Hi,
I was just wondering what was the format and if you had specification of it somewhere, and a way to access it. The idea was to avoid duplicating data and so not use the archive option. We currently have several terabytes (around 10) so if we could avoid to duplicate it, that will save us some storage...
The format of the Pixels file is really pure pixel data (no header etc) since all the metadata, dimensions etc is stored in the database pixels table.
However, your question is quite timely in that we are getting close to the first release candidate of what we've been calling OMERO.FS 'file system'. In OMERO.FS, imported images are simply stored in their original format (and name) and these original files are used to access Pixel data. Therefore, no Pixel objects are created and there is no data duplication. See
http://trac.openmicroscopy.org.uk/ome/milestone/OMERO-5I'm afraid there's no "simple" way to get "Combine_Images.py" to generate multiple images. If you are acquiring your data using a common format (E.g. commercial system) then we should be able to extend Bio-Formats to recognise this and import the data 'correctly' into plates in OMERO. However, if you have you own in-house acquisition and format, then you could either combine the channels before import using ImageJ / Bio-Formats etc on the command line or adapt the Combine_Images script to do what you want.
The Dataset_To_Plate script should certainly handle multiple images per plate. Did you see the notes and demo at
http://www.openmicroscopy.org/site/supp ... ripts.html ?
E.g. if you have these images (in the following order sorted by name)
A1.tif
A2.tif
A3.tif
B1.tif
B2.tif
B3.tif
and you want columns A & B and rows 1,2,3 then you'd simply choose that you want the 'First Axis' to be row and the 'First Axis Count':3. Then choose to name columns by 'letter' and rows by 'number'.