[ome-devel] Fwd: Example Imageset

[Melissa Linkert]

Hi Rubén,

Again, my apologies for not replying to you sooner.

> 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"

Using multiple directories is fine, but you must then use relative
paths in the FileName attribute of UUID.  So in the example dataset,
you would just need to change the UUID elements from this:

<UUID FileName="Test_Ruben_001--W0001--P001--Z001--C01--T00001.ome.tif">

to this:

<UUID FileName="W0001/P001/Test_Ruben_001--W0001--P001--Z001--C01--T00001.ome.tif">

Note that if you are testing against recent trunk builds of
Bio-Formats, multi-file OME-TIFF datasets will not open correctly.
This will be resolved in the upcoming 4.2 release.

Regards,
-Melissa

On Wed, Apr 28, 2010 at 4:49 AM, Rubén Muñoz <ruben.munoz at embl.de> wrote:
> 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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