diff --git a/WellPlateReader/.gitignore b/WellPlateReader/.gitignore
index 0c22d640576a8026664191caddf409543a70bb20..6f248b177d760ff8c511b2cef7655e93e37c6358 100644
--- a/WellPlateReader/.gitignore
+++ b/WellPlateReader/.gitignore
@@ -3,4 +3,5 @@
 bin/
 build/
 .project
-.classpath
\ No newline at end of file
+.classpath
+/ecbuild/
diff --git a/WellPlateReader/build.gradle b/WellPlateReader/build.gradle
index 6b34e90cd8bad15f1eaa3ce9f69646e47ed56c56..9148fef2586a8ff85ad1fa6be6e7c226af697b4e 100644
--- a/WellPlateReader/build.gradle
+++ b/WellPlateReader/build.gradle
@@ -2,31 +2,31 @@ apply plugin: 'java-library'
 apply plugin: 'eclipse'
 
 version = '2.2.3'
-task wrapper(type: Wrapper) {
-	gradleVersion = '4.3'
-}
+
+println "ICY_HOME=${System.env.ICY_HOME}"
+println project.name + " " + version
 
 configurations {
 	extraLibs // configuration that holds jars to include in the jar
+	implementation.extendsFrom(extraLibs)
 }
 
 repositories {
 	jcenter()
 }
 
-println "ICY_HOME=${System.env.ICY_HOME}"
 dependencies {
-	configurations.implementation.extendsFrom(configurations.extraLibs)
 	// 1. External libraries
 	// 2. Icy libraries
-	implementation files("${System.env.ICY_HOME}/icy.jar") // Icy core
-	implementation files("${System.env.ICY_HOME}/plugins/adufour/ezplug/EzPlug.jar") // EzPlug
-	implementation files("${System.env.ICY_HOME}/plugins/adufour/protocols/Protocols.jar") // Protocols
-	implementation files("${System.env.ICY_HOME}/plugins/adufour/blocks/Blocks.jar") // Blocks
 	implementation files("${System.env.ICY_HOME}/lib/bioformats.jar") // Bioformats
 	implementation files("${System.env.ICY_HOME}/lib/flamingo.jar") // Flamingo
 	implementation files("${System.env.ICY_HOME}/lib/jai_core.jar") // JAI
 	implementation files("${System.env.ICY_HOME}/lib/jai_codec.jar") // JAI
+
+	implementation files("${System.env.ICY_HOME}/icy.jar") // Icy core
+	implementation files("${System.env.ICY_HOME}/plugins/adufour/ezplug/EzPlug.jar") // EzPlug
+	implementation files("${System.env.ICY_HOME}/plugins/adufour/protocols/Protocols.jar") // Protocols
+	implementation files("${System.env.ICY_HOME}/plugins/adufour/blocks/Blocks.jar") // Blocks
 	
 	// 3. Test libraries
 	testImplementation 'org.hamcrest:hamcrest-all:1.3'
@@ -35,13 +35,22 @@ dependencies {
 
 // Eclipse project creation
 eclipse {
-	classpath.downloadJavadoc = true
+	classpath {
+		defaultOutputDir = file("ecbuild")
+		file.whenMerged {
+      entries.each {
+        source ->
+          // This seems kludgy.  If the second test is omitted, it fails processing a 'Project Dependency' entry
+          if (source.kind == 'src' && source.toString().contains('output')) {
+            source.output = 'ecbuild'
+          }
+      }
+    }
+		downloadJavadoc = true
+  }
 
 	project {
-		buildCommand 'org.eclipse.buildship.core.gradleprojectbuilder'
-		
 		natures += ['icy.icy4eclipse.core.icynature']
-		natures += ['org.eclipse.buildship.core.gradleprojectnature']
 	}
 }
 
diff --git a/WellPlateReader/gradle/wrapper/gradle-wrapper.jar b/WellPlateReader/gradle/wrapper/gradle-wrapper.jar
deleted file mode 100644
index a5fe1cb94b9ee5ce57e6113458225bcba12d83e3..0000000000000000000000000000000000000000
Binary files a/WellPlateReader/gradle/wrapper/gradle-wrapper.jar and /dev/null differ
diff --git a/WellPlateReader/gradle/wrapper/gradle-wrapper.properties b/WellPlateReader/gradle/wrapper/gradle-wrapper.properties
deleted file mode 100644
index 92165eede80f1d94536089f202478c7adc36a7a3..0000000000000000000000000000000000000000
--- a/WellPlateReader/gradle/wrapper/gradle-wrapper.properties
+++ /dev/null
@@ -1,5 +0,0 @@
-distributionBase=GRADLE_USER_HOME
-distributionPath=wrapper/dists
-zipStoreBase=GRADLE_USER_HOME
-zipStorePath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-4.3-bin.zip
diff --git a/WellPlateReader/gradlew b/WellPlateReader/gradlew
deleted file mode 100644
index cccdd3d517fc5249beaefa600691cf150f2fa3e6..0000000000000000000000000000000000000000
--- a/WellPlateReader/gradlew
+++ /dev/null
@@ -1,172 +0,0 @@
-#!/usr/bin/env sh
-
-##############################################################################
-##
-##  Gradle start up script for UN*X
-##
-##############################################################################
-
-# Attempt to set APP_HOME
-# Resolve links: $0 may be a link
-PRG="$0"
-# Need this for relative symlinks.
-while [ -h "$PRG" ] ; do
-    ls=`ls -ld "$PRG"`
-    link=`expr "$ls" : '.*-> \(.*\)$'`
-    if expr "$link" : '/.*' > /dev/null; then
-        PRG="$link"
-    else
-        PRG=`dirname "$PRG"`"/$link"
-    fi
-done
-SAVED="`pwd`"
-cd "`dirname \"$PRG\"`/" >/dev/null
-APP_HOME="`pwd -P`"
-cd "$SAVED" >/dev/null
-
-APP_NAME="Gradle"
-APP_BASE_NAME=`basename "$0"`
-
-# Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
-DEFAULT_JVM_OPTS=""
-
-# Use the maximum available, or set MAX_FD != -1 to use that value.
-MAX_FD="maximum"
-
-warn () {
-    echo "$*"
-}
-
-die () {
-    echo
-    echo "$*"
-    echo
-    exit 1
-}
-
-# OS specific support (must be 'true' or 'false').
-cygwin=false
-msys=false
-darwin=false
-nonstop=false
-case "`uname`" in
-  CYGWIN* )
-    cygwin=true
-    ;;
-  Darwin* )
-    darwin=true
-    ;;
-  MINGW* )
-    msys=true
-    ;;
-  NONSTOP* )
-    nonstop=true
-    ;;
-esac
-
-CLASSPATH=$APP_HOME/gradle/wrapper/gradle-wrapper.jar
-
-# Determine the Java command to use to start the JVM.
-if [ -n "$JAVA_HOME" ] ; then
-    if [ -x "$JAVA_HOME/jre/sh/java" ] ; then
-        # IBM's JDK on AIX uses strange locations for the executables
-        JAVACMD="$JAVA_HOME/jre/sh/java"
-    else
-        JAVACMD="$JAVA_HOME/bin/java"
-    fi
-    if [ ! -x "$JAVACMD" ] ; then
-        die "ERROR: JAVA_HOME is set to an invalid directory: $JAVA_HOME
-
-Please set the JAVA_HOME variable in your environment to match the
-location of your Java installation."
-    fi
-else
-    JAVACMD="java"
-    which java >/dev/null 2>&1 || die "ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
-
-Please set the JAVA_HOME variable in your environment to match the
-location of your Java installation."
-fi
-
-# Increase the maximum file descriptors if we can.
-if [ "$cygwin" = "false" -a "$darwin" = "false" -a "$nonstop" = "false" ] ; then
-    MAX_FD_LIMIT=`ulimit -H -n`
-    if [ $? -eq 0 ] ; then
-        if [ "$MAX_FD" = "maximum" -o "$MAX_FD" = "max" ] ; then
-            MAX_FD="$MAX_FD_LIMIT"
-        fi
-        ulimit -n $MAX_FD
-        if [ $? -ne 0 ] ; then
-            warn "Could not set maximum file descriptor limit: $MAX_FD"
-        fi
-    else
-        warn "Could not query maximum file descriptor limit: $MAX_FD_LIMIT"
-    fi
-fi
-
-# For Darwin, add options to specify how the application appears in the dock
-if $darwin; then
-    GRADLE_OPTS="$GRADLE_OPTS \"-Xdock:name=$APP_NAME\" \"-Xdock:icon=$APP_HOME/media/gradle.icns\""
-fi
-
-# For Cygwin, switch paths to Windows format before running java
-if $cygwin ; then
-    APP_HOME=`cygpath --path --mixed "$APP_HOME"`
-    CLASSPATH=`cygpath --path --mixed "$CLASSPATH"`
-    JAVACMD=`cygpath --unix "$JAVACMD"`
-
-    # We build the pattern for arguments to be converted via cygpath
-    ROOTDIRSRAW=`find -L / -maxdepth 1 -mindepth 1 -type d 2>/dev/null`
-    SEP=""
-    for dir in $ROOTDIRSRAW ; do
-        ROOTDIRS="$ROOTDIRS$SEP$dir"
-        SEP="|"
-    done
-    OURCYGPATTERN="(^($ROOTDIRS))"
-    # Add a user-defined pattern to the cygpath arguments
-    if [ "$GRADLE_CYGPATTERN" != "" ] ; then
-        OURCYGPATTERN="$OURCYGPATTERN|($GRADLE_CYGPATTERN)"
-    fi
-    # Now convert the arguments - kludge to limit ourselves to /bin/sh
-    i=0
-    for arg in "$@" ; do
-        CHECK=`echo "$arg"|egrep -c "$OURCYGPATTERN" -`
-        CHECK2=`echo "$arg"|egrep -c "^-"`                                 ### Determine if an option
-
-        if [ $CHECK -ne 0 ] && [ $CHECK2 -eq 0 ] ; then                    ### Added a condition
-            eval `echo args$i`=`cygpath --path --ignore --mixed "$arg"`
-        else
-            eval `echo args$i`="\"$arg\""
-        fi
-        i=$((i+1))
-    done
-    case $i in
-        (0) set -- ;;
-        (1) set -- "$args0" ;;
-        (2) set -- "$args0" "$args1" ;;
-        (3) set -- "$args0" "$args1" "$args2" ;;
-        (4) set -- "$args0" "$args1" "$args2" "$args3" ;;
-        (5) set -- "$args0" "$args1" "$args2" "$args3" "$args4" ;;
-        (6) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" ;;
-        (7) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" ;;
-        (8) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" "$args7" ;;
-        (9) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" "$args7" "$args8" ;;
-    esac
-fi
-
-# Escape application args
-save () {
-    for i do printf %s\\n "$i" | sed "s/'/'\\\\''/g;1s/^/'/;\$s/\$/' \\\\/" ; done
-    echo " "
-}
-APP_ARGS=$(save "$@")
-
-# Collect all arguments for the java command, following the shell quoting and substitution rules
-eval set -- $DEFAULT_JVM_OPTS $JAVA_OPTS $GRADLE_OPTS "\"-Dorg.gradle.appname=$APP_BASE_NAME\"" -classpath "\"$CLASSPATH\"" org.gradle.wrapper.GradleWrapperMain "$APP_ARGS"
-
-# by default we should be in the correct project dir, but when run from Finder on Mac, the cwd is wrong
-if [ "$(uname)" = "Darwin" ] && [ "$HOME" = "$PWD" ]; then
-  cd "$(dirname "$0")"
-fi
-
-exec "$JAVACMD" "$@"
diff --git a/WellPlateReader/gradlew.bat b/WellPlateReader/gradlew.bat
deleted file mode 100644
index f9553162f122c71b34635112e717c3e733b5b212..0000000000000000000000000000000000000000
--- a/WellPlateReader/gradlew.bat
+++ /dev/null
@@ -1,84 +0,0 @@
-@if "%DEBUG%" == "" @echo off
-@rem ##########################################################################
-@rem
-@rem  Gradle startup script for Windows
-@rem
-@rem ##########################################################################
-
-@rem Set local scope for the variables with windows NT shell
-if "%OS%"=="Windows_NT" setlocal
-
-set DIRNAME=%~dp0
-if "%DIRNAME%" == "" set DIRNAME=.
-set APP_BASE_NAME=%~n0
-set APP_HOME=%DIRNAME%
-
-@rem Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
-set DEFAULT_JVM_OPTS=
-
-@rem Find java.exe
-if defined JAVA_HOME goto findJavaFromJavaHome
-
-set JAVA_EXE=java.exe
-%JAVA_EXE% -version >NUL 2>&1
-if "%ERRORLEVEL%" == "0" goto init
-
-echo.
-echo ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
-echo.
-echo Please set the JAVA_HOME variable in your environment to match the
-echo location of your Java installation.
-
-goto fail
-
-:findJavaFromJavaHome
-set JAVA_HOME=%JAVA_HOME:"=%
-set JAVA_EXE=%JAVA_HOME%/bin/java.exe
-
-if exist "%JAVA_EXE%" goto init
-
-echo.
-echo ERROR: JAVA_HOME is set to an invalid directory: %JAVA_HOME%
-echo.
-echo Please set the JAVA_HOME variable in your environment to match the
-echo location of your Java installation.
-
-goto fail
-
-:init
-@rem Get command-line arguments, handling Windows variants
-
-if not "%OS%" == "Windows_NT" goto win9xME_args
-
-:win9xME_args
-@rem Slurp the command line arguments.
-set CMD_LINE_ARGS=
-set _SKIP=2
-
-:win9xME_args_slurp
-if "x%~1" == "x" goto execute
-
-set CMD_LINE_ARGS=%*
-
-:execute
-@rem Setup the command line
-
-set CLASSPATH=%APP_HOME%\gradle\wrapper\gradle-wrapper.jar
-
-@rem Execute Gradle
-"%JAVA_EXE%" %DEFAULT_JVM_OPTS% %JAVA_OPTS% %GRADLE_OPTS% "-Dorg.gradle.appname=%APP_BASE_NAME%" -classpath "%CLASSPATH%" org.gradle.wrapper.GradleWrapperMain %CMD_LINE_ARGS%
-
-:end
-@rem End local scope for the variables with windows NT shell
-if "%ERRORLEVEL%"=="0" goto mainEnd
-
-:fail
-rem Set variable GRADLE_EXIT_CONSOLE if you need the _script_ return code instead of
-rem the _cmd.exe /c_ return code!
-if  not "" == "%GRADLE_EXIT_CONSOLE%" exit 1
-exit /b 1
-
-:mainEnd
-if "%OS%"=="Windows_NT" endlocal
-
-:omega
diff --git a/WellPlateReader/src/main/java/plugins/adufour/hcs/io/WellPlateReader_ScanR.java b/WellPlateReader/src/main/java/plugins/adufour/hcs/io/WellPlateReader_ScanR.java
index 706ec49d56a7ea5029206994cf94a5265094bd5e..a89722073dadb785b0f93b9f500683688dd17aa1 100644
--- a/WellPlateReader/src/main/java/plugins/adufour/hcs/io/WellPlateReader_ScanR.java
+++ b/WellPlateReader/src/main/java/plugins/adufour/hcs/io/WellPlateReader_ScanR.java
@@ -95,7 +95,7 @@ public class WellPlateReader_ScanR extends WellPlateReader {
 		// Step 1: read plate info from experiment_descriptor.xml
 		try {
 			Document xml = XMLUtil
-					.createDocument(FileUtils.readFileToString(new File(folder.getPath() + "/experiment_descriptor.xml")));
+					.createDocument(FileUtils.readFileToString(new File(folder.getPath() + "/experiment_descriptor.xml"), "UTF-8"));
 
 			Element rootCluster = XMLUtil.getElement(XMLUtil.getElement(xml, "LVData"), "Cluster");