[ome-devel] questions about the well index

[Bernhard Holländer]

Hi Josh!

>  > Here's the modified code to add well samples to existing wells:
>  >
>  > ws = WellSampleI()
>  > ws.well = WellI(w.id, False) # w comes from the  query above
>  > ws.image = ImageI(image.id, False)
>  > w.addWellSample(ws)
>  > w = self.updates.saveAndReturnObject(w)
>  > ws = w.getWellSample(w.sizeOfWellSamples()-1)
>  > ws = WellSampleI(ws.id.val, False)
>  > # now link ws to a screen acquistion
>
>  > >From your previous post I assume the last sample in the list of well
>  > samples is the newest added?
>
> Not necessarily. This is file format specific, so if you know that the
> format you're working with behaves this way then it's a fine
> assumption. Unfortunately, we can't guarantee it for all formats.

But what if I add the samples with the method above. Is it not
guarantied that the sample I get back from the end of the list of
samples is the one I just added (neglecting concurrency issues)? How
could I otherwise get the id of the new sample which I need to link it
to the screen acquisition?

If you use the well_index to get the same well samples for an entire
plate, do you take care when there is a sample missing in a well. Say
well A1 has four samples but the acquisition in well A2 had problems
and only produced 2 samples, which are e.g the first and the last, the
second and third are missing.

As far as I understand, if a plate is measured multiple times,
different screen acquisitions would be linked against different sets
of well samples. I assume well_index does not start again at 0 for the
other measurement. Eg:

screen acquisition 1 -> ws 1 (well 1, well_index 0)
                                 -> ws 2 (well 1, well_index 1)
screen acquisition 2 -> ws 3 (well 1, well_index 2)  *)
                                 -> ws 4 (well 1, well_index {previous+1})

At *) I would prefer well_index 0 again, since this is the first field
of the second acquisition of well 1.

How about adding another container (WellSampleSet) that holds a
collection of well samples of one acquisition and this would have the
well index field. In addition this would make it easier for us to
store analysis results that are averaged over all samples in a well.
These could be saved as a WellSampleSet annotation.


Thanks again! Bernhard