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LOCI Importer .nd2 and .lsm formats

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LOCI Importer .nd2 and .lsm formats

Cammer, Michael
Dear ImageJers,

Some time between October and January the LOCI importers changed to break the nd2 importer but to fix the lsm importer.

We are using release 4.4.4 revision ccc87b3, 18 Oct 2011
to open .nd2 files but it does not work for .lsm files.

Newer versions of the plugins, such as release 4.4-DEV revision f796122 built 2 Jan 2012
opens most lsm files but opens .nds2 files in the wrong order.  So we have been quitting ImageJ and reinstalling the plugins depending of which project we are working on.

Does anyone know if there a build that opens both formats?

Also, yesterday we got a bunch of files from the Zeiss ELYRA and they don't open properly with the LOCI plugins.  Any help adding this variation of the lsm format to the importers would very much appreciated.

Thank you!


________________________________________________________
Michael Cammer, Assistant Research Scientist
Skirball Institute of Biomolecular Medicine
Lab: (212) 263-3208  Cell: (914) 309-3270
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Re: LOCI Importer .nd2 and .lsm formats

dscho
Dear Michael,

On Fri, 2 Mar 2012, Cammer, Michael wrote:

> Some time between October and January the LOCI importers changed to
> break the nd2 importer but to fix the lsm importer.

I am sure you'll find the Bio-Formats people very helpful in fixing thd
bug once you send them a file explaining what you expect to see.

Ciao,
Johannes
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Re: LOCI Importer .nd2 and .lsm formats

Melissa Linkert-2
In reply to this post by Cammer, Michael
Hi Michael,

> Some time between October and January the LOCI importers changed to break the nd2 importer but to fix the lsm importer.
>
> We are using release 4.4.4 revision ccc87b3, 18 Oct 2011
> to open .nd2 files but it does not work for .lsm files.
>
> Newer versions of the plugins, such as release 4.4-DEV revision f796122 built 2 Jan 2012
> opens most lsm files but opens .nds2 files in the wrong order.  So we have been quitting ImageJ and reinstalling the plugins depending of which project we are working on.
>
> Does anyone know if there a build that opens both formats?

There are several known issues with Nikon ND2 support at the moment:

https://trac.openmicroscopy.org.uk/ome/ticket/7901
https://trac.openmicroscopy.org.uk/ome/ticket/7947

Fixes for these are in progress at the moment, but it basically amounts
to a major reworking of the ND2 reader (and subsequently re-testing ~50
GB of data).  I know that you have already sent several files that
demonstrate various problems, so there is no need to send more .nd2
files at this point.

If you would like automated updates on the progress of either of the
above issues, just let me know and I will CC you on either or both
tickets.

> Also, yesterday we got a bunch of files from the Zeiss ELYRA and they don't open properly with the LOCI plugins.  Any help adding this variation of the lsm format to the importers would very much appreciated.

It would be extremely helpful if you could send one or two of the files
in question, along with the full text of the error message (if any) or a
description of what happens that is not correct.  I believe you already
have all of the details on sending files, but if not please let me know
and I will re-send privately.

Regards,
-Melissa

On Fri, Mar 02, 2012 at 02:25:43PM +0000, Cammer, Michael wrote:

> Dear ImageJers,
>
> Some time between October and January the LOCI importers changed to break the nd2 importer but to fix the lsm importer.
>
> We are using release 4.4.4 revision ccc87b3, 18 Oct 2011
> to open .nd2 files but it does not work for .lsm files.
>
> Newer versions of the plugins, such as release 4.4-DEV revision f796122 built 2 Jan 2012
> opens most lsm files but opens .nds2 files in the wrong order.  So we have been quitting ImageJ and reinstalling the plugins depending of which project we are working on.
>
> Does anyone know if there a build that opens both formats?
>
> Also, yesterday we got a bunch of files from the Zeiss ELYRA and they don't open properly with the LOCI plugins.  Any help adding this variation of the lsm format to the importers would very much appreciated.
>
> Thank you!
>
>
> ________________________________________________________
> Michael Cammer, Assistant Research Scientist
> Skirball Institute of Biomolecular Medicine
> Lab: (212) 263-3208  Cell: (914) 309-3270
>
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