[ome-devel] About SPW 'runs' (and .flex import)

[Anatole Chessel]

Hi all,

    A couple of quick question about SPW: we switched to 4.3.3 recently, 
and 'runs' made their apparition in Insight, I guess corresponding to 
'PlateAcquisition' (they where not there before, right, or did I just 
not saw them?). I am not sure how that work: it seems to be a shortcut 
for a subset of well samples based on dates? So a plate have only one 
well at each position, which have a number of well sample, each with a 
position and a date. They are all equivalent as well samples, and a 
PlateAqusition links to a subset of them between two dates. In insight 
however, a plate is divided in runs and fields, which is done under the 
assumption that the same locations (different fields at the same time) 
are acquired at different time (different runs at the same position). Is 
that right?

   The thing is, in our case different runs correspond to different 
fields, for both technical and biological reasons, so 5 consecutive runs 
of a plate would be done each in a different location in wells, 
corresponding actually to 5 fields (but done plate-wise, not well-wise). 
Data (plain .flex), when imported, used to appear as different plates, 
and I had a script putting them together as different fields of the same 
plate (relinking well-sample of plate B to the wells of plate A). Now 
they appear as different runs of different plate (see screenshot 
attached); I am not sure whether that is an importation bug or an 
expected behaviour given our unexpected data and quite how to deal with 
it (as my script do not seem to be working any more -or at least insight 
is not showing any changes, I am guessing it is confused between runs 
and fields-)...

   Lastly it seems that if an image in a well is tagged, and looked for 
using the search interface, there is no way of knowing where (which 
plate and screen) it comes from, as the only info is about datasets, not 
plates. I reported that a while back (it ended up here I think: 
http://trac.openmicroscopy.org.uk/ome/ticket/3871). Any plans for that? 
It would come in handy...

Hoping I am somewhat understandable,
Many thanks,

Anatole Chessel




-- 
Anatole Chessel
Research associate
The Gurdon Institute
University of Cambridge
Tennis Court Road, Cambridge CB2 1QN
tel: +44 (0)1223 767197

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