ome.xml for adaptive feedback microscopy

[tischi]

Hi All,

We were wondering whether the current ome.xml (or the new version) would be flexible enough to represent our "adaptive feedback microscopy" datasets.

A typical example is:

• Multi-well
  • Multi-position
    • At each position:
      • One low resolution "pre-scan" overview image
      • Several zoomed-in high-resolution time-series "re-scan" datasets, whose positions are somewhere within the low resolution pre-scan image.

[sbesson]

Hi @tischi,

thanks for starting the discussion here.

Part of the requirements for the adaptive feedback microscopy workflow are currently supported in the OME Data Model. The Screen-Plate-Well model allows to structure imaging data in a Plate with multiple Wells. Within this well, you can define multiple WellSamples corresponding to the individual positions.

Minimal examples of such a layout are given in our official OME-XML samples with the SPW structure being expressed as:

<Plate ID="Plate:0">
  <Well ID="Well:0:0" Column="1" Row="1">
    <WellSample ID="WellSample:0:0:0" PositionX="0.0" PositionY="0.0" Index="1"><ImageRef ID="Image:0"/></WellSample>
    <WellSample ID="WellSample:0:0:1" PositionX="0.1" PositionY="0.0" Index="2"><ImageRef ID="Image:1"/></WellSample>
...

For handling the low-resolution overview images, at the moment, you would probably have to create:

• an overview plate with a single field per well containing the pre-scanned images
• a detailed plate with multiple fields per well containing the high-resolution time-series per position.