Possible solution for problems opening confocal files from Zeiss LSM 880 in Neurolucida 360 environment

 The issue: One of the regular users of Neurolucida 360 has noticed that some image files produced by the Zeiss LSM 880 (confocal microscope using ZEN black software) do not open. This happens rarely, but she had five examples of medium sized (tens to hundreds of MB sized, mosaics with multiple z-levels) files that NL360 could not open. 

Diagnose procedure: I tried to open the same files in Fiji and by using Matlabs bformats pack (v7.0.0) and in both cases, I got error messages concerning corrupted data bytes. Nevertheless it was possible to open those files in ZEN blue lite version. That made me hypothesize that there are a few corrupted data bytes in the file, but that ZEN lite can bypass those data points. That lead me to the think that if I tried to save those files again using the "Save as" menu, the files would be saved with the corrected bytes version, and that would make the files whole again. Upon testing this procedure, the files were fixed and could open normally in both NL360, Fiji and by using bformats. 

Solution: try to open the corrupted czi files in ZEN lite and save them again as new czi files, but possibly with a new name (adding a suffix would suffice, for example). Neurolucida 360 should open these new files.  

  

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