[ome-devel] OMERO ScanR import

[Rubén Muñoz]

Hi Melissa,
Nice to meet you. Very kind of you to welcome our contribution, we are  
glad to be of help here.

Currently uploading 5.8G file 161009test2.tar.bz2 (originally from  
ScanR) to the given FTP, also checked out the bioformats trunk and  
work on this same set. As you suggest, to examine the resulting OME- 
TIFFs.

Other sets from ScanR have the similar complexity, so we though that  
is a good example. Please note that the set it's an acquisition of 2  
plates, 2 channels, 3 slices, 30 time points, 5 wells, 3 positions  
each. My colleagues confirm that the directory structure and file  
naming is NOT COMPLETELY standard for every scan. So I will have to  
provide you one more example, if it is Ok.

Other information will be provided, bugs and possible patches in a  
longer term. Testing is the best we can achieve at the moment.

Best regards,
--
Rubén Muñoz
European Molecular Biology Laboratory


On Oct 19, 2009, at 11:29 PM, Melissa Linkert wrote:

> Hi Ruben,
>
>> In other hand, we have multiC and multiD and time-lapse data from  
>> ScanR
>> that want to provide (via FTP or CVS). And help to extend  
>> ScanrReader.java
>> any possible way. I can provide information about ScanR, make test,
>> suggestions and development.
>
> We currently have very little ScanR data, so if you are willing to
> provide additional datasets that would be very helpful.  I will send
> you FTP server information off-list.
>
> The two main things you can do to help with ScanR support are:
>
> 1) Testing with your own data, and reporting any bugs.
>
> 2) Reviewing the metadata displayed in OMERO, and verifying that it
> represents all of the metadata that is present in ScanR files.
>
> At a minimum, it would help to have a list of things that should be
> fixed in the ScanR reader.  We would certainly welcome patches; if you
> are planning on submitting patches to ScanrReader.java (or Bio-Formats
> in general), I would recommend that you read through the developer
> documentation at
>
> http://loci.wisc.edu/ome/formats-library.html
>
> ...in particular, the "Other developer links" section.
>
> If you have any questions, please feel free to ask!
>
> Regards,
> -Melissa
>
> On Mon, Oct 19, 2009 at 2:38 AM, Rubén Muñoz <ruben.munoz at embl.de>  
> wrote:
>> Hello all,
>>
>> I'd like to introduce myself, my name is Ruben. We use OMERO at EMBL,
>> specially since ScanR format is supported!!! It's great.
>>
>> While installing OMERO, I have taken a couple of notes, from
>> [http://www.openmicroscopy.org/site/support/omero4/server/installation 
>> ]
>> that you may like to consider as changes.
>>
>> In other hand, we have multiC and multiD and time-lapse data from  
>> ScanR
>> that want to provide (via FTP or CVS). And help to extend  
>> ScanrReader.java
>> any possible way. I can provide information about ScanR, make test,
>> suggestions and development.
>>
>> Thanks for your work.
>>
>> --
>> Rubén Muñoz
>> European Molecular Biology Laboratory
>>
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>> ome-devel at lists.openmicroscopy.org.uk
>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel
>>
>>