[ome-users] Question about LOCI and Zeiss czi format for SPIM ( light sheet microscope)

[Melissa Linkert]

Hi Jan,

[CC'ing the ome-users mailing list; that is the best place for
Bio-Formats questions, and I know a number of others are interested in
this topic.]

> may I please ask you for your advice regarding the LOCI and Zeiss czi
> format for their new Light Sheet Microscope - which countains
> information about angles and dual view  in addition to x,y,z
> positions.
> 
> You were helping us many times in the past which making LOCI reader
> ready to read new formats. I wonder what you think about the possibility
> to make this new CZI format readable by LOCI?
>
> We recently got new Zeiss light sheet ( SPIM) machine installed and
> we would very much like to use multi-view registration macro of
> Stephan Preibish which is available in Fiji, but currently our new
> SPIM users get slowed down by the fact that we can not read czi
> multiview SPIM format into Fiji. So what our users keep doing is to
> convert data to TIFFs and then load them to Fiji which is not
> omptimal.
> 
> Melissa, may I please ask you for your advice regarding this topic ?
> I wonder what you think about the possibility to make this new CZI
> format readable by LOCI. My understanding is that Zeiss people are
> willing to provide you with all doumentation necessary.
> I am also aware that this is probably a project which might take a
> while. In general your help with this project would be highly
> appreciated. But at the same time I would like to hear back from you
> about what you think will be needed to make this project work from
> your side. Please let me know.

We are certainly going to update Bio-Formats to read these new .czi
files.  Zeiss has already contacted us privately to arrange for sending
official documentation and sample files; we are waiting for that to
happen and then will schedule that work on our issue tracking system.

I do not currently have an estimate of when this work will be completed,
as we haven't received all of the promised information yet (and without
knowing the full scope of the work, it's difficult to say how long it
will take).  The best way for you and anyone else interested is, as
usual, to send representative files.  Files can be uploaded here:

http://qa.openmicroscopy.org.uk/qa/upload/

If that doesn't work, I can send alternate instructions privately.

Regards,
-Melissa

On Wed, Mar 20, 2013 at 11:12:37AM +0100, Jan Peychl wrote:
> Dear Melissa,
> 
> may I please ask you for your advice regarding the LOCI and Zeiss czi
> format for their new Light Sheet Microscope - which countains
> information about angles and dual view  in addition to x,y,z
> positions.
> 
> You were helping us many times in the past which making LOCI reader
> ready to read new formats. I wonder what you think about the possibility
> to make this new CZI format readable by LOCI?
> 
> We recently got new Zeiss light sheet ( SPIM) machine installed and
> we would very much like to use multi-view registration macro of
> Stephan Preibish which is available in Fiji, but currently our new
> SPIM users get slowed down by the fact that we can not read czi
> multiview SPIM format into Fiji. So what our users keep doing is to
> convert data to TIFFs and then load them to Fiji which is not
> omptimal.
> 
> Melissa, may I please ask you for your advice regarding this topic ?
> I wonder what you think about the possibility to make this new CZI
> format readable by LOCI. My understanding is that Zeiss people are
> willing to provide you with all doumentation necessary.
> I am also aware that this is probably a project which might take a
> while. In general your help with this project would be highly
> appreciated. But at the same time I would like to hear back from you
> about what you think will be needed to make this project work from
> your side. Please let me know.
> 
> Thank you  very much.
> 
> 
> Jan
> 
> 
>