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AllenCellModeling / czi-to-ome-xslt

A repository of XSL transform sheets to map CZI metadata to OME.
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Populate `Plate/Well/WellSample` #6

Open MatteBailey opened 3 years ago

MatteBailey commented 3 years ago

CZI contains information about which well each scene comes from in /ImageDocument/Metadata/Information/Image/Dimensions/S/Scenes/Scene/Shape. In OME, this information can be translated to Plate/Well/WellSample, which can refer to an Image representing the relevant scene.

GabeMedrash commented 2 years ago

At least one big open question: In both OME (/Plates/Plate) and Zeiss (/ImageDocument/Metadata/Experiment/ExperimentBlocks/AcquisitionBlock/SubDimensionSetups/RegionsSetup/SampleHolder/Template) metadata, there is allowance for multiple plates. And there are even instances within AICS' data in which this is the case!1 But because wells (within Zeiss metadata, /ImageDocument/.../Information/.../Scene/Shape) are not linked to plates (/ImageDocment/.../Experiment/.../Template), either hierarchically or by reference, how are we supposed to connect which wells correspond to which plates?

1 In a random sample of ~1100 CZI images from various data collection eras/modalities I pulled from FMS on Feb. 4, 2022, nearly 200 of them had multiple plates in their metadata.