[ome-devel] Fwd: Example Imageset

[Rubén Muñoz]

Begin forwarded message:

> From: "Josh Moore" <josh at glencoesoftware.com>
> Date: April 28, 2010 11:17:25 AM GMT+02:00
> To: Rubén Muñoz <ruben.munoz at embl.de>
> Subject: Example Imageset
> 
> Rubén Muñoz writes:
>> Hi Josh, 
>> 
>> How are you? 
> 
> Hi Ruben.

Josh, awaited your reply but the circumstances that you have commented in your previous e-mail worried me. I hope that everything is fine at home now and wish you a happy return to Germany. 

When you settle and have time we may also give a call, so that we know that everything is fine.

> 
>> Some time ago we decided to re-take our discussion on OME-TIF files
>> that would be compatible with OMERO.Fs and with our local systems,
>> we are very interested in being compliant with the upcoming
>> standard.  I hope that you are still interested in having a look
>> into our data. Please understand that the delay was caused by a bug
>> introduced in the OME-XML header that prevented me from loading
>> this in OMERO server. Now fixed.
> 
> This means that your previous email from Apr. 7, "OME-TIFs", is no longer
> an issue? If so, how did you fix it?

Yes. I was creating wrong tags in the OME.XML header of the OME.TIF files. Very newby mistake by the way (see next):

	FirstC="1" FirstT="1" FirstZ="1" were wrong values for TiffData tag. FirstC="0" FirstT="0" FirstZ="0" replaced that in my headers as solution to the problem.

By now the datasets are O.K. for loading with all OME.TIF compatible software.

> 
>> We will use a folder arrangement to store OME-TIF
>> datasets. Currently those will only load in OMERO when placed in
>> the same folder, the subfolders are a major requirement here. And a
>> question would be, will FileName attribute admit relative paths to
>> files?
> 
>> Like for example "../P002/example_name.ome.xml"
>> 
>> I am currently uploading a dataset to the typical ftp server with the name Test_Ruben_001.zip
> 
> The answer seems to be yes, but I'll forward this to Melissa and have
> her look at it. To avoid time delays, you should really use the forums
> and/or mailing lists with these questions. I think the community would
> be interested to hear what you are planning on doing. Do you want to
> forward this email to the list yourself?

That would be great. Lately during the Hackathon I commented this to Curtis, he also considered it a good idea back then.

As commented many times, with or without, we find the format a perfect choice for every acquisition. Also we will like to make the files accessible to OMERO.

> 
>> Thank you for listening to our case,
>> Rubén
> 
> Take care,

Be well, and let us know if you are.

Rubén

> ~Josh.

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