idea what the problem could be? or do you definitely need
> the large data set, to check this? If yes, I will also upload this one.

Thank you for the bug report.  Yes, we will need to see the original
larger .czi file.  As it's too large for our QA system (and probably
inconvenient for Dropbox?), I am sending FTP server credentials in a
private mail.

Regards,
-Melissa

On Thu, Oct 09, 2014 at 05:49:04PM +0200, Sebastian Rhode wrote:
> I have acquired a 2.6 GB Timelapse CZI file with 3 Channel and 300 Frames.
> 
> When I open this via BioFormats in Fiji the images itself is "assembled"
> wrong (i found no better term to put) --> see the screenshot attached.
> 
> When I export the CZI from ZEN as OME-TIFF (is them 1.92 GB) it works fine
> with Fiji.
> 
> When I cut out the first 3 TimePoints in ZEN, save the CZI again and open
> the short version og the CZI in Fiji via BioFormats it looks fine. This CZI
> can be found here:
> 
> https://dl.dropboxusercontent.com/u/623476/ADD_Ute_TL_GFP_mCherry_3frames_10s.czi
> 
> 
> Do you have any idea what the problem could be? or do you definitely need
> the large data set, to check this? If yes, I will also upload this one.
> 
> Cheers,  Sebi
> 
> PS: I use BioFormats 5.0.5-DEV, revision 440626c on a Win/, 64bit system
> with 8GB RAM.


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