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OMERO.mde

Extension of OMERO.importer to get an overview of available metadata provided by the selected image container and annotate images at import step by standardized key-value templates. Changes of metadata provided by image will save as key-value pairs.

Customize MDE

Save mdeConfiguration.xml in the directory /omero/ to specify available objects and how the looks like. You can use the mdeConfiguration.xml example file or create a new under OMERO.importer>MDE>Configuration...>Save To File.

The microscope element can be understood more generally as a template category.

mdeConfiguration.xml: Element MDEObjects (in progress)

Default:

<Microscope Name="Universal">

hold all available object specifications. Predefined are most of objects specified in the ome schema (https://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome.html).

You can add a child

<Object Type=<yourObjectName>> 

in this element to create a new custom object with key-values as TagData elements (see example object Available InputFields in mdeConfiguration.xml in this repository). Please specify an insertion point for every object by defining a parent object. E.g. object OME:Detector has the insertion OME:Channel - that means that OME:Detector can only be a subobject of an OME:Channel object.

<Parents Values="OME:Channel" />

For any new microscope you add to the xml MDEObject element you can specify which of these objects are available and how the looks like (overwrite TagData properties by defining TagDataProp to hide a TagData or change default unit).

TagData

There are different editor input field types for TagData:

TextField define like:

  <TagData DefaultValues="" 
            Name="Tag of Type TextField" 
            Type="TextField" 
            Unit=""
            Value="" 
            Visible="true" />

TextField with unit define like:

  <TagData DefaultValues="" 
            Name="Tag of Type TextField with unit" 
            Type="TextField" 
            Unit="nm"
            Value="" 
            Visible="true" />

TextArea define like:

  <TagData DefaultValues="" 
            Name="Tag of Type TextArea" 
            Type="TextArea"
            Unit="" 
            Value="" 
            Visible="true" />

ArrayField define like (for an array of 2 elements):

<TagData DefaultValues="2" 
          Name="Tag of Type ArrayField"
          Type="ArrayField" 
          Unit="" 
      Value="" 
          Visible="true" />

ArrayField with unit define like (for an array of 3 elements):

<TagData DefaultValues="3" 
          Name="Tag of Type ArrayField with unit"
          Type="ArrayField" 
          Unit="s" 
      Value="" 
          Visible="true" />

ComboBox define like:

<TagData DefaultValues="Value1,Value2,Value3"
	      Name="tag of Type ComboBox" 
          Type="ComboBox" 
          Unit="" 
          Value="Value1"
          Visible="true" />

TimeStamp define like:

<TagData DefaultValues="" 
          Name="Tag of Type TimeStamp"
          Type="TimeStamp" 
          Unit="" 
          Value="" 
          Visible="true" />

mdeConfiguration.xml: Element MDEHardwareConfiguration

List of available instruments (==objects) for specified microscope. E.g. LeicaLSM SP5 instruments:

OME:Dichroic,OME:Detector,OME:Laser,OME:Arc,OME:Objective,OME:Filter

Please specify new elements by using the `Configuration` dialog in MDE.

Licensing

This software is licensed under the terms of the GNU General Public License (GPL), the full text of which can be found in the top level LICENSE.txt. See https://www.openmicroscopy.org/licensing/ for further details.

Copyright

Copyright (C) 2006-2019 University Osnabrueck. All rights reserved.