ome · jburel · Dec 17, 2019 · Aug 21, 2019 · Aug 21, 2019 · Aug 21, 2019
diff --git a/README.md b/README.md
@@ -27,9 +27,9 @@
   automated by means of a Gradle (https://gradle.org/) build file.
   In order to perform a build, all you need is
   a JDK -- version 1.8 or later. From the command line, enter:
-  
+
      gradle build
-  
+
   This will compile, build, test and create a distribution bundle.
   To run OMERO.insight from the distribution bundle unzip
   `omero-insight.zip` then go to the `omero-insight` directory and from
@@ -48,81 +48,92 @@
   To run OMERO.importer, from the command line, enter:
 
      gradle runImporter
-     
+
   Packaging OMERO.insight
   -----------------------
-  
+
   OMERO.insight uses the Gradle [java-packager-plugin](https://github.com/ome/omero-javapackager-plugin)
-  and is capable of creating an installer for the platform the deployment task is run on. 
-  
+  and is capable of creating an installer for the platform the deployment task is run on.
+
   __Note, a Java runtime is included with the bundled installer. It is recommended to use
   [OpenJDK](https://openjdk.java.net) as the system's JRE to avoid potential licensing issues.__
-  
+
   In order to be able to successfully create an installer, a JDK with
   [`javapackager`](https://docs.oracle.com/javase/8/docs/technotes/tools/unix/javapackager.html) or
   an [OpenJFX SDK](https://gluonhq.com/products/javafx/) matching the version of the system JDK
   is required (particularly if you intend to build with JDK 11 or higher).
-  
+
   ### OSX
-  
+
   If you are using [Homebrew](https://brew.sh/), you can install, for example, [OpenJDK 8](https://www.azul.com/downloads/zulu/)
   which comes bundled with JavaFX.
   To install run:
 
       brew cask install zulu8
-      
+
   ### Windows
-  
+
   #### Scoop:
-  
+
       scoop bucket add java
-  
+
       scoop install zulufx8
-  
+
   #### Chocolatey:
-  
+
       choco install zulu8
 
-  #### Manually:     
-  
-  To set up a build environment with Windows without using a package manager such as [Scoop](https://scoop.sh) or 
-  [Chocolatey](https://chocolatey.org) perform the following: 
+  #### Manually:
+
+  To set up a build environment with Windows without using a package manager such as [Scoop](https://scoop.sh) or
+  [Chocolatey](https://chocolatey.org) perform the following:
 
   **JDK:**
-  
+
   1. Download [ojdkbuild](https://github.com/ojdkbuild/ojdkbuild/releases/download/1.8.0.191-1/java-1.8.0-openjdk-1.8.0.191-1.b12.ojdkbuild.windows.x86_64.msi).
   2. Run the installer.
-  3. Once at the _custom setup_ page of the setup select the _OpenJDK Runtime_ drop-down and install the _JAVA_HOME_ 
+  3. Once at the _custom setup_ page of the setup select the _OpenJDK Runtime_ drop-down and install the _JAVA_HOME_
      feature.
   4. Whilst on the _custom setup_ page, select to include the _OpenJFX Runtime_.
-  
+
   **Inno Setup (required to create .exe installer):**
-  
+
   1. Download and install [Inno Setup](http://www.jrsoftware.org/isdl.php).
   2. Add the Inno Setup install directory (default `C:\Program Files (x86)\Inno Setup 5`) to the PATH.
-  
+
   **WiX (required to build .msi installer):**
-  
+
   1. Download and install [WiX 3.0 or greater](http://wixtoolset.org/).
   2. Add WiX to the PATH.
- 
+
   ### Packaging
-  
+
   To run the application packager, from the command line enter:
-  
+
   **Windows**
-  
+
      gradle packageApplicationExe
-     
+
   **OSX**
-    
+
      gradle packageApplicationDmg
 
   Developing OMERO.insight
   ------------------------
 
   See https://docs.openmicroscopy.org/latest/omero/developers/index.html#insight.
 
+  OMERO.insight extension
+  -----------------------
+
+  1. To use the metadata extension [OMERO.mde](mde-extension.md),
+  set the following entry in [container.xml](src/config/container.xml) or in
+  [containerImporter.xml](src/config/containerImporter.xml) to `true`:
+  ```
+  <entry name="omero.client.import.mde.enabled" type="boolean">false</entry>
+  ```
+
+
   Licensing
   ---------
 

diff --git a/images/ArrayField.PNG b/images/ArrayField.PNG
diff --git a/images/AvailableInputFields.PNG b/images/AvailableInputFields.PNG
diff --git a/images/ComboBox1.PNG b/images/ComboBox1.PNG
diff --git a/images/ConfigurationPanel.PNG b/images/ConfigurationPanel.PNG
diff --git a/images/MDE1.PNG b/images/MDE1.PNG
diff --git a/images/MDE2.PNG b/images/MDE2.PNG
diff --git a/images/MDE3.PNG b/images/MDE3.PNG
diff --git a/images/TextArea.PNG b/images/TextArea.PNG
diff --git a/images/TextField.PNG b/images/TextField.PNG
diff --git a/mde-extension.md b/mde-extension.md
@@ -0,0 +1,163 @@
+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 be saved as key-value pairs.
+
+Workflow example
+----------------
+In this example we load data from an Olympus TIRF Setup. There is no information about
+the objective in the image container.
+
+<p align="center">
+  <img src="images/MDE1.PNG" width="550" >
+  </p>
+When you have specified your objectives for your Olympus TIRF Setup (see section Customize MDE), you can load these objectives by choosing object specification: Olympus TIRF. Now one of the objectives could be adopt from the list of available Elements or you can add manually the missing information.
+   <p align="center">
+  <img src="images/MDE2.PNG" width="550" >
+  </p>
+After the import you will find your annotation under General>Key-Value Pairs.
+   <p align="center">
+  <img src="images/MDE3.PNG" width="550" >
+  </p>
+
+Customize MDE
+-------------
+Save mdeConfiguration.xml in the directory &lt;user &gt;/omero/ to specify available objects and
+how the looks like. You can edit the mdeConfiguration.xml to configure your personal MDE.
+
+You can configure different setups for different object subsets and layouts.
+
+
+
+mdeConfiguration.xml: Element MDEObjects (in progress)
+------------------------------------------------------
+First you can specify which objects are general available: 
+```
+    <Definitions>
+	   <ObjectDef Type=<yourObjectName>>
+	   	...
+	   </ObjectDef>
+	   ...
+    </Definitions>
+```
+
+You can add a child 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
+sub-object of an OME:Channel object.
+```
+    <Parents Values="OME:Channel" />
+```
+Predefined are most of objects specified in the [ome schema](https://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome.html).
+
+You can specify different setup to use only subsets of objects or present different layout of defined objects:
+```
+	<Configurations>
+		<SetupConf Name=<yourSetupName>>
+			...
+		</SetupConf>
+		...
+	</Configurations>
+```
+For any new setup you added to the xml Configuration element you can specify which of objects
+are available for this setup by add an element
+```
+	<ObjectConf Type=<yourObjectName>>
+		...
+	</ObjectConf>
+``` 
+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:
+
+  <p align="center">
+  <img src="images/AvailableInputFields.PNG" width="550" >
+  </p>
+
+`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 MDEPredefinitions 
+-----------------------------------------------
+Here you can specify predefined values for your object for different setups.
+```
+<MDEPredefinitions>
+	<SetupPre Name=<yourSetupName>>
+		<ObjectPre Type=<yourObjectName>>
+			<TagData .../>
+			...
+		</ObjectPre>
+		...
+	</SetupPre>
+	....
+</MDEPredefinitions>
+```