Repository: mobie/mobie-viewer-fiji (language: python)

Issue:
manual transform moves segmentation sources when they are not selected
HI,

I want to register a fluorescence image with a segmentation in EM. When I enable manual transforms, the segmentation moves with the active source.

example data:
https://github.com/mobie/environmental-dinoflagellate-vCLEM

any FM channels and EM segmentation "Chloroplast"



Discussion / hints:

Fix patch:
diff --git a/install.sh b/install.sh
index 1ed4394fc..a4e987711 100755
--- a/install.sh
+++ b/install.sh
@@ -1,10 +1,10 @@
 #!/bin/bash
 # This script is shamelessly adapted from https://github.com/saalfeldlab/n5-utils, thanks @axtimwalde & co!
 
-VERSION="3.0.7-SNAPSHOT"
+VERSION=$1
 MEM=8 # FIXME
 
-mvn clean install -Denforcer.skip
+mvn clean install -Denforcer.skip -Dmaven.test.skip=true
 mvn -Dmdep.outputFile=cp.txt -Dmdep.includeScope=runtime dependency:build-classpath
 
 echo '#!/bin/bash' > mobie
@@ -22,7 +22,7 @@ echo ""
 echo "Installed MoBIE in current directory."
 echo "Type ./mobie to see all options"
 echo "Example call:"
-echo "./mobie -i \"./src/test/resources/golgi-intensities.tif\" -s \"./src/test/resources/golgi-cell-labels.tif\""
+echo "./mobie -i \"./src/test/resources/input/mlj-2d-tiff/image.tif\" -s \"./src/test/resources/input/mlj-2d-tiff/segmentation.tif\" -t \"./src/test/resources/input/mlj-2d-tiff/table-mlj.csv\""
 echo ""
 
 rm cp.txt
\ No newline at end of file
diff --git a/mobie b/mobie
index f41a4cead..63d4618f1 100755
--- a/mobie
+++ b/mobie
@@ -1,8 +1,8 @@
 #!/bin/bash
 
-JAR=$HOME/.m2/repository/org/embl/mobie/mobie-viewer-fiji/3.0.7-SNAPSHOT/mobie-viewer-fiji-3.0.7-SNAPSHOT.jar
+JAR=$HOME/.m2/repository/org/embl/mobie/mobie-viewer-fiji/3.0.10-SNAPSHOT/mobie-viewer-fiji-3.0.10-SNAPSHOT.jar
 java \
   -Xmx8g \
   -XX:+UseConcMarkSweepGC \
-  -cp $JAR:/Users/tischer/.m2/repository/net/imagej/imagej-legacy/0.39.2/imagej-legacy-0.39.2.jar:/Users/tischer/.m2/repository/io/scif/scifio/0.43.2/scifio-0.43.2.jar:/Users/tischer/.m2/repository/io/scif/scifio-jai-imageio/1.1.1/scifio-jai-imageio-1.1.1.jar:/Users/tischer/.m2/repository/net/imagej/ij1-patcher/1.2.2/ij1-patcher-1.2.2.jar:/Users/tischer/.m2/repository/net/imagej/imagej-common/0.35.0/imagej-common-0.35.0.jar:/Users/tischer/.m2/repository/edu/ucar/udunits/4.3.18/udunits-4.3.18.jar:/Users/tischer/.m2/repository/net/imagej/imagej-deprecated/0.1.5/imagej-deprecated-0.1.5.jar:/Users/tischer/.m2/repository/net/imglib2/imglib2-ij/2.0.0/imglib2-ij-2.0.0.jar:/Users/tischer/.m2/repository/net/imglib2/imglib2-realtransform/3.1.2/imglib2-realtransform-3.1.2.jar:/Users/tischer/.m2/repository/jitk/jitk-tps/3.0.3/jitk-tps-3.0.3.jar:/Users/tischer/.m2/repository/net/imglib2/imglib2-roi/0.12.1/imglib2-roi-0.12.1.jar:/Users/tischer/.m2/repository/org/scijava/scijava-common/2.89.0/scijava-common-2.89.0.jar:/Users/tischer/.m2/repository/org/scijava/parsington/3.0.0/parsington-3.0.0.jar:/Users/tischer/.m2/repository/org/bushe/eventbus/1.4/eventbus-1.4.jar:/Users/tischer/.m2/repository/org/scijava/scijava-search/1.0.0/scijava-search-1.0.0.jar:/Users/tischer/.m2/repository/org/ocpsoft/prettytime/prettytime/4.0.1.Final/prettytime-4.0.1.Final.jar:/Users/tischer/.m2/repository/org/scijava/scijava-table/0.7.0/scijava-table-0.7.0.jar:/Users/tischer/.m2/repository/org/scijava/scijava-ui-awt/0.1.7/scijava-ui-awt-0.1.7.jar:/Users/tischer/.m2/repository/org/scijava/scijava-ui-swing/0.17.1/scijava-ui-swing-0.17.1.jar:/Users/tischer/.m2/repository/org/scijava/scijava-plot/0.2.0/scijava-plot-0.2.0.jar:/Users/tischer/.m2/repository/org/scijava/swing-checkbox-tree/1.0.2/swing-checkbox-tree-1.0.2.jar:/Users/tischer/.m2/repository/org/jfree/jfreechart/1.5.3/jfreechart-1.5.3.jar:/Users/tischer/.m2/repository/org/jfree/jfreesvg/3.4.1/jfreesvg-3.4.1.jar:/Users/tischer/.m2/repository/com/github/sbridges/object-inspector/object-inspector/0.1/object-inspector-0.1.jar:/Users/tischer/.m2/repository/net/sourceforge/jdatepicker/jdatepicker/1.3.2/jdatepicker-1.3.2.jar:/Users/tischer/.m2/repository/org/scijava/script-editor/0.7.8/script-editor-0.7.8.jar:/Users/tischer/.m2/repository/org/scijava/scripting-java/0.4.1/scripting-java-0.4.1.jar:/Users/tischer/.m2/repository/org/scijava/minimaven/2.2.2/minimaven-2.2.2.jar:/Users/tischer/.m2/repository/org/scijava/batch-processor/0.4.2/batch-processor-0.4.2.jar:/Users/tischer/.m2/repository/com/fifesoft/autocomplete/3.1.5/autocomplete-3.1.5.jar:/Users/tischer/.m2/repository/com/fifesoft/languagesupport/3.1.4/languagesupport-3.1.4.jar:/Users/tischer/.m2/repository/org/mozilla/rhino/1.7.6/rhino-1.7.6.jar:/Users/tischer/.m2/repository/com/fifesoft/rsyntaxtextarea/3.1.6/rsyntaxtextarea-3.1.6.jar:/Users/tischer/.m2/repository/com/miglayout/miglayout-swing/5.2/miglayout-swing-5.2.jar:/Users/tischer/.m2/repository/com/miglayout/miglayout-core/5.2/miglayout-core-5.2.jar:/Users/tischer/.m2/repository/net/sf/trove4j/trove4j/3.0.3/trove4j-3.0.3.jar:/Users/tischer/.m2/repository/org/javassist/javassist/3.28.0-GA/javassist-3.28.0-GA.jar:/Users/tischer/.m2/repository/sc/fiji/bigdataviewer-playground/0.6.0/bigdataviewer-playground-0.6.0.jar:/Users/tischer/.m2/repository/org/scijava/ui-behaviour/2.0.7/ui-behaviour-2.0.7.jar:/Users/tischer/.m2/repository/org/yaml/snakeyaml/1.29/snakeyaml-1.29.jar:/Users/tischer/.m2/repository/ch/epfl/biop/bigdataviewer-selector/0.2.1/bigdataviewer-selector-0.2.1.jar:/Users/tischer/.m2/repository/sc/fiji/bigvolumeviewer/0.2.0/bigvolumeviewer-0.2.0.jar:/Users/tischer/.m2/repository/commons-lang/commons-lang/2.6/commons-lang-2.6.jar:/Users/tischer/.m2/repository/org/antlr/ST4/4.0.8/ST4-4.0.8.jar:/Users/tischer/.m2/repository/org/antlr/antlr-runtime/3.5.2/antlr-runtime-3.5.2.jar:/Users/tischer/.m2/repository/org/jogamp/gluegen/gluegen-rt-main/2.3.2/gluegen-rt-main-2.3.2.jar:/Users/tischer/.m2/repository/org/jogamp/gluegen/gluegen-rt/2.3.2/gluegen-rt-2.3.2-natives-android-aarch64.jar:/Users/tischer/.m2/repository/org/jogamp/gluegen/gluegen-rt/2.3.2/gluegen-rt-2.3.2-natives-android-armv6.jar:/Users/tischer/.m2/repository/org/jogamp/gluegen/gluegen-rt/2.3.2/gluegen-rt-2.3.2-natives-linux-amd64.jar:/Users/tischer/.m2/repository/org/jogamp/gluegen/gluegen-rt/2.3.2/gluegen-rt-2.3.2-natives-linux-armv6.jar:/Users/tischer/.m2/repository/org/jogamp/gluegen/gluegen-rt/2.3.2/gluegen-rt-2.3.2-natives-linux-armv6hf.jar:/Users/tischer/.m2/repository/org/jogamp/gluegen/gluegen-rt/2.3.2/gluegen-rt-2.3.2-natives-linux-i586.jar:/Users/tischer/.m2/repository/org/jogamp/gluegen/gluegen-rt/2.4.0-rc-20210111/gluegen-rt-2.4.0-rc-20210111-natives-macosx-universal.jar:/Users/tischer/.m2/repository/org/jogamp/gluegen/gluegen-rt/2.3.2/gluegen-rt-2.3.2-natives-solaris-amd64.jar:/Users/tischer/.m2/repository/org/jogamp/gluegen/gluegen-rt/2.3.2/gluegen-rt-2.3.2-natives-solaris-i586.jar:/Users/tischer/.m2/repository/org/jogamp/gluegen/gluegen-rt/2.3.2/gluegen-rt-2.3.2-natives-windows-amd64.jar:/Users/tischer/.m2/repository/org/jogamp/gluegen/gluegen-rt/2.3.2/gluegen-rt-2.3.2-natives-windows-i586.jar:/Users/tischer/.m2/repository/org/jogamp/jogl/jogl-all-main/2.3.2/jogl-all-main-2.3.2.jar:/Users/tischer/.m2/repository/org/jogamp/jogl/jogl-all/2.3.2/jogl-all-2.3.2-natives-android-aarch64.jar:/Users/tischer/.m2/repository/org/jogamp/jogl/jogl-all/2.3.2/jogl-all-2.3.2-natives-android-armv6.jar:/Users/tischer/.m2/repository/org/jogamp/jogl/jogl-all/2.3.2/jogl-all-2.3.2-natives-linux-amd64.jar:/Users/tischer/.m2/repository/org/jogamp/jogl/jogl-all/2.3.2/jogl-all-2.3.2-natives-linux-armv6.jar:/Users/tischer/.m2/repository/org/jogamp/jogl/jogl-all/2.3.2/jogl-all-2.3.2-natives-linux-armv6hf.jar:/Users/tischer/.m2/repository/org/jogamp/jogl/jogl-all/2.3.2/jogl-all-2.3.2-natives-linux-i586.jar:/Users/tischer/.m2/repository/org/jogamp/jogl/jogl-all/2.4.0-rc-20210111/jogl-all-2.4.0-rc-20210111-natives-macosx-universal.jar:/Users/tischer/.m2/repository/org/jogamp/jogl/jogl-all/2.3.2/jogl-all-2.3.2-natives-solaris-amd64.jar:/Users/tischer/.m2/repository/org/jogamp/jogl/jogl-all/2.3.2/jogl-all-2.3.2-natives-solaris-i586.jar:/Users/tischer/.m2/repository/org/jogamp/jogl/jogl-all/2.3.2/jogl-all-2.3.2-natives-windows-amd64.jar:/Users/tischer/.m2/repository/org/jogamp/jogl/jogl-all/2.3.2/jogl-all-2.3.2-natives-windows-i586.jar:/Users/tischer/.m2/repository/org/joml/joml/1.10.2/joml-1.10.2.jar:/Users/tischer/.m2/repository/sc/fiji/bigwarp_fiji/7.0.6/bigwarp_fiji-7.0.6.jar:/Users/tischer/.m2/repository/sc/fiji/fiji-lib/2.1.3/fiji-lib-2.1.3.jar:/Users/tischer/.m2/repository/mpicbg/mpicbg/1.4.2/mpicbg-1.4.2.jar:/Users/tischer/.m2/repository/org/janelia/saalfeldlab/n5-ij/3.2.2/n5-ij-3.2.2.jar:/Users/tischer/.m2/repository/org/janelia/saalfeldlab/n5-google-cloud/3.3.2/n5-google-cloud-3.3.2.jar:/Users/tischer/.m2/repository/org/janelia/saalfeldlab/n5-hdf5/1.4.2/n5-hdf5-1.4.2.jar:/Users/tischer/.m2/repository/com/google/cloud/google-cloud-resourcemanager/0.117.2-alpha/google-cloud-resourcemanager-0.117.2-alpha.jar:/Users/tischer/.m2/repository/com/google/api/api-common/1.8.1/api-common-1.8.1.jar:/Users/tischer/.m2/repository/org/threeten/threetenbp/1.4.1/threetenbp-1.4.1.jar:/Users/tischer/.m2/repository/com/google/apis/google-api-services-cloudresourcemanager/v1-rev20200210-1.30.9/google-api-services-cloudresourcemanager-v1-rev20200210-1.30.9.jar:/Users/tischer/.m2/repository/com/google/http-client/google-http-client-jackson2/1.40.0/google-http-client-jackson2-1.40.0.jar:/Users/tischer/.m2/repository/com/google/auth/google-auth-library-oauth2-http/0.20.0/google-auth-library-oauth2-http-0.20.0.jar:/Users/tischer/.m2/repository/com/google/auto/value/auto-value-annotations/1.7/auto-value-annotations-1.7.jar:/Users/tischer/.m2/repository/com/google/cloud/google-cloud-core/1.93.2/google-cloud-core-1.93.2.jar:/Users/tischer/.m2/repository/com/google/api/grpc/proto-google-common-protos/1.17.0/proto-google-common-protos-1.17.0.jar:/Users/tischer/.m2/repository/com/google/cloud/google-cloud-core-http/1.93.2/google-cloud-core-http-1.93.2.jar:/Users/tischer/.m2/repository/com/google/http-client/google-http-client-appengine/1.40.0/google-http-client-appengine-1.40.0.jar:/Users/tischer/.m2/repository/com/google/api/gax-httpjson/0.71.0/gax-httpjson-0.71.0.jar:/Users/tischer/.m2/repository/com/google/cloud/google-cloud-storage/1.108.0/google-cloud-storage-1.108.0.jar:/Users/tischer/.m2/repository/com/google/api-client/google-api-client/1.30.9/google-api-client-1.30.9.jar:/Users/tischer/.m2/repository/com/google/oauth-client/google-oauth-client/1.30.5/google-oauth-client-1.30.5.jar:/Users/tischer/.m2/repository/com/google/apis/google-api-services-storage/v1-rev20200326-1.30.9/google-api-services-storage-v1-rev20200326-1.30.9.jar:/Users/tischer/.m2/repository/com/google/auth/google-auth-library-credentials/0.20.0/google-auth-library-credentials-0.20.0.jar:/Users/tischer/.m2/repository/com/google/api/grpc/proto-google-iam-v1/0.13.0/proto-google-iam-v1-0.13.0.jar:/Users/tischer/.m2/repository/com/google/protobuf/protobuf-java-util/3.11.4/protobuf-java-util-3.11.4.jar:/Users/tischer/.m2/repository/com/google/api/gax/1.56.0/gax-1.56.0.jar:/Users/tischer/.m2/repository/ome/formats-api/6.10.1/formats-api-6.10.1.jar:/Users/tischer/.m2/repository/org/openmicroscopy/ome-codecs/0.3.2/ome-codecs-0.3.2.jar:/Users/tischer/.m2/repository/org/openmicroscopy/ome-jai/0.1.3/ome-jai-0.1.3.jar:/Users/tischer/.m2/repository/ome/formats-bsd/6.10.1/formats-bsd-6.10.1.jar:/Users/tischer/.m2/repository/org/openmicroscopy/specification/6.3.1/specification-6.3.1.jar:/Users/tischer/.m2/repository/ome/turbojpeg/6.10.1/turbojpeg-6.10.1.jar:/Users/tischer/.m2/repository/org/scijava/native-lib-loader/2.4.0/native-lib-loader-2.4.0.jar:/Users/tischer/.m2/repository/com/esotericsoftware/kryo/4.0.2/kryo-4.0.2.jar:/Users/tischer/.m2/repository/com/esotericsoftware/reflectasm/1.11.3/reflectasm-1.11.3.jar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al.jar:/Users/tischer/.m2/repository/io/netty/netty-common/4.1.45.Final/netty-common-4.1.45.Final.jar:/Users/tischer/.m2/repository/io/netty/netty-handler/4.1.45.Final/netty-handler-4.1.45.Final.jar:/Users/tischer/.m2/repository/io/netty/netty-resolver/4.1.45.Final/netty-resolver-4.1.45.Final.jar:/Users/tischer/.m2/repository/io/netty/netty-transport/4.1.45.Final/netty-transport-4.1.45.Final.jar:/Users/tischer/.m2/repository/org/apache/ant/ant/1.9.7/ant-1.9.7.jar:/Users/tischer/.m2/repository/org/apache/ant/ant-launcher/1.9.7/ant-launcher-1.9.7.jar:/Users/tischer/.m2/repository/org/scijava/scripting-renjin/0.2.3/scripting-renjin-0.2.3.jar:/Users/tischer/.m2/repository/org/renjin/renjin-script-engine/0.8.1906/renjin-script-engine-0.8.1906.jar:/Users/tischer/.m2/repository/org/renjin/renjin-core/0.8.1906/renjin-core-0.8.1906.jar:/Users/tischer/.m2/repository/org/apache/commons/commons-math/2.2/commons-math-2.2.jar:/Users/tischer/.m2/repository/org/renjin/gcc-runtime/0.8.1906/gcc-runtime-0.8.1906.jar:/Users/tischer/.m2/repository/org/netlib/netlib-java/0.9.3-renjin-patched-2/netlib-java-0.9.3-renjin-patched-2.jar:/Users/tischer/.m2/repository/org/netlib/lapack/0.8/lapack-0.8.jar:/Users/tischer/.m2/repository/org/netlib/f2jutil/0.8/f2jutil-0.8.jar:/Users/tischer/.m2/repository/org/netlib/xerbla/0.8/xerbla-0.8.jar:/Users/tischer/.m2/repository/org/netlib/blas/0.8/blas-0.8.jar:/Users/tischer/.m2/repository/org/apache/commons/commons-vfs2/2.0/commons-vfs2-2.0.jar:/Users/tischer/.m2/repository/org/apache/maven/scm/maven-scm-api/1.4/maven-scm-api-1.4.jar:/Users/tischer/.m2/repository/org/codehaus/plexus/plexus-utils/1.5.6/plexus-utils-1.5.6.jar:/Users/tischer/.m2/repository/org/apache/maven/scm/maven-scm-provider-svnexe/1.4/maven-scm-provider-svnexe-1.4.jar:/Users/tischer/.m2/repository/org/apache/maven/scm/maven-scm-provider-svn-commons/1.4/maven-scm-provider-svn-commons-1.4.jar:/Users/tischer/.m2/repository/regexp/regexp/1.3/regexp-1.3.jar:/Users/tischer/.m2/repository/edu/emory/mathcs/jtransforms/2.4/jtransforms-2.4.jar:/Users/tischer/.m2/repository/net/sf/jung/jung-api/2.0.1/jung-api-2.0.1.jar:/Users/tischer/.m2/repository/net/sourceforge/collections/collections-generic/4.01/collections-generic-4.01.jar:/Users/tischer/.m2/repository/net/sf/jung/jung-graph-impl/2.0.1/jung-graph-impl-2.0.1.jar:/Users/tischer/.m2/repository/com/sun/codemodel/codemodel/2.6/codemodel-2.6.jar:/Users/tischer/.m2/repository/org/renjin/stats/0.8.1906/stats-0.8.1906.jar:/Users/tischer/.m2/repository/org/renjin/renjin-appl/0.8.1906/renjin-appl-0.8.1906.jar:/Users/tischer/.m2/repository/org/renjin/renjin-gnur-runtime/0.8.1906/renjin-gnur-runtime-0.8.1906.jar:/Users/tischer/.m2/repository/org/renjin/methods/0.8.1906/methods-0.8.1906.jar:/Users/tischer/.m2/repository/org/renjin/datasets/0.8.1906/datasets-0.8.1906.jar:/Users/tischer/.m2/repository/org/renjin/utils/0.8.1906/utils-0.8.1906.jar:/Users/tischer/.m2/repository/org/renjin/grDevices/0.8.1906/grDevices-0.8.1906.jar:/Users/tischer/.m2/repository/org/renjin/graphics/0.8.1906/graphics-0.8.1906.jar:/Users/tischer/.m2/repository/org/scijava/scripting-scala/0.2.2/scripting-scala-0.2.2.jar:/Users/tischer/.m2/repository/org/scala-lang/scala-compiler/2.12.1/scala-compiler-2.12.1.jar:/Users/tischer/.m2/repository/org/scala-lang/scala-library/2.12.1/scala-library-2.12.1.jar:/Users/tischer/.m2/repository/org/scala-lang/scala-reflect/2.12.1/scala-reflect-2.12.1.jar:/Users/tischer/.m2/repository/org/scala-lang/modules/scala-xml_2.12/1.0.6/scala-xml_2.12-1.0.6.jar:/Users/tischer/.m2/repository/net/imagej/imagej-ui-swing/0.23.3/imagej-ui-swing-0.23.3.jar:/Users/tischer/.m2/repository/org/jhotdraw/jhotdraw/7.6.0/jhotdraw-7.6.0.jar:/Users/tischer/.m2/repository/net/imagej/imagej-ui-awt/0.3.1/imagej-ui-awt-0.3.1.jar:/Users/tischer/.m2/repository/org/scijava/scijava-io-http/0.2.1/scijava-io-http-0.2.1.jar:/Users/tischer/.m2/repository/com/squareup/okhttp3/okhttp/4.7.2/okhttp-4.7.2.jar:/Users/tischer/.m2/repository/com/squareup/okio/okio/2.6.0/okio-2.6.0.jar:/Users/tischer/.m2/repository/org/jetbrains/kotlin/kotlin-stdlib-common/1.4.21/kotlin-stdlib-common-1.4.21.jar:/Users/tischer/.m2/repository/org/jetbrains/kotlin/kotlin-stdlib/1.4.21/kotlin-stdlib-1.4.21.jar:/Users/tischer/.m2/repository/org/scijava/scijava-plugins-commands/0.2.3/scijava-plugins-commands-0.2.3.jar:/Users/tischer/.m2/repository/org/scijava/scijava-plugins-io-table/0.4.0/scijava-plugins-io-table-0.4.0.jar:/Users/tischer/.m2/repository/org/scijava/scijava-plugins-platforms/0.3.1/scijava-plugins-platforms-0.3.1.jar:/Users/tischer/.m2/repository/org/scijava/scijava-plugins-text-markdown/0.1.3/scijava-plugins-text-markdown-0.1.3.jar:/Users/tischer/.m2/repository/org/markdownj/markdownj/0.3.0-1.0.2b4/markdownj-0.3.0-1.0.2b4.jar:/Users/tischer/.m2/repository/org/scijava/scijava-plugins-text-plain/0.1.3/scijava-plugins-text-plain-0.1.3.jar:/Users/tischer/.m2/repository/org/junit/jupiter/junit-jupiter-api/5.4.2/junit-jupiter-api-5.4.2.jar:/Users/tischer/.m2/repository/org/apiguardian/apiguardian-api/1.0.0/apiguardian-api-1.0.0.jar:/Users/tischer/.m2/repository/org/opentest4j/opentest4j/1.1.1/opentest4j-1.1.1.jar:/Users/tischer/.m2/repository/org/junit/platform/junit-platform-commons/1.4.2/junit-platform-commons-1.4.2.jar:/Users/tischer/.m2/repository/org/junit/jupiter/junit-jupiter-engine/5.4.2/junit-jupiter-engine-5.4.2.jar:/Users/tischer/.m2/repository/org/junit/platform/junit-platform-engine/1.4.2/junit-platform-engine-1.4.2.jar:/Users/tischer/.m2/repository/com/github/erosb/everit-json-schema/1.14.1/everit-json-schema-1.14.1.jar:/Users/tischer/.m2/repository/org/json/json/20220320/json-20220320.jar:/Users/tischer/.m2/repository/commons-validator/commons-validator/1.7/commons-validator-1.7.jar:/Users/tischer/.m2/repository/commons-digester/commons-digester/2.1/commons-digester-2.1.jar:/Users/tischer/.m2/repository/com/damnhandy/handy-uri-templates/2.1.8/handy-uri-templates-2.1.8.jar:/Users/tischer/.m2/repository/joda-time/joda-time/2.10.6/joda-time-2.10.6.jar:/Users/tischer/.m2/repository/com/google/re2j/re2j/1.6/re2j-1.6.jar \
-  org.embl.mobie.cmd.MoBIECommandLineInterface "$@"
+  -cp $JAR:/Users/tischer/.m2/repository/net/imagej/imagej-legacy/0.39.2/imagej-legacy-0.39.2.jar:/Users/tischer/.m2/repository/io/scif/scifio/0.43.2/scifio-0.43.2.jar:/Users/tischer/.m2/repository/io/scif/scifio-jai-imageio/1.1.1/scifio-jai-imageio-1.1.1.jar:/Users/tischer/.m2/repository/net/imagej/ij1-patcher/1.2.2/ij1-patcher-1.2.2.jar:/Users/tischer/.m2/repository/net/imagej/imagej-common/0.35.0/imagej-common-0.35.0.jar:/Users/tischer/.m2/repository/edu/ucar/udunits/4.3.18/udunits-4.3.18.jar:/Users/tischer/.m2/repository/net/imagej/imagej-deprecated/0.1.5/imagej-deprecated-0.1.5.jar:/Users/tischer/.m2/repository/net/imglib2/imglib2-ij/2.0.0/imglib2-ij-2.0.0.jar:/Users/tischer/.m2/repository/net/imglib2/imglib2-realtransform/3.1.2/imglib2-realtransform-3.1.2.jar:/Users/tischer/.m2/repository/jitk/jitk-tps/3.0.3/jitk-tps-3.0.3.jar:/Users/tischer/.m2/repository/net/imglib2/imglib2-roi/0.12.1/imglib2-roi-0.12.1.jar:/Users/tischer/.m2/repository/org/scijava/scijava-common/2.89.0/scijava-common-2.89.0.jar:/Users/tischer/.m2/repository/org/scijava/parsington/3.0.0/parsington-3.0.0.jar:/Users/tischer/.m2/repository/org/bushe/eventbus/1.4/eventbus-1.4.jar:/Users/tischer/.m2/repository/org/scijava/scijava-search/1.0.0/scijava-search-1.0.0.jar:/Users/tischer/.m2/repository/org/ocpsoft/prettytime/prettytime/4.0.1.Final/prettytime-4.0.1.Final.jar:/Users/tischer/.m2/repository/org/scijava/scijava-table/0.7.0/scijava-table-0.7.0.jar:/Users/tischer/.m2/repository/org/scijava/scijava-ui-awt/0.1.7/scijava-ui-awt-0.1.7.jar:/Users/tischer/.m2/repository/org/scijava/scijava-ui-swing/0.17.1/scijava-ui-swing-0.17.1.jar:/Users/tischer/.m2/repository/org/scijava/scijava-plot/0.2.0/scijava-plot-0.2.0.jar:/Users/tischer/.m2/repository/org/scijava/swing-checkbox-tree/1.0.2/swing-checkbox-tree-1.0.2.jar:/Users/tischer/.m2/repository/org/jfree/jfreechart/1.5.3/jfreechart-1.5.3.jar:/Users/tischer/.m2/repository/org/jfree/jfreesvg/3.4.1/jfreesvg-3.4.1.jar:/Users/tischer/.m2/repository/com/github/sbridges/object-inspector/object-inspector/0.1/object-inspector-0.1.jar:/Users/tischer/.m2/repository/net/sourceforge/jdatepicker/jdatepicker/1.3.2/jdatepicker-1.3.2.jar:/Users/tischer/.m2/repository/org/scijava/script-editor/0.7.8/script-editor-0.7.8.jar:/Users/tischer/.m2/repository/org/scijava/scripting-java/0.4.1/scripting-java-0.4.1.jar:/Users/tischer/.m2/repository/org/scijava/minimaven/2.2.2/minimaven-2.2.2.jar:/Users/tischer/.m2/repository/org/scijava/batch-processor/0.4.2/batch-processor-0.4.2.jar:/Users/tischer/.m2/repository/com/fifesoft/autocomplete/3.1.5/autocomplete-3.1.5.jar:/Users/tischer/.m2/repository/com/fifesoft/languagesupport/3.1.4/languagesupport-3.1.4.jar:/Users/tischer/.m2/repository/org/mozilla/rhino/1.7.6/rhino-1.7.6.jar:/Users/tischer/.m2/repository/com/fifesoft/rsyntaxtextarea/3.1.6/rsyntaxtextarea-3.1.6.jar:/Users/tischer/.m2/repository/com/miglayout/miglayout-swing/5.2/miglayout-swing-5.2.jar:/Users/tischer/.m2/repository/com/miglayout/miglayout-core/5.2/miglayout-core-5.2.jar:/Users/tischer/.m2/repository/net/sf/trove4j/trove4j/3.0.3/trove4j-3.0.3.jar:/Users/tischer/.m2/repository/org/javassist/javassist/3.28.0-GA/javassist-3.28.0-GA.jar:/Users/tischer/.m2/repository/sc/fiji/bigdataviewer-playground/0.6.0/bigdataviewer-playground-0.6.0.jar:/Users/tischer/.m2/repository/org/scijava/ui-behaviour/2.0.7/ui-behaviour-2.0.7.jar:/Users/tischer/.m2/repository/org/yaml/snakeyaml/1.29/snakeyaml-1.29.jar:/Users/tischer/.m2/repository/ch/epfl/biop/bigdataviewer-selector/0.2.1/bigdataviewer-selector-0.2.1.jar:/Users/tischer/.m2/repository/sc/fiji/bigvolumeviewer/0.2.0/bigvolumeviewer-0.2.0.jar:/Users/tischer/.m2/repository/commons-lang/commons-lang/2.6/commons-lang-2.6.jar:/Users/tischer/.m2/repository/org/antlr/ST4/4.0.8/ST4-4.0.8.jar:/Users/tischer/.m2/repository/org/antlr/antlr-runtime/3.5.2/antlr-runtime-3.5.2.jar:/Users/tischer/.m2/repository/org/jogamp/gluegen/gluegen-rt-main/2.3.2/gluegen-rt-main-2.3.2.jar:/Users/tischer/.m2/repository/org/jogamp/gluegen/gluegen-rt/2.3.2/gluegen-rt-2.3.2-natives-android-aarch64.jar:/Users/tischer/.m2/repository/org/jogamp/gluegen/gluegen-rt/2.3.2/gluegen-rt-2.3.2-natives-android-armv6.jar:/Users/tischer/.m2/repository/org/jogamp/gluegen/gluegen-rt/2.3.2/gluegen-rt-2.3.2-natives-linux-amd64.jar:/Users/tischer/.m2/repository/org/jogamp/gluegen/gluegen-rt/2.3.2/gluegen-rt-2.3.2-natives-linux-armv6.jar:/Users/tischer/.m2/repository/org/jogamp/gluegen/gluegen-rt/2.3.2/gluegen-rt-2.3.2-natives-linux-armv6hf.jar:/Users/tischer/.m2/repository/org/jogamp/gluegen/gluegen-rt/2.3.2/gluegen-rt-2.3.2-natives-linux-i586.jar:/Users/tischer/.m2/repository/org/jogamp/gluegen/gluegen-rt/2.4.0-rc-20210111/gluegen-rt-2.4.0-rc-20210111-natives-macosx-universal.jar:/Users/tischer/.m2/repository/org/jogamp/gluegen/gluegen-rt/2.3.2/gluegen-rt-2.3.2-natives-solaris-amd64.jar:/Users/tischer/.m2/repository/org/jogamp/gluegen/gluegen-rt/2.3.2/gluegen-rt-2.3.2-natives-solaris-i586.jar:/Users/tischer/.m2/repository/org/j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on/4.1.45.Final/netty-common-4.1.45.Final.jar:/Users/tischer/.m2/repository/io/netty/netty-handler/4.1.45.Final/netty-handler-4.1.45.Final.jar:/Users/tischer/.m2/repository/io/netty/netty-resolver/4.1.45.Final/netty-resolver-4.1.45.Final.jar:/Users/tischer/.m2/repository/io/netty/netty-transport/4.1.45.Final/netty-transport-4.1.45.Final.jar:/Users/tischer/.m2/repository/org/apache/ant/ant/1.9.7/ant-1.9.7.jar:/Users/tischer/.m2/repository/org/apache/ant/ant-launcher/1.9.7/ant-launcher-1.9.7.jar:/Users/tischer/.m2/repository/org/scijava/scripting-renjin/0.2.3/scripting-renjin-0.2.3.jar:/Users/tischer/.m2/repository/org/renjin/renjin-script-engine/0.8.1906/renjin-script-engine-0.8.1906.jar:/Users/tischer/.m2/repository/org/renjin/renjin-core/0.8.1906/renjin-core-0.8.1906.jar:/Users/tischer/.m2/repository/org/apache/commons/commons-math/2.2/commons-math-2.2.jar:/Users/tischer/.m2/repository/org/renjin/gcc-runtime/0.8.1906/gcc-runtime-0.8.1906.jar:/Users/tischer/.m2/repository/org/netlib/netlib-java/0.9.3-renjin-patched-2/netlib-java-0.9.3-renjin-patched-2.jar:/Users/tischer/.m2/repository/org/netlib/lapack/0.8/lapack-0.8.jar:/Users/tischer/.m2/repository/org/netlib/f2jutil/0.8/f2jutil-0.8.jar:/Users/tischer/.m2/repository/org/netlib/xerbla/0.8/xerbla-0.8.jar:/Users/tischer/.m2/repository/org/netlib/blas/0.8/blas-0.8.jar:/Users/tischer/.m2/repository/org/apache/commons/commons-vfs2/2.0/commons-vfs2-2.0.jar:/Users/tischer/.m2/repository/org/apache/maven/scm/maven-scm-api/1.4/maven-scm-api-1.4.jar:/Users/tischer/.m2/repository/org/codehaus/plexus/plexus-utils/1.5.6/plexus-utils-1.5.6.jar:/Users/tischer/.m2/repository/org/apache/maven/scm/maven-scm-provider-svnexe/1.4/maven-scm-provider-svnexe-1.4.jar:/Users/tischer/.m2/repository/org/apache/maven/scm/maven-scm-provider-svn-commons/1.4/maven-scm-provider-svn-commons-1.4.jar:/Users/tischer/.m2/repository/regexp/regexp/1.3/regexp-1.3.jar:/Users/tischer/.m2/repository/edu/emory/mathcs/jtransforms/2.4/jtransforms-2.4.jar:/Users/tischer/.m2/repository/net/sf/jung/jung-api/2.0.1/jung-api-2.0.1.jar:/Users/tischer/.m2/repository/net/sourceforge/collections/collections-generic/4.01/collections-generic-4.01.jar:/Users/tischer/.m2/repository/net/sf/jung/jung-graph-impl/2.0.1/jung-graph-impl-2.0.1.jar:/Users/tischer/.m2/repository/com/sun/codemodel/codemodel/2.6/codemodel-2.6.jar:/Users/tischer/.m2/repository/org/renjin/stats/0.8.1906/stats-0.8.1906.jar:/Users/tischer/.m2/repository/org/renjin/renjin-appl/0.8.1906/renjin-appl-0.8.1906.jar:/Users/tischer/.m2/repository/org/renjin/renjin-gnur-runtime/0.8.1906/renjin-gnur-runtime-0.8.1906.jar:/Users/tischer/.m2/repository/org/renjin/methods/0.8.1906/methods-0.8.1906.jar:/Users/tischer/.m2/repository/org/renjin/datasets/0.8.1906/datasets-0.8.1906.jar:/Users/tischer/.m2/repository/org/renjin/utils/0.8.1906/utils-0.8.1906.jar:/Users/tischer/.m2/repository/org/renjin/grDevices/0.8.1906/grDevices-0.8.1906.jar:/Users/tischer/.m2/repository/org/renjin/graphics/0.8.1906/graphics-0.8.1906.jar:/Users/tischer/.m2/repository/org/scijava/scripting-scala/0.2.2/scripting-scala-0.2.2.jar:/Users/tischer/.m2/repository/org/scala-lang/scala-compiler/2.12.1/scala-compiler-2.12.1.jar:/Users/tischer/.m2/repository/org/scala-lang/scala-library/2.12.1/scala-library-2.12.1.jar:/Users/tischer/.m2/repository/org/scala-lang/scala-reflect/2.12.1/scala-reflect-2.12.1.jar:/Users/tischer/.m2/repository/org/scala-lang/modules/scala-xml_2.12/1.0.6/scala-xml_2.12-1.0.6.jar:/Users/tischer/.m2/repository/net/imagej/imagej-ui-swing/0.23.3/imagej-ui-swing-0.23.3.jar:/Users/tischer/.m2/repository/org/jhotdraw/jhotdraw/7.6.0/jhotdraw-7.6.0.jar:/Users/tischer/.m2/repository/net/imagej/imagej-ui-awt/0.3.1/imagej-ui-awt-0.3.1.jar:/Users/tischer/.m2/repository/org/scijava/scijava-io-http/0.2.1/scijava-io-http-0.2.1.jar:/Users/tischer/.m2/repository/com/squareup/okhttp3/okhttp/4.7.2/okhttp-4.7.2.jar:/Users/tischer/.m2/repository/com/squareup/okio/okio/2.6.0/okio-2.6.0.jar:/Users/tischer/.m2/repository/org/jetbrains/kotlin/kotlin-stdlib-common/1.4.21/kotlin-stdlib-common-1.4.21.jar:/Users/tischer/.m2/repository/org/jetbrains/kotlin/kotlin-stdlib/1.4.21/kotlin-stdlib-1.4.21.jar:/Users/tischer/.m2/repository/org/scijava/scijava-plugins-commands/0.2.3/scijava-plugins-commands-0.2.3.jar:/Users/tischer/.m2/repository/org/scijava/scijava-plugins-io-table/0.4.0/scijava-plugins-io-table-0.4.0.jar:/Users/tischer/.m2/repository/org/scijava/scijava-plugins-platforms/0.3.1/scijava-plugins-platforms-0.3.1.jar:/Users/tischer/.m2/repository/org/scijava/scijava-plugins-text-markdown/0.1.3/scijava-plugins-text-markdown-0.1.3.jar:/Users/tischer/.m2/repository/org/markdownj/markdownj/0.3.0-1.0.2b4/markdownj-0.3.0-1.0.2b4.jar:/Users/tischer/.m2/repository/org/scijava/scijava-plugins-text-plain/0.1.3/scijava-plugins-text-plain-0.1.3.jar:/Users/tischer/.m2/repository/org/junit/jupiter/junit-jupiter-api/5.4.2/junit-jupiter-api-5.4.2.jar:/Users/tischer/.m2/repository/org/apiguardian/apiguardian-api/1.0.0/apiguardian-api-1.0.0.jar:/Users/tischer/.m2/repository/org/opentest4j/opentest4j/1.1.1/opentest4j-1.1.1.jar:/Users/tischer/.m2/repository/org/junit/platform/junit-platform-commons/1.4.2/junit-platform-commons-1.4.2.jar:/Users/tischer/.m2/repository/org/junit/jupiter/junit-jupiter-engine/5.4.2/junit-jupiter-engine-5.4.2.jar:/Users/tischer/.m2/repository/org/junit/platform/junit-platform-engine/1.4.2/junit-platform-engine-1.4.2.jar:/Users/tischer/.m2/repository/com/github/erosb/everit-json-schema/1.14.1/everit-json-schema-1.14.1.jar:/Users/tischer/.m2/repository/org/json/json/20220320/json-20220320.jar:/Users/tischer/.m2/repository/commons-validator/commons-validator/1.7/commons-validator-1.7.jar:/Users/tischer/.m2/repository/commons-digester/commons-digester/2.1/commons-digester-2.1.jar:/Users/tischer/.m2/repository/com/damnhandy/handy-uri-templates/2.1.8/handy-uri-templates-2.1.8.jar:/Users/tischer/.m2/repository/joda-time/joda-time/2.10.6/joda-time-2.10.6.jar:/Users/tischer/.m2/repository/com/google/re2j/re2j/1.6/re2j-1.6.jar \
+  org.embl.mobie.cmd.MoBIECmd "$@"
diff --git a/pom.xml b/pom.xml
index 676f39e5f..0205370bc 100644
--- a/pom.xml
+++ b/pom.xml
@@ -9,9 +9,9 @@
 
     <groupId>org.embl.mobie</groupId>
     <artifactId>mobie-viewer-fiji</artifactId>
-    <version>3.0.10-SNAPSHOT</version>
+    <version>3.0.11-SNAPSHOT</version>
 
-    <!--  ../scijava-scripts/release-version.sh - -skip-version-check - -skip-license-update - -skip-branch-check  -->
+    <!--  ../scijava-scripts/release-version.sh - -skip-version-check - -skip-license-update -->
     <!-- mvn javadoc:javadoc -Denforcer.skip | grep error -->
     <!-- mvn clean compile -Dmaven.test.skip=true -->
     <!-- mvn clean install -Dscijava.app.directory=/Users/tischer/Desktop/Fiji/Fiji-MoBIE-beta.app -->
@@ -86,7 +86,7 @@
 
         <bigdataviewer-playground.version>0.6.0</bigdataviewer-playground.version>
         <imagej-utils.version>0.6.9</imagej-utils.version>
-        <mobie-io.version>2.0.10-SNAPSHOT</mobie-io.version>
+        <mobie-io.version>2.0.10</mobie-io.version>
 
         <!-- Version 1.6.0-scijava-3-SNAPSHOT of j3dcore addresses a minor issue
         https://github.com/fiji/3D_Viewer/issues/26
diff --git a/src/main/java/org/embl/mobie/cmd/MoBIECmd.java b/src/main/java/org/embl/mobie/cmd/MoBIECmd.java
index c3575bc4f..83a154da9 100644
--- a/src/main/java/org/embl/mobie/cmd/MoBIECmd.java
+++ b/src/main/java/org/embl/mobie/cmd/MoBIECmd.java
@@ -6,35 +6,52 @@
 import picocli.CommandLine;
 import picocli.CommandLine.Option;
 
+import java.io.IOException;
 import java.util.concurrent.Callable;
 
-
+@CommandLine.Command(name = "mobie", mixinStandardHelpOptions = true, version = "3.0.11",
+		description = "Visualise multi-modal big image data, see https://mobie.github.io/")
 public class MoBIECmd implements Callable<Void> {
 
 	// FIXME: https://github.com/mobie/mobie-viewer-fiji/issues/926
 
-	@Option(names = {"-i", "--image"}, required = false, description = "intensity image, e.g. -i /home/image.tif")
-	private String[] images = null;
+	@Option(names = {"-p", "--project"}, required = false, description = "project, e.g. -p \"https://github.com/mobie/platybrowser-datasets\"")
+	public String project = null;
+
+	@Option(names = {"-i", "--image"}, required = false, description = "intensity image, e.g. -i \"/home/image.tif\"")
+	public String[] images = null;
 
-	@Option(names = {"-s", "--segmentation"}, required = false, description = "segmentation label mask image, e.g. -s /home/labels.tif")
-	private String[] segmentations = null;
+	@Option(names = {"-s", "--segmentation"}, required = false, description = "segmentation label mask image, e.g. -s \"/home/labels.tif\"")
+	public String[] segmentations = null;
 
-	@Option(names = {"-t", "--table"}, required = false, description = "segments feature table, e.g. -t /home/features.csv")
-	private String[] tables = null;
+	@Option(names = {"-t", "--table"}, required = false, description = "segments feature table, e.g. -t \"/home/features.csv\"")
+	public String[] tables = null;
 
 	@Override
 	public Void call() throws Exception {
-		run( images, segmentations, tables );
-		return null;
-	}
 
-	public void run( String[] images, String[] segmentations, String[] tables ) throws SpimDataException
-	{
-		new ImageJ();// init SciJava services
-		new MoBIE( "", images, segmentations, tables );
+		// I don't understand whether I should use callable or runnable
+		// Runnable does not allow me to throw an Exception
+		// Callable wants to return something, but what?
+
+		if ( project != null )
+			new MoBIE( project );
+		else
+			new MoBIE( "", images, segmentations, tables );
+
+		return null;
 	}
 
 	public static final void main( final String... args ) {
-		new CommandLine( new MoBIECmd() ).execute( args );
+
+		// Show help if there are no arguments
+		if ( args == null || args.length == 0 )
+		{
+			final int exitCode = new CommandLine( new MoBIECmd() ).execute( "--help" );
+			System.exit( exitCode );
+		}
+
+		final int exitCode = new CommandLine( new MoBIECmd() ).execute( args );
+		System.exit( exitCode );
 	}
 }
\ No newline at end of file
diff --git a/src/main/java/org/embl/mobie/viewer/MoBIE.java b/src/main/java/org/embl/mobie/viewer/MoBIE.java
index 5363dc197..1e8bc5db8 100644
--- a/src/main/java/org/embl/mobie/viewer/MoBIE.java
+++ b/src/main/java/org/embl/mobie/viewer/MoBIE.java
@@ -38,11 +38,11 @@
 import mpicbg.spim.data.sequence.ImgLoader;
 import net.imglib2.Dimensions;
 import org.apache.commons.io.FilenameUtils;
+import org.embl.mobie.viewer.io.IOHelper;
 import org.embl.mobie.io.ImageDataFormat;
 import org.embl.mobie.io.SpimDataOpener;
 import org.embl.mobie.io.github.GitHubUtils;
 import org.embl.mobie.io.ome.zarr.loaders.N5OMEZarrImageLoader;
-import org.embl.mobie.io.util.IOHelper;
 import org.embl.mobie.io.util.S3Utils;
 import org.embl.mobie.viewer.annotation.AnnotatedSegment;
 import org.embl.mobie.viewer.annotation.AnnotatedSpot;
@@ -65,6 +65,7 @@
 import org.embl.mobie.viewer.serialize.SegmentationDataSource;
 import org.embl.mobie.viewer.serialize.SpotDataSource;
 import org.embl.mobie.viewer.serialize.View;
+import org.embl.mobie.viewer.serialize.display.Display;
 import org.embl.mobie.viewer.serialize.display.ImageDisplay;
 import org.embl.mobie.viewer.serialize.display.SegmentationDisplay;
 import org.embl.mobie.viewer.io.StorageLocation;
@@ -158,9 +159,9 @@ public MoBIE( String projectLocation, MoBIESettings settings ) throws IOExceptio
 		setS3Credentials( settings );
 		setProjectImageAndTableRootLocations();
 		registerProjectPlugins( settings.values.getProjectLocation() );
-		project = new ProjectJsonParser().parseProject( IOHelper.combinePath( projectRoot,  "project.json" ) );
+		project = new ProjectJsonParser().parseProject( org.embl.mobie.io.util.IOHelper.combinePath( projectRoot,  "project.json" ) );
 		if ( project.getName() == null )
-			project.setName( IOHelper.getFileName( projectLocation ) );
+			project.setName( org.embl.mobie.io.util.IOHelper.getFileName( projectLocation ) );
 		setImageDataFormats( projectLocation );
 		settings.addTableDataFormat( TableDataFormat.TSV );
 
@@ -168,10 +169,19 @@ public MoBIE( String projectLocation, MoBIESettings settings ) throws IOExceptio
 	}
 
 	// use this constructor from the command line
-	public MoBIE( String projectName, String[] imagePaths, String[] segmentationPaths, String[] tablePaths ) throws SpimDataException
+	public MoBIE( String projectName, String[] imagePaths, String[] segmentationPaths, String[] tablePaths ) throws SpimDataException, IOException
 	{
 		initProject( projectName );
 
+		if ( imagePaths[ 0 ].contains( "*" ) )
+			imagePaths = IOHelper.getPaths( imagePaths[ 0 ] );
+
+		if ( segmentationPaths[ 0 ].contains( "*" ) )
+			segmentationPaths = IOHelper.getPaths( segmentationPaths[ 0 ] );
+
+		if ( tablePaths[ 0 ].contains( "*" ) )
+			tablePaths = IOHelper.getPaths( tablePaths[ 0 ] );
+
 		// images
 		for ( String path : imagePaths )
 		{
@@ -203,7 +213,32 @@ public MoBIE( String projectName, String[] imagePaths, String[] segmentationPath
 			}
 		}
 
-		initUIandShowAllViews();
+		// combine image and segmentation views into segmented image views, if possible
+		final String[] views = dataset.views.keySet().toArray( new String[ 0 ] );
+		Arrays.sort( views );
+		String segmentedImageView = null;
+		for ( int viewIndex = 0; viewIndex < views.length; viewIndex+=2 )
+		{
+			final Display< ? > displayA = dataset.views.get( views[ viewIndex ] ).displays().get( 0 );
+			final Display< ? > displayB = dataset.views.get( views[ viewIndex + 1 ] ).displays().get( 0 );
+
+			if ( (     displayA instanceof ImageDisplay
+					&& displayB instanceof SegmentationDisplay )
+			     || (  displayB instanceof ImageDisplay
+					&& displayA instanceof SegmentationDisplay )
+			)
+			{
+				final String name = displayA.getName() + "-" + displayB.getName();
+				final ArrayList< Display< ? > > displays = new ArrayList<>();
+				displays.add( displayA );
+				displays.add( displayB );
+				final View combinedView = new View( displayA.getName(), "segmented image", displays, null, true );
+				segmentedImageView = name;
+				dataset.views.put( name, combinedView );
+			}
+		}
+
+		initUIandShowViews( segmentedImageView );
 	}
 
 	// use this constructor from the Fiji UI
@@ -227,14 +262,22 @@ public MoBIE( String projectName, AbstractSpimData< ? > image, AbstractSpimData<
 
 		addSpimDataImages( segmentation, true, tableStorageLocation, tableDataFormat );
 
-		initUIandShowAllViews();
+		initUIandShowViews( null );
 	}
 
-	private void initUIandShowAllViews()
+	private void initUIandShowViews( @Nullable String view )
 	{
 		initUI();
-		for ( String viewName : dataset.views.keySet() )
-			viewManager.show( getView( viewName, dataset ) );
+		if ( view == null )
+		{
+			// show all views
+			for ( String viewName : dataset.views.keySet() )
+				viewManager.show( getView( viewName, dataset ) );
+		}
+		else
+		{
+			viewManager.show( getView( view, dataset ) );
+		}
 	}
 
 	private void initProject( String projectName )
@@ -276,12 +319,12 @@ private void addSpimDataImages(
 			if ( isSegmentation )
 			{
 				dataSource = new SegmentationDataSource( imageName, imageDataFormat, storageLocation, tableDataFormat, tableStorageLocation );
-				addSegmentationDisplayToDataset( dataSource.getName(), spimData, setupIndex );
+				addSegmentationView( dataSource.getName(), spimData, setupIndex );
 			}
 			else
 			{
 				dataSource = new ImageDataSource( imageName, imageDataFormat, storageLocation );
-				addImageDisplayToDataset( spimData, setupIndex, imageName );
+				addImageView( spimData, setupIndex, imageName );
 			}
 
 			dataSource.preInit( true );
@@ -289,7 +332,7 @@ private void addSpimDataImages(
 		}
 	}
 
-	private void addImageDisplayToDataset( AbstractSpimData< ? > spimData, int imageIndex, String imageName )
+	private void addImageView( AbstractSpimData< ? > spimData, int imageIndex, String imageName )
 	{
 		final Displaysettings displaysettings = spimData.getSequenceDescription().getViewSetupsOrdered().get( imageIndex ).getAttribute( Displaysettings.class );
 
@@ -315,7 +358,7 @@ private String getImageName( String imagePath, int numImages, int imageIndex )
 		return imageName;
 	}
 
-	private void addSegmentationDisplayToDataset( String imageName, AbstractSpimData< ? > spimData, int setupId  )
+	private void addSegmentationView( String imageName, AbstractSpimData< ? > spimData, int setupId  )
 	{
 		final SegmentationDisplay< ? > display = new SegmentationDisplay<>( imageName, Arrays.asList( imageName ) );
 
@@ -415,27 +458,27 @@ private void setProjectImageAndTableRootLocations( )
 				settings.values.getProjectLocation(),
 				settings.values.getProjectBranch() );
 
-		if( ! IOHelper.exists( IOHelper.combinePath( projectRoot, "project.json" ) ) )
+		if( ! org.embl.mobie.io.util.IOHelper.exists( org.embl.mobie.io.util.IOHelper.combinePath( projectRoot, "project.json" ) ) )
 		{
-			projectRoot = IOHelper.combinePath( projectRoot, "data" );
+			projectRoot = org.embl.mobie.io.util.IOHelper.combinePath( projectRoot, "data" );
 		}
 
 		imageRoot = createPath(
 				settings.values.getImageDataLocation(),
 				settings.values.getImageDataBranch() );
 
-		if( ! IOHelper.exists( IOHelper.combinePath( imageRoot, "project.json" ) ) )
+		if( ! org.embl.mobie.io.util.IOHelper.exists( org.embl.mobie.io.util.IOHelper.combinePath( imageRoot, "project.json" ) ) )
 		{
-			imageRoot = IOHelper.combinePath( imageRoot, "data" );
+			imageRoot = org.embl.mobie.io.util.IOHelper.combinePath( imageRoot, "data" );
 		}
 
 		tableRoot = createPath(
 				settings.values.getTableDataLocation(),
 				settings.values.getTableDataBranch() );
 
-		if( ! IOHelper.exists( IOHelper.combinePath( tableRoot, "project.json" ) ) )
+		if( ! org.embl.mobie.io.util.IOHelper.exists( org.embl.mobie.io.util.IOHelper.combinePath( tableRoot, "project.json" ) ) )
 		{
-			tableRoot = IOHelper.combinePath( tableRoot, "data" );
+			tableRoot = org.embl.mobie.io.util.IOHelper.combinePath( tableRoot, "data" );
 		}
 	}
 
@@ -518,7 +561,7 @@ private String createPath( String rootLocation, String githubBranch, String... f
 		final ArrayList< String > strings = new ArrayList<>();
 		strings.add( rootLocation );
 		Collections.addAll( strings, files );
-		final String path = IOHelper.combinePath( strings.toArray( new String[0] ) );
+		final String path = org.embl.mobie.io.util.IOHelper.combinePath( strings.toArray( new String[0] ) );
 
 		return path;
 	}
@@ -653,7 +696,7 @@ public StorageLocation getTableLocation( Map< TableDataFormat, StorageLocation >
 		if ( storageLocation.relativePath != null )
 		{
 			storageLocation.defaultChunk = TableDataFormat.MOBIE_DEFAULT_CHUNK;
-			storageLocation.absolutePath = IOHelper.combinePath( tableRoot, currentDatasetName, storageLocation.relativePath );
+			storageLocation.absolutePath = org.embl.mobie.io.util.IOHelper.combinePath( tableRoot, currentDatasetName, storageLocation.relativePath );
 			return storageLocation;
 		}
 
@@ -662,7 +705,7 @@ public StorageLocation getTableLocation( Map< TableDataFormat, StorageLocation >
 
 	public String getDatasetPath( String... files )
 	{
-		final String datasetRoot = IOHelper.combinePath( projectRoot, getCurrentDatasetName() );
+		final String datasetRoot = org.embl.mobie.io.util.IOHelper.combinePath( projectRoot, getCurrentDatasetName() );
 		return createPath( datasetRoot, files );
 	}
 
@@ -670,7 +713,7 @@ private String createPath( String root, String[] files )
 	{
 		String location = root;
 		for ( String file : files )
-			location = IOHelper.combinePath( location, file );
+			location = org.embl.mobie.io.util.IOHelper.combinePath( location, file );
 		return location;
 	}
 
@@ -711,7 +754,7 @@ public synchronized String getImageLocation( ImageDataFormat imageDataFormat, St
 			case OmeZarr:
             	if ( storageLocation.absolutePath != null  )
 					return storageLocation.absolutePath;
-                return IOHelper.combinePath( imageRoot, getCurrentDatasetName(), storageLocation.relativePath );
+                return org.embl.mobie.io.util.IOHelper.combinePath( imageRoot, getCurrentDatasetName(), storageLocation.relativePath );
             case OpenOrganelleS3:
             case OmeZarrS3:
                 return storageLocation.s3Address;
diff --git a/src/main/java/org/embl/mobie/viewer/bdv/view/AnnotationSliceView.java b/src/main/java/org/embl/mobie/viewer/bdv/view/AnnotationSliceView.java
index b3d8563f9..9893e6124 100644
--- a/src/main/java/org/embl/mobie/viewer/bdv/view/AnnotationSliceView.java
+++ b/src/main/java/org/embl/mobie/viewer/bdv/view/AnnotationSliceView.java
@@ -28,6 +28,7 @@
  */
 package org.embl.mobie.viewer.bdv.view;
 
+import bdv.tools.transformation.TransformedSource;
 import bdv.util.BdvHandle;
 import bdv.viewer.Source;
 import bdv.viewer.SourceAndConverter;
@@ -103,6 +104,7 @@ private SourceAndConverter createSourceAndConverter( AbstractAnnotationDisplay<
 		final Source< AnnotationType< A > > source = image.getSourcePair().getSource();
 		final BoundarySource boundarySource = new BoundarySource( source, false, 0.0F, image.getMask() );
 		final Converter< AnnotationType< A >, ARGBType > annotationARGBConverter = new AnnotationARGBConverter<>( display.coloringModel );
+		final TransformedSource transformedSource = new TransformedSource( boundarySource );
 
 		// create volatile sac
 		//
@@ -112,15 +114,18 @@ private SourceAndConverter createSourceAndConverter( AbstractAnnotationDisplay<
 			final Source< ? extends Volatile< ? extends AnnotationType< ? > > > volatileSource = image.getSourcePair().getVolatileSource();
 			final VolatileBoundarySource volatileBoundarySource = new VolatileBoundarySource( volatileSource, false, 1.0F, image.getMask() );
 			final VolatileAnnotationARGBConverter volatileAnnotationConverter = new VolatileAnnotationARGBConverter( display.coloringModel );
-			SourceAndConverter volatileSourceAndConverter = new SourceAndConverter( volatileBoundarySource, volatileAnnotationConverter );
+			final TransformedSource volatileTransformedSource = new TransformedSource( volatileBoundarySource, transformedSource );
+			SourceAndConverter volatileSourceAndConverter = new SourceAndConverter( volatileTransformedSource, volatileAnnotationConverter );
 
 			// combine non-volatile and volatile sac
 			//
-			return new SourceAndConverter( boundarySource, annotationARGBConverter, volatileSourceAndConverter );
+			final SourceAndConverter combinedSAC = new SourceAndConverter( transformedSource, annotationARGBConverter, volatileSourceAndConverter );
+			return combinedSAC;
 		}
 
 		// only non-volatile sac
-		return new SourceAndConverter( boundarySource, annotationARGBConverter );
+		final SourceAndConverter sac = new SourceAndConverter( transformedSource, annotationARGBConverter );
+		return sac;
 	}
 
 	private void show( SourceAndConverter< ? > sourceAndConverter )
diff --git a/src/main/java/org/embl/mobie/viewer/command/ManualRegistrationCommand.java b/src/main/java/org/embl/mobie/viewer/command/ManualRegistrationCommand.java
index c923bb456..bafd3a1be 100644
--- a/src/main/java/org/embl/mobie/viewer/command/ManualRegistrationCommand.java
+++ b/src/main/java/org/embl/mobie/viewer/command/ManualRegistrationCommand.java
@@ -36,7 +36,6 @@
 @Plugin(type = BdvPlaygroundActionCommand.class, menuPath = CommandConstants.CONTEXT_MENU_ITEMS_ROOT + "Transform>Registration - Manual")
 public class ManualRegistrationCommand implements BdvPlaygroundActionCommand
 {
-
 	private AffineTransform3D originalFixedTransform;
 
 	@Override
diff --git a/src/main/java/org/embl/mobie/viewer/io/IOHelper.java b/src/main/java/org/embl/mobie/viewer/io/IOHelper.java
new file mode 100644
index 000000000..4b71dd537
--- /dev/null
+++ b/src/main/java/org/embl/mobie/viewer/io/IOHelper.java
@@ -0,0 +1,60 @@
+package org.embl.mobie.viewer.io;
+
+import java.io.File;
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Paths;
+import java.util.Arrays;
+import java.util.stream.Collectors;
+
+public class IOHelper
+{
+	// from https://stackoverflow.com/questions/28734455/java-converting-file-pattern-to-regular-expression-pattern
+	public static String wildcardToRegex(String wildcard){
+		StringBuffer s = new StringBuffer(wildcard.length());
+		s.append('^');
+		for (int i = 0, is = wildcard.length(); i < is; i++) {
+			char c = wildcard.charAt(i);
+			switch(c) {
+				case '*':
+					s.append(".*");
+					break;
+				case '?':
+					s.append(".");
+					break;
+				case '^': // escape character in cmd.exe
+					s.append("\\");
+					break;
+				// escape special regexp-characters
+				case '(': case ')': case '[': case ']': case '$':
+				case '.': case '{': case '}': case '|':
+				case '\\':
+					s.append("\\");
+					s.append(c);
+					break;
+				default:
+					s.append(c);
+					break;
+			}
+		}
+		s.append('$');
+		return(s.toString());
+	}
+
+	public static String[] getPaths( String imagePath ) throws IOException
+	{
+		final String regExPath = imagePath;
+
+		final String dir = new File( regExPath ).getParent();
+		String name = new File( regExPath ).getName();
+		final String regex = wildcardToRegex( name );
+
+		final String[] paths = Files.find( Paths.get( dir ), 999,
+				( path, basicFileAttribute ) -> basicFileAttribute.isRegularFile()
+						&& path.getFileName().toString().matches( regex ) ).map( path -> path.toString() ).collect( Collectors.toList() ).toArray( new String[ 0 ] );
+
+		Arrays.sort( paths );
+
+		return paths;
+	}
+}
diff --git a/src/main/java/org/embl/mobie/viewer/serialize/View.java b/src/main/java/org/embl/mobie/viewer/serialize/View.java
index 9b51ec340..535d5b228 100644
--- a/src/main/java/org/embl/mobie/viewer/serialize/View.java
+++ b/src/main/java/org/embl/mobie/viewer/serialize/View.java
@@ -77,7 +77,7 @@ public Map< String, Object > getSources()
 	{
 		final Map< String, Object > sources = new HashMap<>();
 
-		for ( Display< ? > display : getDisplays() )
+		for ( Display< ? > display : displays() )
 		{
 			for ( String source : display.getSources() )
 			{
@@ -127,7 +127,7 @@ public List< Transformation > getTransformations()
 			return sourceTransforms;
 	}
 
-	public List< Display< ? > > getDisplays()
+	public List< Display< ? > > displays()
 	{
 		if ( sourceDisplays == null )
 			return new ArrayList<>();
diff --git a/src/main/java/org/embl/mobie/viewer/view/ViewManager.java b/src/main/java/org/embl/mobie/viewer/view/ViewManager.java
index 7cd55a3d1..858a42f1d 100644
--- a/src/main/java/org/embl/mobie/viewer/view/ViewManager.java
+++ b/src/main/java/org/embl/mobie/viewer/view/ViewManager.java
@@ -273,7 +273,7 @@ public synchronized void show( View view )
 		initData( view );
 
 		// display the data
-		final List< Display< ? > > displays = view.getDisplays();
+		final List< Display< ? > > displays = view.displays();
 		for ( Display< ? > display : displays )
 			show( display );
 
@@ -459,7 +459,7 @@ else if ( transformation instanceof GridTransformation )
 		// instantiate {@code RegionDisplay}
 		// note that this could not be done already in MoBIE.initData()
 		// because we needed to wait until all images are present
-		for ( Display< ? > display : view.getDisplays() )
+		for ( Display< ? > display : view.displays() )
 		{
 			// https://github.com/mobie/mobie-viewer-fiji/issues/818
 			if ( display instanceof RegionDisplay )


Test patch:
diff --git a/src/test/java/org/embl/mobie/cmd/CommandLineMorphoLibJ2DTIFF.java b/src/test/java/org/embl/mobie/cmd/CommandLineMorphoLibJ2DTIFF.java
index 006297e6f..06d79f0d5 100644
--- a/src/test/java/org/embl/mobie/cmd/CommandLineMorphoLibJ2DTIFF.java
+++ b/src/test/java/org/embl/mobie/cmd/CommandLineMorphoLibJ2DTIFF.java
@@ -2,18 +2,19 @@
 
 import mpicbg.spim.data.SpimDataException;
 
+import java.io.IOException;
+
 class CommandLineMorphoLibJ2DTIFF
 {
 	public static final String ROOT = "/Users/tischer/Documents/mobie/";
 	public static final String DIR = "src/test/resources/input/mlj-2d-tiff/";
 
-	public static void main( String[] args ) throws SpimDataException
+	public static void main( String[] args ) throws Exception
 	{
-		final MoBIECmd commandLineInterface = new MoBIECmd();
-		commandLineInterface.run(
-				new String[]{ ROOT + DIR + "image.tif" },
-				new String[]{ ROOT + DIR + "segmentation.tif" },
-				new String[]{ ROOT + DIR + "table-mlj.csv" }
-				);
+		final MoBIECmd cmd = new MoBIECmd();
+		cmd.images = new String[]{ ROOT + DIR + "image.tif" };
+		cmd.segmentations = new String[]{ ROOT + DIR + "segmentation.tif" };
+		cmd.tables = new String[]{ ROOT + DIR + "table-mlj.csv" };
+		cmd.call();
 	}
 }
\ No newline at end of file
diff --git a/src/test/java/org/embl/mobie/cmd/CommandLineNoArgs.java b/src/test/java/org/embl/mobie/cmd/CommandLineNoArgs.java
new file mode 100644
index 000000000..634b4d21c
--- /dev/null
+++ b/src/test/java/org/embl/mobie/cmd/CommandLineNoArgs.java
@@ -0,0 +1,14 @@
+package org.embl.mobie.cmd;
+
+import mpicbg.spim.data.SpimDataException;
+
+import java.io.IOException;
+
+class CommandLineNoArgs
+{
+	public static void main( String[] args ) throws Exception
+	{
+		final MoBIECmd cmd = new MoBIECmd();
+		cmd.call();
+	}
+}
\ No newline at end of file
diff --git a/src/test/java/org/embl/mobie/cmd/CommandLineSkimage2DTIFF.java b/src/test/java/org/embl/mobie/cmd/CommandLineSkimage2DTIFF.java
index be539f7e4..911caf614 100644
--- a/src/test/java/org/embl/mobie/cmd/CommandLineSkimage2DTIFF.java
+++ b/src/test/java/org/embl/mobie/cmd/CommandLineSkimage2DTIFF.java
@@ -2,18 +2,19 @@
 
 import mpicbg.spim.data.SpimDataException;
 
+import java.io.IOException;
+
 class CommandLineSkimage2DTIFF
 {
 	public static final String ROOT = "/Users/tischer/Documents/mobie/";
 	public static final String DIR = "src/test/resources/input/skimage-2d-tiff/";
 
-	public static void main( String[] args ) throws SpimDataException
+	public static void main( String[] args ) throws Exception
 	{
-		final MoBIECmd commandLineInterface = new MoBIECmd();
-		commandLineInterface.run(
-				new String[]{ ROOT + DIR + "image.tif" },
-				new String[]{ ROOT + DIR + "segmentation.tif" },
-				new String[]{ ROOT + DIR + "table.tsv" }
-				);
+		final MoBIECmd cmd = new MoBIECmd();
+		cmd.images = new String[]{ ROOT + DIR + "image.tif" };
+		cmd.segmentations = new String[]{ ROOT + DIR + "segmentation.tif" };
+		cmd.tables = new String[]{ ROOT + DIR + "table.tsv" };
+		cmd.call();
 	}
 }
\ No newline at end of file
diff --git a/src/test/java/org/embl/mobie/cmd/CommandLineSkimage2DTZarr.java b/src/test/java/org/embl/mobie/cmd/CommandLineSkimage2DTZarr.java
index bb58be7b7..62285182c 100644
--- a/src/test/java/org/embl/mobie/cmd/CommandLineSkimage2DTZarr.java
+++ b/src/test/java/org/embl/mobie/cmd/CommandLineSkimage2DTZarr.java
@@ -2,18 +2,19 @@
 
 import mpicbg.spim.data.SpimDataException;
 
+import java.io.IOException;
+
 class CommandLineSkimage2DTZarr
 {
 	public static final String ROOT = "/Users/tischer/Documents/mobie/";
 	public static final String DIR = "src/test/resources/input/skimage-2dt-zarr/";
 
-	public static void main( String[] args ) throws SpimDataException
+	public static void main( String[] args ) throws Exception
 	{
-		final MoBIECmd commandLineInterface = new MoBIECmd();
-		commandLineInterface.run(
-				new String[]{ ROOT + DIR + "image.ome.zarr" },
-				new String[]{ ROOT + DIR + "segmentation.ome.zarr" },
-				new String[]{ ROOT + DIR + "table.tsv" }
-				);
+		final MoBIECmd cmd = new MoBIECmd();
+		cmd.images = new String[]{ ROOT + DIR + "image.ome.zarr" };
+		cmd.segmentations = new String[]{ ROOT + DIR + "segmentation.ome.zarr" };
+		cmd.tables = new String[]{ ROOT + DIR + "table.tsv" };
+		cmd.call();
 	}
 }
\ No newline at end of file
diff --git a/src/test/java/org/embl/mobie/cmd/CommandLineSkimage3DN5.java b/src/test/java/org/embl/mobie/cmd/CommandLineSkimage3DN5.java
index d46b8f541..c7d2d1278 100644
--- a/src/test/java/org/embl/mobie/cmd/CommandLineSkimage3DN5.java
+++ b/src/test/java/org/embl/mobie/cmd/CommandLineSkimage3DN5.java
@@ -2,18 +2,19 @@
 
 import mpicbg.spim.data.SpimDataException;
 
+import java.io.IOException;
+
 class CommandLineSkimage3DN5
 {
 	public static final String ROOT = "/Users/tischer/Documents/mobie/";
 	public static final String DIR = "src/test/resources/input/skimage-3d-n5/";
 
-	public static void main( String[] args ) throws SpimDataException
+	public static void main( String[] args ) throws Exception
 	{
-		final MoBIECmd commandLineInterface = new MoBIECmd();
-		commandLineInterface.run(
-				new String[]{ ROOT + DIR + "image.xml" },
-				new String[]{ ROOT + DIR + "segmentation.xml" },
-				new String[]{ ROOT + DIR + "table.tsv" }
-				);
+		final MoBIECmd cmd = new MoBIECmd();
+		cmd.images = new String[]{ ROOT + DIR + "image.xml" };
+		cmd.segmentations = new String[]{ ROOT + DIR + "segmentation.xml" };
+		cmd.tables = new String[]{ ROOT + DIR + "table.tsv" };
+		cmd.call();
 	}
 }
\ No newline at end of file
diff --git a/src/test/java/org/embl/mobie/cmd/CommandLineWildcardMovies.java b/src/test/java/org/embl/mobie/cmd/CommandLineWildcardMovies.java
new file mode 100644
index 000000000..50e1efa8f
--- /dev/null
+++ b/src/test/java/org/embl/mobie/cmd/CommandLineWildcardMovies.java
@@ -0,0 +1,19 @@
+package org.embl.mobie.cmd;
+
+import mpicbg.spim.data.SpimDataException;
+
+import java.io.IOException;
+
+class CommandLineWildcardMovies
+{
+	public static final String DIR = "/Users/tischer/Desktop/Kristina/2022_11_18/";
+
+	public static void main( String[] args ) throws Exception
+	{
+		final MoBIECmd cmd = new MoBIECmd();
+		cmd.images = new String[]{ DIR + "*-pro.tif" };
+		cmd.segmentations = new String[]{ DIR + "*-seg.tif" };
+		cmd.tables = new String[]{ DIR + "*.csv" };
+		cmd.call();
+	}
+}
\ No newline at end of file
diff --git a/src/test/java/projects/OpenRemoteDynoflagellate.java b/src/test/java/projects/OpenRemoteDynoflagellate.java
new file mode 100644
index 000000000..9746a88d3
--- /dev/null
+++ b/src/test/java/projects/OpenRemoteDynoflagellate.java
@@ -0,0 +1,45 @@
+/*-
+ * #%L
+ * Fiji viewer for MoBIE projects
+ * %%
+ * Copyright (C) 2018 - 2022 EMBL
+ * %%
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ * 
+ * 1. Redistributions of source code must retain the above copyright notice,
+ *    this list of conditions and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above copyright notice,
+ *    this list of conditions and the following disclaimer in the documentation
+ *    and/or other materials provided with the distribution.
+ * 
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+ * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
+ * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+ * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+ * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ * POSSIBILITY OF SUCH DAMAGE.
+ * #L%
+ */
+package projects;
+
+import net.imagej.ImageJ;
+import org.embl.mobie.viewer.MoBIE;
+import org.embl.mobie.viewer.MoBIESettings;
+
+import java.io.IOException;
+
+public class OpenRemoteDynoflagellate
+{
+	public static void main( String[] args ) throws IOException
+	{
+		final ImageJ imageJ = new ImageJ();
+		imageJ.ui().showUI();
+		new MoBIE( "https://github.com/mobie/environmental-dinoflagellate-vCLEM" );
+	}
+}
diff --git a/src/test/java/projects/OpenRemoteMalariaWithCredentials.java b/src/test/java/projects/OpenRemoteMalariaWithCredentials.java
new file mode 100644
index 000000000..c4c76c29d
--- /dev/null
+++ b/src/test/java/projects/OpenRemoteMalariaWithCredentials.java
@@ -0,0 +1,52 @@
+/*-
+ * #%L
+ * Fiji viewer for MoBIE projects
+ * %%
+ * Copyright (C) 2018 - 2022 EMBL
+ * %%
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ * 
+ * 1. Redistributions of source code must retain the above copyright notice,
+ *    this list of conditions and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above copyright notice,
+ *    this list of conditions and the following disclaimer in the documentation
+ *    and/or other materials provided with the distribution.
+ * 
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+ * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
+ * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+ * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+ * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ * POSSIBILITY OF SUCH DAMAGE.
+ * #L%
+ */
+package projects;
+
+import net.imagej.ImageJ;
+import org.embl.mobie.io.ImageDataFormat;
+import org.embl.mobie.viewer.MoBIE;
+import org.embl.mobie.viewer.MoBIESettings;
+
+import java.io.IOException;
+
+public class OpenRemoteMalariaWithCredentials
+{
+	public static void main( String[] args )
+	{
+		final ImageJ imageJ = new ImageJ();
+		imageJ.ui().showUI();
+
+		try {
+			new MoBIE("https://s3.embl.de/plasmodium-oocysts/mobie",
+					MoBIESettings.settings().s3AccessAndSecretKey( new String[]{ "DstL6Ju", "r4bqZzZsyJde9"} ) );
+		} catch (IOException e) {
+			e.printStackTrace();
+		}
+	}
+}
diff --git a/src/test/java/projects/OpenRemotePlatynereis.java b/src/test/java/projects/OpenRemotePlatynereis.java
index e3350c2ac..500b2af5f 100644
--- a/src/test/java/projects/OpenRemotePlatynereis.java
+++ b/src/test/java/projects/OpenRemotePlatynereis.java
@@ -41,6 +41,6 @@ public static void main( String[] args ) throws IOException
 		imageJ.ui().showUI();
 
 		final MoBIE moBIE = new MoBIE( "https://github.com/platybrowser/platybrowser");
-		moBIE.getViewManager().show( "cells" );
+		//moBIE.getViewManager().show( "cells" );
 	}
 }
diff --git a/src/test/java/users/kristina/CommandLineFlatwormKristina.java b/src/test/java/users/kristina/CommandLineFlatwormKristina.java
index 370dc38df..9ccc5b708 100644
--- a/src/test/java/users/kristina/CommandLineFlatwormKristina.java
+++ b/src/test/java/users/kristina/CommandLineFlatwormKristina.java
@@ -3,18 +3,18 @@
 import mpicbg.spim.data.SpimDataException;
 import org.embl.mobie.cmd.MoBIECmd;
 
+import java.io.IOException;
+
 class CommandLineFlatwormKristina
 {
-	public static final String ROOT = "/Users/tischer/Desktop/Kristina/output/";
-	public static final String DATASET = "large-worm";
+	public static final String DIR = "/Users/tischer/Desktop/Kristina/2022_11_18/";
 
-	public static void main( String[] args ) throws SpimDataException
+	public static void main( String[] args ) throws Exception
 	{
-		final MoBIECmd commandLineInterface = new MoBIECmd();
-		commandLineInterface.run(
-				new String[]{ ROOT + DATASET + "-pro.tif" },
-				new String[]{ ROOT + DATASET + "-seg.tif" },
-				new String[]{ ROOT + DATASET + ".csv" }
-				);
+		final MoBIECmd cmd = new MoBIECmd();
+		cmd.images = new String[]{ DIR + "*-pro.tif" };
+		cmd.segmentations = new String[]{ DIR + "*-seg.tif" };
+		cmd.tables = new String[]{ DIR + "*.csv" };
+		cmd.call();
 	}
 }
\ No newline at end of file
diff --git a/src/test/resources/input/mlj-2d-tiff/.image.tif.bfmemo b/src/test/resources/input/mlj-2d-tiff/.image.tif.bfmemo
new file mode 100644
index 000000000..dfa01f856
Binary files /dev/null and b/src/test/resources/input/mlj-2d-tiff/.image.tif.bfmemo differ
diff --git a/src/test/resources/input/mlj-2d-tiff/.segmentation.tif.bfmemo b/src/test/resources/input/mlj-2d-tiff/.segmentation.tif.bfmemo
new file mode 100644
index 000000000..e2f97f441
Binary files /dev/null and b/src/test/resources/input/mlj-2d-tiff/.segmentation.tif.bfmemo differ