[ome-users] import of single Zeiss LSM files

[Will Moore]

Hi Martin,

  I think what we will do for now is what I described below (for LSMs)  
which should fix most of your issues. E.g. If you select all (or one  
or more) of the LSM files within a directory, with or without an mdb  
present, then we import just those LSMs (ignore the mdb and any other  
LSMs it references).
Ticket for this is http://trac.openmicroscopy.org.uk/omero/ticket/3701

For handling situations where you select the mdb AND a lsm contained  
within it, this would require a bit more work to remove duplicates. We  
probably won't do this unless people tell us it's a common problem.
And to fix the same situation for SP2 format is even more tricky (when  
you select a tiff AND the lei container).
However, in both these situations where you choose to import  
everything in the directory (select the directory itself for import)  
we do parse all the files to make sure that we don't import duplicates  
etc.

A message for every file type is a bit of an overkill, since only a  
handful of formats (out of more than 100 that we support) have  
multiple images per file.
We might consider a pop-up for explicitly choosing images (in the  
style of the ImageJ LOCI importer) if we continue to have these  
problems, but hopefully we can fix them by simply changing the  
behavior to make it more predictable.

   Cheers,

    Will.



Begin forwarded message:

> From: Martin Spitaler <m.spitaler at imperial.ac.uk>
> Date: 14 December 2010 10:25:40 GMT
> To: Will Moore <will at lifesci.dundee.ac.uk>
> Subject: Re: [ome-users] import of single Zeiss LSM files
>
> Hi,
>
>  funny how different people's thoughts are, that's why it's good to  
> have these discussions.
>
>  My personal logic is clear: If I add one or two LSM files to the  
> queue, I want those one or two LSM files imported, otherwise I would  
> select all files.
>
> Talking about selecting all files: Have you noticed that at the  
> moment that multiplies the files? When a user wants to import Zeiss  
> LSM files, goes to the folder with the files and selects them all,  
> because s/he wants to import them all, the importer starts with the  
> MDB database and imports all LSM files, then goes to the first LSM  
> files and again imports all LSM files and so on, which produces as  
> many versions of each file as there are files in the folder.
>
>  So in my opinion the best solution is to import whatever is in the  
> queue, irrespective of what's in the MDB. I understand that this can  
> produce confusion when both MDB and LSMs are selected. You would  
> either need to automatically check whether a file has already been  
> imported in the queue, or ignore the MDB and require the user to  
> select the LSM.
>
>  Of course that's even more complicated with the old Leica SP2  
> format (and maybe others?) where each frame is saved as a separate  
> TIF, in the Zeiss format at least all frames belonging to one series  
> are in one LSM files.
>
>  My idea for a quick fix: When selecting the format in the pull-down  
> menu below the folder tree of the IMPORTER, show a little  
> explanatory text specific for that file type.
>
>  My idea for a long-term solution, completely unambiguous and user  
> friendly: When importing these file types, pop up a window with tick  
> boxes for all files contained in the MDB, and SELECT ALL and  
> DESELECT ALL buttons. Actually exactly how the ImageJ Loci Importer  
> works, that's perfect.
>
> Best,
>
> Martin
>
> On 14/12/2010 03:05, Will Moore wrote:
>>
>> Hi Martin,
>>
>>  I discussed this with Melissa today and we thought of a possible  
>> solution.
>> - If mdb is present, and you choose the mdb file, then import all  
>> the images in the file
>> - If you choose an LSM file, only import the LSM itself, even if  
>> the mdb is present and includes other LSMs.
>>
>> The only caveat of this approach is that it might confuse users who  
>> are expecting all the LSMs from an mdb to be imported - even when  
>> selecting a single image.
>> But I think most users could get used to the proposed change in  
>> behavior pretty easily.
>>
>> What do you think?
>>
>>  Cheers,
>>
>>   Will.
>>
>>
>> On 13 Dec 2010, at 18:36, Martin Spitaler wrote:
>>
>>> I have noticed that IMPORTER does not allow to import single LSM  
>>> files: When I add a single LSM file to the queue, it correctly  
>>> lists that file in the queue, but upon IMPORT it looks up the  
>>> connected *.MDB database and uploads all images in that database.  
>>> While that might not be problem usually, occasionally it is useful  
>>> to be able to select specific files, especially if the whole  
>>> collection of files is very large,
>>>
>>> Martin
>>> -- 
>>> Martin Spitaler, PhD
>>> FILM - Facility for Imaging by Light Microscopy
>>> - Facility Manager -
>>> Sir Alexander Fleming Building, desk 401
>>> Imperial College London / South Kensington
>>> Exhibition Road
>>> London SW7 2AZ
>>> UK
>>>
>>> Tel. +44-(0)20-759-42023
>>> E-mail m.spitaler at imperial.ac.uk
>>> Website: http://imperial.ac.uk/imagingfacility
>>>
>>>
>>> _______________________________________________
>>> ome-users mailing list
>>> ome-users at lists.openmicroscopy.org.uk
>>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>>
>> William Moore
>> Wellcome Trust Centre for Gene Regulation & Expression
>> College of Life Sciences
>> MSI/WTB/JBC Complex
>> University of Dundee
>> Dow Street
>> Dundee  DD1 5EH
>> United Kingdom
>>
>> Phone 01382 386364
>> http://openmicroscopy.org.uk
>>
>>
>>
>>

William Moore
Wellcome Trust Centre for Gene Regulation & Expression
College of Life Sciences
MSI/WTB/JBC Complex
University of Dundee
Dow Street
Dundee  DD1 5EH
United Kingdom

Phone 01382 386364
http://openmicroscopy.org





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