Closed erjel closed 6 years ago
Hi @erjel,
sorry to hear about these issues. I agree that the reported version number is suspicious. To help troubleshooting this issue, could you send us the content of
>> javaclasspath
in order to confirm there is nothing in the static of the dynamic Java class path that would shadow the content of bioformats_package
you downloaded?
Hi @sbesson ,
>> javaclasspath
STATIC JAVA PATH
C:\Micro-Manager-2.0beta\plugins\Micro-Manager\guava-17.0.jar
C:\Program Files\MATLAB\R2017b\java\patch
C:\Program Files\MATLAB\R2017b\java\jarext\ant.jar
C:\Program Files\MATLAB\R2017b\java\jarext\ant-launcher.jar
C:\Program Files\MATLAB\R2017b\java\jarext\antlr.jar
C:\Program Files\MATLAB\R2017b\java\jarext\felix.jar
C:\Program Files\MATLAB\R2017b\java\jarext\scr.jar
C:\Program Files\MATLAB\R2017b\java\jarext\axis2\activation.jar
C:\Program Files\MATLAB\R2017b\java\jarext\axis2\axiom-api.jar
C:\Program Files\MATLAB\R2017b\java\jarext\axis2\axiom-impl.jar
C:\Program Files\MATLAB\R2017b\java\jarext\axis2\axis2-adb.jar
C:\Program Files\MATLAB\R2017b\java\jarext\axis2\axis2-kernel.jar
C:\Program Files\MATLAB\R2017b\java\jarext\axis2\axis2-transport-http.jar
C:\Program Files\MATLAB\R2017b\java\jarext\axis2\axis2-transport-local.jar
C:\Program Files\MATLAB\R2017b\java\jarext\axis2\commons-httpclient.jar
C:\Program Files\MATLAB\R2017b\java\jarext\axis2\geronimo-stax-api.jar
C:\Program Files\MATLAB\R2017b\java\jarext\axis2\httpcore.jar
C:\Program Files\MATLAB\R2017b\java\jarext\axis2\mail.jar
C:\Program Files\MATLAB\R2017b\java\jarext\axis2\neethi.jar
C:\Program Files\MATLAB\R2017b\java\jarext\axis2\wsdl4j.jar
C:\Program Files\MATLAB\R2017b\java\jarext\axis2\wstx-asl.jar
C:\Program Files\MATLAB\R2017b\java\jarext\axis2\XmlSchema.jar
C:\Program Files\MATLAB\R2017b\java\jarext\batik-anim.jar
C:\Program Files\MATLAB\R2017b\java\jarext\batik-extension.jar
C:\Program Files\MATLAB\R2017b\java\jarext\batik-dom.jar
C:\Program Files\MATLAB\R2017b\java\jarext\batik-transcoder.jar
C:\Program Files\MATLAB\R2017b\java\jarext\batik-awt-util.jar
C:\Program Files\MATLAB\R2017b\java\jarext\batik-bridge.jar
C:\Program Files\MATLAB\R2017b\java\jarext\batik-gvt.jar
C:\Program Files\MATLAB\R2017b\java\jarext\batik-css.jar
C:\Program Files\MATLAB\R2017b\java\jarext\batik-parser.jar
C:\Program Files\MATLAB\R2017b\java\jarext\batik-ext.jar
C:\Program Files\MATLAB\R2017b\java\jarext\batik-gui-util.jar
C:\Program Files\MATLAB\R2017b\java\jarext\batik-svggen.jar
C:\Program Files\MATLAB\R2017b\java\jarext\batik-codec.jar
C:\Program Files\MATLAB\R2017b\java\jarext\batik-svg-dom.jar
C:\Program Files\MATLAB\R2017b\java\jarext\batik-script.jar
C:\Program Files\MATLAB\R2017b\java\jarext\batik-util.jar
C:\Program Files\MATLAB\R2017b\java\jarext\batik-swing.jar
C:\Program Files\MATLAB\R2017b\java\jarext\batik-xml.jar
C:\Program Files\MATLAB\R2017b\java\jarext\bluecove-emu.jar
C:\Program Files\MATLAB\R2017b\java\jarext\bluecove.jar
C:\Program Files\MATLAB\R2017b\java\jarext\commons-cli.jar
C:\Program Files\MATLAB\R2017b\java\jarext\commons-codec.jar
C:\Program Files\MATLAB\R2017b\java\jarext\commons-collections-generic.jar
C:\Program Files\MATLAB\R2017b\java\jarext\commons-collections.jar
C:\Program Files\MATLAB\R2017b\java\jarext\commons-compress.jar
C:\Program Files\MATLAB\R2017b\java\jarext\commons-io.jar
C:\Program Files\MATLAB\R2017b\java\jarext\commons-lang.jar
C:\Program Files\MATLAB\R2017b\java\jarext\commons-logging.jar
C:\Program Files\MATLAB\R2017b\java\jarext\commons-net.jar
C:\Program Files\MATLAB\R2017b\java\jarext\dom4j.jar
C:\Program Files\MATLAB\R2017b\java\jarext\fop-pdf-images.jar
C:\Program Files\MATLAB\R2017b\java\jarext\fop.jar
C:\Program Files\MATLAB\R2017b\java\jarext\avalon-framework-api.jar
C:\Program Files\MATLAB\R2017b\java\jarext\avalon-framework-impl.jar
C:\Program Files\MATLAB\R2017b\java\jarext\foxtrot.jar
C:\Program Files\MATLAB\R2017b\java\jarext\geotools\geoapi-nogenerics.jar
C:\Program Files\MATLAB\R2017b\java\jarext\geotools\gt2-api.jar
C:\Program Files\MATLAB\R2017b\java\jarext\geotools\gt2-coverage.jar
C:\Program Files\MATLAB\R2017b\java\jarext\geotools\gt2-main.jar
C:\Program Files\MATLAB\R2017b\java\jarext\geotools\gt2-referencing.jar
C:\Program Files\MATLAB\R2017b\java\jarext\geotools\gt2-referencing3D.jar
C:\Program Files\MATLAB\R2017b\java\jarext\geotools\gt2-wms.jar
C:\Program Files\MATLAB\R2017b\java\jarext\geotools\jts.jar
C:\Program Files\MATLAB\R2017b\java\jarext\glazedlists_java15.jar
C:\Program Files\MATLAB\R2017b\java\jarext\google-collect.jar
C:\Program Files\MATLAB\R2017b\java\jarext\gson.jar
C:\Program Files\MATLAB\R2017b\java\jarext\guice\aopalliance.jar
C:\Program Files\MATLAB\R2017b\java\jarext\guice\guice.jar
C:\Program Files\MATLAB\R2017b\java\jarext\guice\guice-assistedinject.jar
C:\Program Files\MATLAB\R2017b\java\jarext\guice\javax.inject.jar
C:\Program Files\MATLAB\R2017b\java\jarext\distcomp\h2mig_pagestore_addon.jar
C:\Program Files\MATLAB\R2017b\java\jarext\distcomp\h2.jar
C:\Program Files\MATLAB\R2017b\java\jarext\ice\ice.jar
C:\Program Files\MATLAB\R2017b\java\jarext\ice\ib6core.jar
C:\Program Files\MATLAB\R2017b\java\jarext\ice\ib6extra.jar
C:\Program Files\MATLAB\R2017b\java\jarext\ice\ib6http.jar
C:\Program Files\MATLAB\R2017b\java\jarext\ice\ib6https.jar
C:\Program Files\MATLAB\R2017b\java\jarext\ice\ib6js.jar
C:\Program Files\MATLAB\R2017b\java\jarext\ice\ib6swing.jar
C:\Program Files\MATLAB\R2017b\java\jarext\ice\ib6util.jar
C:\Program Files\MATLAB\R2017b\java\jarext\ice\ib6xalan.jar
C:\Program Files\MATLAB\R2017b\java\jarext\ice\icessl.jar
C:\Program Files\MATLAB\R2017b\java\jarext\jackson\jackson-annotations.jar
C:\Program Files\MATLAB\R2017b\java\jarext\jackson\jackson-core.jar
C:\Program Files\MATLAB\R2017b\java\jarext\jackson\jackson-databind.jar
C:\Program Files\MATLAB\R2017b\java\jarext\jackson\jackson-jaxrs-base.jar
C:\Program Files\MATLAB\R2017b\java\jarext\jackson\jackson-jaxrs-json-provider.jar
C:\Program Files\MATLAB\R2017b\java\jarext\jackson\jackson-module-jaxb-annotations.jar
C:\Program Files\MATLAB\R2017b\java\jarext\access-bridge.jar
C:\Program Files\MATLAB\R2017b\java\jarext\jaccess-1_4.jar
C:\Program Files\MATLAB\R2017b\java\jarext\jaxen.jar
C:\Program Files\MATLAB\R2017b\java\jarext\jdom.jar
C:\Program Files\MATLAB\R2017b\java\jarext\annotations.jar
C:\Program Files\MATLAB\R2017b\java\jarext\jgit\jgit.jar
C:\Program Files\MATLAB\R2017b\java\jarext\jgit\jgitui.jar
C:\Program Files\MATLAB\R2017b\java\jarext\jgoodies-forms.jar
C:\Program Files\MATLAB\R2017b\java\jarext\jgoodies-looks.jar
C:\Program Files\MATLAB\R2017b\java\jarext\jide\jide-action.jar
C:\Program Files\MATLAB\R2017b\java\jarext\jide\jide-charts.jar
C:\Program Files\MATLAB\R2017b\java\jarext\jide\jide-common.jar
C:\Program Files\MATLAB\R2017b\java\jarext\jide\jide-components.jar
C:\Program Files\MATLAB\R2017b\java\jarext\jide\jide-dialogs.jar
C:\Program Files\MATLAB\R2017b\java\jarext\jide\jide-dock.jar
C:\Program Files\MATLAB\R2017b\java\jarext\jide\jide-properties.jar
C:\Program Files\MATLAB\R2017b\java\jarext\jide\jide-grids.jar
C:\Program Files\MATLAB\R2017b\java\jarext\jide\jide-shortcut.jar
C:\Program Files\MATLAB\R2017b\java\jarext\distcomp\jini2\lib\fiddler-dl.jar
C:\Program Files\MATLAB\R2017b\java\jarext\distcomp\jini2\lib\phoenix-dl.jar
C:\Program Files\MATLAB\R2017b\java\jarext\distcomp\jini2\lib\mahalo.jar
C:\Program Files\MATLAB\R2017b\java\jarext\distcomp\jini2\lib\destroy.jar
C:\Program Files\MATLAB\R2017b\java\jarext\distcomp\jini2\lib\jsk-platform.jar
C:\Program Files\MATLAB\R2017b\java\jarext\distcomp\jini2\lib\jini-ext.jar
C:\Program Files\MATLAB\R2017b\java\jarext\distcomp\jini2\lib\jini-core.jar
C:\Program Files\MATLAB\R2017b\java\jarext\distcomp\jini2\lib\reggie-dl.jar
C:\Program Files\MATLAB\R2017b\java\jarext\distcomp\jini2\lib\norm-dl.jar
C:\Program Files\MATLAB\R2017b\java\jarext\distcomp\jini2\lib\browser-dl.jar
C:\Program Files\MATLAB\R2017b\java\jarext\distcomp\jini2\lib\sdm-dl.jar
C:\Program Files\MATLAB\R2017b\java\jarext\distcomp\jini2\lib\norm.jar
C:\Program Files\MATLAB\R2017b\java\jarext\distcomp\jini2\lib\mahalo-dl.jar
C:\Program Files\MATLAB\R2017b\java\jarext\distcomp\jini2\lib\group.jar
C:\Program Files\MATLAB\R2017b\java\jarext\distcomp\jini2\lib\phoenix-init.jar
C:\Program Files\MATLAB\R2017b\java\jarext\distcomp\jini2\lib\browser.jar
C:\Program Files\MATLAB\R2017b\java\jarext\distcomp\jini2\lib\reggie.jar
C:\Program Files\MATLAB\R2017b\java\jarext\distcomp\jini2\lib\fiddler.jar
C:\Program Files\MATLAB\R2017b\java\jarext\distcomp\jini2\lib\phoenix-group.jar
C:\Program Files\MATLAB\R2017b\java\jarext\distcomp\jini2\lib\sun-util.jar
C:\Program Files\MATLAB\R2017b\java\jarext\distcomp\jini2\lib\jsk-policy.jar
C:\Program Files\MATLAB\R2017b\java\jarext\distcomp\jini2\lib\group-dl.jar
C:\Program Files\MATLAB\R2017b\java\jarext\distcomp\jini2\lib\sharedvm.jar
C:\Program Files\MATLAB\R2017b\java\jarext\distcomp\jini2\lib\start.jar
C:\Program Files\MATLAB\R2017b\java\jarext\distcomp\jini2\lib\jsk-resources.jar
C:\Program Files\MATLAB\R2017b\java\jarext\distcomp\jini2\lib\phoenix.jar
C:\Program Files\MATLAB\R2017b\java\jarext\Jmol.jar
C:\Program Files\MATLAB\R2017b\java\jarext\Acme.jar
C:\Program Files\MATLAB\R2017b\java\jarext\gluegen-rt.jar
C:\Program Files\MATLAB\R2017b\java\jarext\jogl-all.jar
C:\Program Files\MATLAB\R2017b\java\jarext\jsch.jar
C:\Program Files\MATLAB\R2017b\java\jarext\jung\jung-3d.jar
C:\Program Files\MATLAB\R2017b\java\jarext\jung\jung-algorithms.jar
C:\Program Files\MATLAB\R2017b\java\jarext\jung\jung-api.jar
C:\Program Files\MATLAB\R2017b\java\jarext\jung\jung-graph-impl.jar
C:\Program Files\MATLAB\R2017b\java\jarext\jung\jung-io.jar
C:\Program Files\MATLAB\R2017b\java\jarext\jung\jung-jai.jar
C:\Program Files\MATLAB\R2017b\java\jarext\jung\jung-visualization.jar
C:\Program Files\MATLAB\R2017b\java\jarext\jxbrowser-chromium\jxbrowser-chromium.jar
C:\Program Files\MATLAB\R2017b\java\jarext\jxbrowser-chromium\runtime.jar
C:\Program Files\MATLAB\R2017b\java\jarext\jxbrowser-chromium\jxbrowser-linux64.jar
C:\Program Files\MATLAB\R2017b\java\jarext\jxbrowser\comfyj.jar
C:\Program Files\MATLAB\R2017b\java\jarext\jxbrowser\engine-gecko.jar
C:\Program Files\MATLAB\R2017b\java\jarext\jxbrowser\engine-gecko15.jar
C:\Program Files\MATLAB\R2017b\java\jarext\jxbrowser\engine-ie.jar
C:\Program Files\MATLAB\R2017b\java\jarext\jxbrowser\engine-webkit.jar
C:\Program Files\MATLAB\R2017b\java\jarext\jxbrowser\jniwrap.jar
C:\Program Files\MATLAB\R2017b\java\jarext\jxbrowser\jxbrowser.jar
C:\Program Files\MATLAB\R2017b\java\jarext\jxbrowser\runtime.jar
C:\Program Files\MATLAB\R2017b\java\jarext\jxbrowser\winpack.jar
C:\Program Files\MATLAB\R2017b\java\jarext\log4j.jar
C:\Program Files\MATLAB\R2017b\java\jarext\lucene-analyzers-common.jar
C:\Program Files\MATLAB\R2017b\java\jarext\lucene-core.jar
C:\Program Files\MATLAB\R2017b\java\jarext\lucene-queryparser.jar
C:\Program Files\MATLAB\R2017b\java\jarext\lucene-highlighter.jar
C:\Program Files\MATLAB\R2017b\java\jarext\lucene-queries.jar
C:\Program Files\MATLAB\R2017b\java\jarext\lucene-suggest.jar
C:\Program Files\MATLAB\R2017b\java\jarext\lucene-memory.jar
C:\Program Files\MATLAB\R2017b\java\jarext\lucene-sandbox.jar
C:\Program Files\MATLAB\R2017b\java\jarext\nekohtml.jar
C:\Program Files\MATLAB\R2017b\java\jarext\openxml4j.jar
C:\Program Files\MATLAB\R2017b\java\jarext\pdfbox.jar
C:\Program Files\MATLAB\R2017b\java\jarext\pdfbox-tools.jar
C:\Program Files\MATLAB\R2017b\java\jarext\fontbox.jar
C:\Program Files\MATLAB\R2017b\java\jarext\xmpbox.jar
C:\Program Files\MATLAB\R2017b\java\jarext\rfa.jar
C:\Program Files\MATLAB\R2017b\toolbox\datafeed\datafeed\config_editor.jar
C:\Program Files\MATLAB\R2017b\java\jarext\rosjava\apache_xmlrpc_client.jar
C:\Program Files\MATLAB\R2017b\java\jarext\rosjava\apache_xmlrpc_common.jar
C:\Program Files\MATLAB\R2017b\java\jarext\rosjava\apache_xmlrpc_server.jar
C:\Program Files\MATLAB\R2017b\java\jarext\rosjava\commons-pool.jar
C:\Program Files\MATLAB\R2017b\java\jarext\rosjava\dnsjava.jar
C:\Program Files\MATLAB\R2017b\java\jarext\rosjava\gradle_plugins.jar
C:\Program Files\MATLAB\R2017b\java\jarext\rosjava\message_generation.jar
C:\Program Files\MATLAB\R2017b\java\jarext\rosjava\netty.jar
C:\Program Files\MATLAB\R2017b\java\jarext\rosjava\rosjava.jar
C:\Program Files\MATLAB\R2017b\java\jarext\rosjava\rosjava_actionlib.jar
C:\Program Files\MATLAB\R2017b\java\jarext\rosjava\rosjava_geometry.jar
C:\Program Files\MATLAB\R2017b\java\jarext\rosjava\rosjava_messages.jar
C:\Program Files\MATLAB\R2017b\java\jarext\rosjava\rosjava_tf2.jar
C:\Program Files\MATLAB\R2017b\java\jarext\rosjava\ws-commons-util.jar
C:\Program Files\MATLAB\R2017b\java\jarext\RXTXcomm.jar
C:\Program Files\MATLAB\R2017b\java\jarext\saxon9-dom.jar
C:\Program Files\MATLAB\R2017b\java\jarext\saxon9-dom4j.jar
C:\Program Files\MATLAB\R2017b\java\jarext\saxon9-jdom.jar
C:\Program Files\MATLAB\R2017b\java\jarext\saxon9-s9api.jar
C:\Program Files\MATLAB\R2017b\java\jarext\saxon9-sql.jar
C:\Program Files\MATLAB\R2017b\java\jarext\saxon9-xom.jar
C:\Program Files\MATLAB\R2017b\java\jarext\saxon9-xpath.jar
C:\Program Files\MATLAB\R2017b\java\jarext\saxon9-xqj.jar
C:\Program Files\MATLAB\R2017b\java\jarext\saxon9.jar
C:\Program Files\MATLAB\R2017b\java\jarext\slf4j\slf4j-api.jar
C:\Program Files\MATLAB\R2017b\java\jarext\slf4j\slf4j-log4j12.jar
C:\Program Files\MATLAB\R2017b\java\jarext\sqlite4java\sqlite4java.jar
C:\Program Files\MATLAB\R2017b\java\jarext\svnkit\svnkit.jar
C:\Program Files\MATLAB\R2017b\java\jarext\svnkit\svnkit-cli.jar
C:\Program Files\MATLAB\R2017b\java\jarext\svnkit\sqljet.jar
C:\Program Files\MATLAB\R2017b\java\jarext\svnkit\jna.jar
C:\Program Files\MATLAB\R2017b\java\jarext\svnkit\jna-platform.jar
C:\Program Files\MATLAB\R2017b\java\jarext\svnkit\trilead.jar
C:\Program Files\MATLAB\R2017b\java\jarext\svnkit\sequence.jar
C:\Program Files\MATLAB\R2017b\java\jarext\swing-layout.jar
C:\Program Files\MATLAB\R2017b\java\jarext\swingx.jar
C:\Program Files\MATLAB\R2017b\java\jarext\tablelayout.jar
C:\Program Files\MATLAB\R2017b\java\jarext\TimingFramework.jar
C:\Program Files\MATLAB\R2017b\java\jarext\j2ee\jsp-api.jar
C:\Program Files\MATLAB\R2017b\java\jarext\j2ee\servlet-api.jar
C:\Program Files\MATLAB\R2017b\java\jarext\distcomp\wrapper.jar
C:\Program Files\MATLAB\R2017b\java\jarext\xercesImpl.jar
C:\Program Files\MATLAB\R2017b\java\jarext\xml-apis.jar
C:\Program Files\MATLAB\R2017b\java\jarext\xml-apis-ext.jar
C:\Program Files\MATLAB\R2017b\java\jarext\xmlgraphics-commons.jar
C:\Program Files\MATLAB\R2017b\java\jar\instwiz.jar
C:\Program Files\MATLAB\R2017b\java\jarext\webservices\activationws_client\activationws_client.jar
C:\Program Files\MATLAB\R2017b\java\jar\addonsinstallerclient.jar
C:\Program Files\MATLAB\R2017b\java\jar\addons_app.jar
C:\Program Files\MATLAB\R2017b\java\jar\addons_common.jar
C:\Program Files\MATLAB\R2017b\java\jar\addons_import.jar
C:\Program Files\MATLAB\R2017b\java\jar\addons_import_api.jar
C:\Program Files\MATLAB\R2017b\java\jar\addons.jar
C:\Program Files\MATLAB\R2017b\java\jar\addons_mlconnector.jar
C:\Program Files\MATLAB\R2017b\java\jar\addons_product.jar
C:\Program Files\MATLAB\R2017b\java\jar\addons_search_path_writer.jar
C:\Program Files\MATLAB\R2017b\java\jar\hwsmanagement.jar
C:\Program Files\MATLAB\R2017b\java\jar\addons_toolbox.jar
C:\Program Files\MATLAB\R2017b\java\jar\addons_zip.jar
C:\Program Files\MATLAB\R2017b\java\jar\addon_enable_disable_management.jar
C:\Program Files\MATLAB\R2017b\java\jar\addon_matlab_path_service_provider.jar
C:\Program Files\MATLAB\R2017b\java\jar\addon_service_management_api.jar
C:\Program Files\MATLAB\R2017b\java\jar\toolbox\parallel\admincenter.jar
C:\Program Files\MATLAB\R2017b\java\jar\toolbox\matlab\appdesigner.jar
C:\Program Files\MATLAB\R2017b\java\jar\appmanagement.jar
C:\Program Files\MATLAB\R2017b\java\jar\toolbox\apps.jar
C:\Program Files\MATLAB\R2017b\java\jarext\webservices\authenticationws_client\authenticationws_client.jar
C:\Program Files\MATLAB\R2017b\java\jar\bde.jar
C:\Program Files\MATLAB\R2017b\java\jar\toolbox\bioinfo.jar
C:\Program Files\MATLAB\R2017b\java\jar\toolbox\matlab\webwindow.jar
C:\Program Files\MATLAB\R2017b\java\jar\toolbox\matlab\cefclient_java.jar
C:\Program Files\MATLAB\R2017b\java\jar\cfbutils.jar
C:\Program Files\MATLAB\R2017b\java\jarext\webservices\cloud_console\cloud-console-client.jar
C:\Program Files\MATLAB\R2017b\java\jar\toolbox\coder.jar
C:\Program Files\MATLAB\R2017b\java\jar\toolbox\comm.jar
C:\Program Files\MATLAB\R2017b\java\jar\comparisons.jar
C:\Program Files\MATLAB\R2017b\java\jar\toolbox\difflink\util.jar
C:\Program Files\MATLAB\R2017b\java\jar\toolbox\difflink\client.jar
C:\Program Files\MATLAB\R2017b\java\jar\toolbox\difflink\server.jar
C:\Program Files\MATLAB\R2017b\java\jar\toolbox\compilersdk.jar
C:\Program Files\MATLAB\R2017b\java\jar\toolbox\compiler.jar
C:\Program Files\MATLAB\R2017b\java\jar\toolbox\shared\computils.jar
C:\Program Files\MATLAB\R2017b\java\jarext\connector_api\connector_api_java\connector_interface.jar
C:\Program Files\MATLAB\R2017b\java\jarext\connector_api\connector_api_java\message_service_interface.jar
C:\Program Files\MATLAB\R2017b\java\jar\connector_api\editor_api.jar
C:\Program Files\MATLAB\R2017b\java\jar\connector_api\client_services_api.jar
C:\Program Files\MATLAB\R2017b\java\jar\connector_api\gson.jar
C:\Program Files\MATLAB\R2017b\java\jar\connector_api\framework_api.jar
C:\Program Files\MATLAB\R2017b\java\jar\connector_api\standalone_host_api.jar
C:\Program Files\MATLAB\R2017b\java\jar\connector_api\jni_cosg_api.jar
C:\Program Files\MATLAB\R2017b\java\jar\connector_api\jni_json_api.jar
C:\Program Files\MATLAB\R2017b\java\jar\connector_api\jni_message_service_api.jar
C:\Program Files\MATLAB\R2017b\java\jar\connector_api\jni_native_bridge_api.jar
C:\Program Files\MATLAB\R2017b\java\jarext\connector_api\cosg_api_java\cosg_java_api.jar
C:\Program Files\MATLAB\R2017b\java\jar\toolbox\curvefit.jar
C:\Program Files\MATLAB\R2017b\java\jar\toolbox\database.jar
C:\Program Files\MATLAB\R2017b\java\jar\toolbox\datafeed.jar
C:\Program Files\MATLAB\R2017b\java\jar\datatools\variableeditor.jar
C:\Program Files\MATLAB\R2017b\java\jarext\webservices\dduxws_installer_client\dduxws-installer-client.jar
C:\Program Files\MATLAB\R2017b\java\jar\ddux_api.jar
C:\Program Files\MATLAB\R2017b\java\jar\toolbox\distcomp.jar
C:\Program Files\MATLAB\R2017b\java\jar\dynamic_resource.jar
C:\Program Files\MATLAB\R2017b\java\jar\toolbox\eml.jar
C:\Program Files\MATLAB\R2017b\java\jarext\epsnotificationclient_api\epsnotificationclient_api.jar
C:\Program Files\MATLAB\R2017b\java\jar\explorer.jar
C:\Program Files\MATLAB\R2017b\java\jar\explorer_api.jar
C:\Program Files\MATLAB\R2017b\java\jar\explorer_resources.jar
C:\Program Files\MATLAB\R2017b\java\jar\explorer_widget.jar
C:\Program Files\MATLAB\R2017b\java\jar\filechooser.jar
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C:\Program Files\MATLAB\R2017b\java\jarext\webservices\ws_client_core\mw-service-client-core.jar
C:\Program Files\MATLAB\R2017b\java\jarext\webservices\ws_usagedata_client\usagedata-client.jar
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C:\Micro-Manager-2.0beta\ij.jar
C:\Micro-Manager-2.0beta\plugins\Micro-Manager\Big.jar
C:\Micro-Manager-2.0beta\plugins\Micro-Manager\MMAcqEngine.jar
C:\Micro-Manager-2.0beta\plugins\Micro-Manager\MMCoreJ.jar
C:\Micro-Manager-2.0beta\plugins\Micro-Manager\MMJ_.jar
C:\Micro-Manager-2.0beta\plugins\Micro-Manager\Projector.jar
C:\Micro-Manager-2.0beta\plugins\Micro-Manager\TSFProto-SVN.jar
C:\Micro-Manager-2.0beta\plugins\Micro-Manager\bsh-2.0b6.jar
C:\Micro-Manager-2.0beta\plugins\Micro-Manager\clojure-1.3.0.jar
C:\Micro-Manager-2.0beta\plugins\Micro-Manager\commons-math-2.2.jar
C:\Micro-Manager-2.0beta\plugins\Micro-Manager\commons-math3-3.4.1.jar
C:\Micro-Manager-2.0beta\plugins\Micro-Manager\core.cache-0.6.2.jar
C:\Micro-Manager-2.0beta\plugins\Micro-Manager\core.memoize-0.5.2.jar
C:\Micro-Manager-2.0beta\plugins\Micro-Manager\data.json-0.1.1.jar
C:\Micro-Manager-2.0beta\plugins\Micro-Manager\eventbus-1.4.jar
C:\Micro-Manager-2.0beta\plugins\Micro-Manager\formats-api-5.1.1.jar
C:\Micro-Manager-2.0beta\plugins\Micro-Manager\formats-common-5.1.1.jar
C:\Micro-Manager-2.0beta\plugins\Micro-Manager\gentyref-1.1.0.jar
C:\Micro-Manager-2.0beta\plugins\Micro-Manager\gson-2.2.4.jar
C:\Micro-Manager-2.0beta\plugins\Micro-Manager\iconloader-GIT.jar
C:\Micro-Manager-2.0beta\plugins\Micro-Manager\jcommon-1.0.23.jar
C:\Micro-Manager-2.0beta\plugins\Micro-Manager\jfreechart-1.0.19.jar
C:\Micro-Manager-2.0beta\plugins\Micro-Manager\joda-time-2.2.jar
C:\Micro-Manager-2.0beta\plugins\Micro-Manager\kryo-2.24.0.jar
C:\Micro-Manager-2.0beta\plugins\Micro-Manager\logback-classic-1.1.1.jar
C:\Micro-Manager-2.0beta\plugins\Micro-Manager\logback-core-1.1.1.jar
C:\Micro-Manager-2.0beta\plugins\Micro-Manager\miglayout-core-4.2.jar
C:\Micro-Manager-2.0beta\plugins\Micro-Manager\miglayout-swing-4.2.jar
C:\Micro-Manager-2.0beta\plugins\Micro-Manager\minlog-1.2.jar
C:\Micro-Manager-2.0beta\plugins\Micro-Manager\objenesis-2.1.jar
C:\Micro-Manager-2.0beta\plugins\Micro-Manager\ome-xml-5.1.1.jar
C:\Micro-Manager-2.0beta\plugins\Micro-Manager\protobuf-java-2.5.0.jar
C:\Micro-Manager-2.0beta\plugins\Micro-Manager\rsyntaxtextarea-2.5.2.jar
C:\Micro-Manager-2.0beta\plugins\Micro-Manager\scijava-common-2.46.0.jar
C:\Micro-Manager-2.0beta\plugins\Micro-Manager\serializer-2.7.1.jar
C:\Micro-Manager-2.0beta\plugins\Micro-Manager\slf4j-api-1.7.6.jar
C:\Micro-Manager-2.0beta\plugins\Micro-Manager\swingx-0.9.5.jar
C:\Micro-Manager-2.0beta\plugins\Micro-Manager\xalan-2.7.1.jar
C:\Micro-Manager-2.0beta\plugins\Micro-Manager\xml-apis-1.3.04.jar
DYNAMIC JAVA PATH
F:\###\z_MATLAB_Analysis\bfmatlab\bioformats_package.jar
Thank you for your help! Eric
Hi @erjel
C:\Micro-Manager-2.0beta\plugins\Micro-Manager\formats-api-5.1.1.jar
C:\Micro-Manager-2.0beta\plugins\Micro-Manager\formats-common-5.1.1.jar
largely explains the issue you are describing. Micro-Manager 1.4 and 2.0-beta both use and ship an older version of Bio-Formats. If you want to use a recent version of Bio-Formats for reading files, you will need to remove the Micro-Manager JARs (at least the Bio-Formats ones) from your static Java path.
Thank you for your quick response! I commented the corresponding lines in javaclasspath.txt
.
As expected this solved the problem with the used bioformats version:
version =
'5.9.2'
Unfortunately I ran into a different problem:
Error using bfGetReader (line 75)
Java exception occurred:
java.lang.NoSuchFieldError: MICROMETER
at loci.formats.in.NiftiReader.<init>(NiftiReader.java:78)
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
at java.lang.Class.newInstance(Class.java:442)
at loci.formats.ImageReader.<init>(ImageReader.java:129)
at loci.formats.in.FilePatternReader.<init>(FilePatternReader.java:77)
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
at java.lang.Class.newInstance(Class.java:442)
at loci.formats.ImageReader.<init>(ImageReader.java:129)
at loci.formats.ImageReader.<init>(ImageReader.java:116)
at loci.formats.ReaderWrapper.<init>(ReaderWrapper.java:61)
at loci.formats.ChannelFiller.<init>(ChannelFiller.java:71)
Do you have any idea why the NiftiReader
is used? I tested bfopen
also with a matlab-generated .tif-file to make sure that my .nd2 file is not corrupted. It produces the same error message.
The above is actually related to the same problem. The Bio-Formats 5.1.1 JARs shipped with Micro-Manager depend on the ome-xml:5.1.1
component which is an older version of the OME model. Removing:
C:\Micro-Manager-2.0beta\plugins\Micro-Manager\ome-xml-5.1.1.jar
should allow to import the latest classes included in bioformats_package
.
Thank you a lot! It solved the problem.
Summary:
1.) Inspect the javaclasspath
in matlab
>> javaclasspath
2.) In case multiple versions of bioformats are present comment/ delete them.
>> cd(prefdir)
>> edit javaclasspath.txt
In my case we changed corresponding lines to:
[...]
#C:\Micro-Manager-2.0beta\plugins\Micro-Manager\formats-api-5.1.1.jar
#C:\Micro-Manager-2.0beta\plugins\Micro-Manager\formats-common-5.1.1.jar
[...]
#C:\Micro-Manager-2.0beta\plugins\Micro-Manager\ome-xml-5.1.1.jar
[...]
I would like to use the Bio-Format MATLAB Toolbox for automatically convert
.nd2
to.tif
files with a small script. Unfortunately I could not even mange to read the files. The script:produces the error message
The first thing which puzzles me is the version number
'5.1.1'
: I downloadedbioformats_package.jar
several times either bundled in the MATLAB Toolbox, as Java Bio-Formats Package and copy-pasted it in the toolbox folder and finally even downloaded legacy versions (5.7.0) just to check whether the version number changes. It does not ...Since I only care about a working script and not so much about a single version number, I focused on the error message: It seems like no reader can be connected to the .nd2 file type in line 181 in ImageReader.java. But if manually check it
I get a positiv result:
On the other hand a
will result in the same error message like above.
I thought that I have followed the documentation as closely as possible. But somewhere I missed something out. I already tested it on two systems: MATLAB 2017b with WIndows 10 64-bit and the latest Java JDK 10 (binary directory
C:\Program Files\java\jre-10.0.2\bin
added toPATH
environment variable) MATLAB 2017a with Debian 9 stretch 64-bit with openjdk version "1.8.0_181"Can anyone help me?