SLIM curve plugin - batch mode issue

slim-plugin
batch-processing
Tags: #<Tag:0x00007fd53e52b3e8> #<Tag:0x00007fd53e52b208>

#1

I have recently started doing TCSPC-FLIM FRET imaging and I am looking for an efficient way to analyze directories of .sdt lifetime images. I stumbled over the SLIM-curve plugin which seems appropriate for the task (comparable to SPCimage which the lab I’m visiting is currently using).

I would like to use a macro or script (scripting in python based of the macro calls in the wiki, I couldn’t find an API) that batch processes efficiently, this is where I hit the wall. When I try to run batch from the gui I get the following error:

[INFO] Reading SDT header
Library not on path Unable to load library 'slim-curve-1.0-SNAPSHOT': Native library (win32-x86-64/slim-curve-1.0-SNAPSHOT.dll) not found in resource path ([file:/C:/Users/Groed/Desktop/Fiji.app/jars/imagej-launcher-4.0.5.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/ahocorasick-0.2.4.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/akutan-1.0.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/args4j-2.0.25.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/asm-4.0.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/asm-analysis-4.0.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/asm-commons-4.0.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/asm-tree-4.0.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/asm-util-4.0.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/autocomplete-2.6.1.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/base64-2.3.8.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/batik-anim-1.9.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/batik-awt-util-1.9.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/batik-bridge-1.9.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/batik-codec-1.9.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/batik-constants-1.9.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/batik-css-1.9.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/batik-dom-1.9.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/batik-ext-1.9.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/batik-gvt-1.9.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/batik-i18n-1.9.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/batik-parser-1.9.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/batik-script-1.9.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/batik-svg-dom-1.9.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/batik-svggen-1.9.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/batik-transcoder-1.9.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/batik-util-1.9.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/batik-xml-1.9.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/bigdataviewer-core-4.1.0.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/bigdataviewer-vistools-1.0.0-beta-5.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/bio-formats/formats-api-5.7.1.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/bio-formats/formats-bsd-5.7.1.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/bio-formats/formats-common-5.1.10.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/bio-formats/formats-gpl-5.7.1.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/bio-formats/jai_imageio-5.5.3.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/bio-formats/jxrlib-all-0.2.1.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/bio-formats/mdbtools-java-5.1.10.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/bio-formats/metakit-5.3.0.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/bio-formats/ome-codecs-0.2.0.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/bio-formats/ome-common-5.3.2.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/bio-formats/ome-jai-0.1.0.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/bio-formats/ome-mdbtools-5.3.0.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/bio-formats/ome-poi-5.3.1.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/bio-formats/ome-xml-5.5.4.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/bio-formats/specification-5.5.4.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/bio-formats/turbojpeg-5.7.1.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/blas-0.8.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/bounce-0.18.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/bsh-2.0b6.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/bytelist-1.0.11.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/caffeine-2.4.0.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/clojure-1.8.0.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/codemodel-2.6.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/collections-generic-4.01.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/colt-1.2.0.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/commons-beanutils-1.9.3.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/commons-codec-1.10.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/commons-collections-3.2.2.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/commons-compress-1.4.1.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/commons-io-1.3.1.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/commons-lang3-3.5.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/commons-logging-1.2.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/commons-math-2.2.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/commons-math3-3.6.1.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/commons-vfs2-2.0.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/concurrent-1.3.4.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/curve-fitter-1.0.0-SNAPSHOT-with-libs.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/datasets-0.8.1906.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/ejml-0.24.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/eventbus-1.4.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/f2jutil-0.8.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/ffmpeg-2.6.1-0.11.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/fiji-2.0.0-SNAPSHOT.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/fiji-compat-2.0.3.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/fiji-lib-2.1.2.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/filters-2.0.235.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/gcc-runtime-0.8.1906.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/gentyref-1.1.0.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/gluegen-rt-2.3.2.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/gluegen-rt-main-2.3.2.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/graphics-0.8.1906.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/grDevices-0.8.1906.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/groovy-2.4.8.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/gson-2.8.0.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/guava-21.0.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/ij-1.51n.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/ij1-patcher-0.12.6.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/image4j-0.7.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/imagej-2.0.0-rc-61.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/imagej-common-0.24.4.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/imagej-deprecated-0.1.2.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/imagej-legacy-0.25.0.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/imagej-notebook-0.2.2.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/imagej-ops-0.38.0.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/imagej-plugins-commands-0.7.1.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/imagej-plugins-tools-0.3.1.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/imagej-plugins-uploader-ssh-0.3.2.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/imagej-plugins-uploader-webdav-0.2.2.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/imagej-scripting-0.6.0.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/imagej-ui-awt-0.3.1.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/imagej-ui-swing-0.21.2.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/imagej-updater-0.8.3.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/imglib2-4.2.1.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/imglib2-algorithm-0.8.0.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/imglib2-algorithm-fft-0.1.4.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/imglib2-algorithm-gpl-0.2.1.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/imglib2-cache-1.0.0-beta-7.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/imglib2-ij-2.0.0-beta-37.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/imglib2-realtransform-2.0.0-beta-37.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/imglib2-roi-0.4.6.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/imglib2-ui-2.0.0-beta-33.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/invokebinder-1.2.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/itextpdf-5.5.11.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/ivy-2.2.0.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/j3dcore-1.6.0-scijava-2.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/j3dutils-1.6.0-scijava-2.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/jai-codec-1.1.3.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/jai-core-1.1.3.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/jama-1.0.3.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/javacpp-0.11.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/javassist-3.22.0-CR1.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/jcodings-1.0.10.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/jcommander-1.48.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/jcommon-1.0.24.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/jdatepicker-1.3.2.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/jdom2-2.0.6.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/jep-2.4.2.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/jffi-1.2.7-native.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/jffi-1.2.7.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/jfreechart-1.0.19.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/jgoodies-common-1.7.0.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/jgoodies-forms-1.7.2.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/jgrapht-0.8.3.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/jgraphx-3.4.1.3.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/jhdf5-14.12.5.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/jhotdraw-7.6.0.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/jitk-tps-2.1.1.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/jna-4.4.0.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/jnr-constants-0.8.5.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/jnr-enxio-0.4.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/jnr-ffi-1.0.7.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/jnr-netdb-1.1.2.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/jnr-posix-3.0.1.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/jnr-unixsocket-0.3.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/jnr-x86asm-1.0.2.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/joal-2.3.2.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/joal-main-2.3.2.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/jocl-2.3.2.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/jocl-main-2.3.2.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/joda-time-2.9.9.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/jogl-all-2.3.2.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/jogl-all-main-2.3.2.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/joni-2.1.1.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/jpedalSTD-2.80b11.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/jruby-core-1.7.12.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/jruby-stdlib-1.7.12.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/jsch-0.1.54.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/jsoup-1.7.2.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/jtransforms-2.4.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/jung-api-2.0.1.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/jung-graph-impl-2.0.1.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/JWlz-1.4.0.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/jxlayer-3.0.4.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/jython-shaded-2.7.0.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/jzlib-1.1.3.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/kryo-2.24.0.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/languagesupport-2.6.0.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/lapack-0.8.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/legacy-imglib1-1.1.8.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/lma-1.3.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/log4j-1.2.17.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/logback-classic-1.2.3.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/logback-core-1.2.3.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/mapdb-1.0.3.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/markdownj-0.3.0-1.0.2b4.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/maven-scm-api-1.4.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/maven-scm-provider-svn-commons-1.4.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/maven-scm-provider-svnexe-1.4.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/metadata-extractor-2.6.2.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/methods-0.8.1906.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/miglayout-3.7.4-swing.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/mines-jtk-20151125.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/minimaven-2.2.1.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/minlog-1.2.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/mpicbg-1.1.1.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/mtj-1.0.4.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/nailgun-server-0.9.1.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/native-lib-loader-2.1.5.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/netcdf-4.3.22.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/netlib-java-0.9.3-renjin-patched-2.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/object-inspector-0.1.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/objenesis-2.1.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/ojalgo-43.0.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/op-finder-0.1.3.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/opencsv-3.9.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/options-1.1.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/pal-optimization-2.0.1.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/parsington-1.0.1.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/perf4j-0.9.13.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/plexus-utils-1.5.6.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/postgresql-9.1-901-1.jdbc4.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/regexp-1.3.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/renjin-appl-0.8.1906.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/renjin-core-0.8.1906.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/renjin-gnur-runtime-0.8.1906.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/renjin-script-engine-0.8.1906.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/rhino-1.7.6.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/rsyntaxtextarea-2.6.1.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/scala-compiler-2.12.1.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/scala-library-2.12.1.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/scala-reflect-2.12.1.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/scala-xml_2.12-1.0.6.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/scifio-0.32.0.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/scifio-bf-compat-2.0.3.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/scifio-cli-0.3.4.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/scifio-hdf5-0.1.2.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/scifio-jai-imageio-1.1.1.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/scifio-lifesci-0.7.1.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/scifio-ome-xml-0.14.3.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/scijava-common-2.64.0.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/scijava-config-2.0.2.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/scijava-plugins-commands-0.2.3.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/scijava-plugins-platforms-0.3.0.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/scijava-plugins-text-markdown-0.1.3.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/scijava-plugins-text-plain-0.1.3.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/scijava-ui-awt-0.1.6.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/scijava-ui-swing-0.9.2.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/script-editor-0.1.4.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/scripting-beanshell-0.3.2.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/scripting-clojure-0.1.6.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/scripting-groovy-0.2.6.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/scripting-java-0.4.1.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/scripting-javascript-0.4.4.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/scripting-jruby-0.2.5.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/scripting-jython-0.4.1.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/scripting-renjin-0.2.2.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/scripting-scala-0.2.1.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/sezpoz-1.9-imagej.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/slf4j-api-1.7.25.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/snakeyaml-1.13.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/spim_data-2.2.0.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/stats-0.8.1906.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/swing-checkbox-tree-1.0.2.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/swing-worker-1.1.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/swingx-1.6.1.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/T2-NIT-1.1.2.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/T2-TreelineGraph-1.1.2.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/trakem2-transform-1.0.0.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/trove4j-3.0.3.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/udunits-4.3.18.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/ui-behaviour-1.3.0.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/utils-0.8.1906.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/vecmath-1.6.0-scijava-2.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/VectorString-2.0.1.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/VIB-lib-2.1.2.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/weave_jy2java-2.1.0.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/weka-dev-3.9.1.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/win64/ffmpeg-2.6.1-0.11-windows-x86_64.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/win64/gluegen-rt-2.3.2-natives-windows-amd64.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/win64/joal-2.3.2-natives-windows-amd64.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/win64/jocl-2.3.2-natives-windows-amd64.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/win64/jogl-all-2.3.2-natives-windows-amd64.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/xerbla-0.8.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/xercesImpl-2.8.1.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/xml-apis-ext-1.3.04.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/xmlgraphics-commons-2.2.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/xmpcore-5.1.2.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/xz-1.0.jar, file:/C:/Users/Groed/Desktop/Fiji.app/jars/yecht-1.0.jar, file:/C:/Users/Groed/Desktop/Fiji.app/plugins/3D_Blob_Segmentation-3.0.1.jar, file:/C:/Users/Groed/Desktop/Fiji.app/plugins/3D_Objects_Counter-2.0.1.jar, file:/C:/Users/Groed/Desktop/Fiji.app/plugins/3D_Viewer-4.0.2.jar, file:/C:/Users/Groed/Desktop/Fiji.app/plugins/AnalyzeSkeleton_-3.1.3.jar, file:/C:/Users/Groed/Desktop/Fiji.app/plugins/Anisotropic_Diffusion_2D-2.0.1.jar, file:/C:/Users/Groed/Desktop/Fiji.app/plugins/Archipelago_Plugins-0.5.4.jar, file:/C:/Users/Groed/Desktop/Fiji.app/plugins/Arrow_-2.0.2.jar, file:/C:/Users/Groed/Desktop/Fiji.app/plugins/Auto_Threshold-1.16.5.jar, file:/C:/Users/Groed/Desktop/Fiji.app/plugins/BalloonSegmentation_-3.0.1.jar, file:/C:/Users/Groed/Desktop/Fiji.app/plugins/bigdataviewer_fiji-4.0.1.jar, file:/C:/Users/Groed/Desktop/Fiji.app/plugins/bigwarp_fiji-3.0.0.jar, file:/C:/Users/Groed/Desktop/Fiji.app/plugins/bio-formats_plugins-5.7.1.jar, file:/C:/Users/Groed/Desktop/Fiji.app/plugins/blockmatching_-2.1.2.jar, file:/C:/Users/Groed/Desktop/Fiji.app/plugins/Bug_Submitter-2.1.1.jar, file:/C:/Users/Groed/Desktop/Fiji.app/plugins/bUnwarpJ_-2.6.9.jar, file:/C:/Users/Groed/Desktop/Fiji.app/plugins/Calculator_Plus-2.0.1.jar, file:/C:/Users/Groed/Desktop/Fiji.app/plugins/Cell_Counter-2.2.2.jar, file:/C:/Users/Groed/Desktop/Fiji.app/plugins/Colocalisation_Analysis-3.0.0.jar, file:/C:/Users/Groed/Desktop/Fiji.app/plugins/Color_Histogram-2.0.7.jar, file:/C:/Users/Groed/Desktop/Fiji.app/plugins/Color_Inspector_3D-2.3.2.jar, file:/C:/Users/Groed/Desktop/Fiji.app/plugins/Colour_Deconvolution-3.0.2.jar, file:/C:/Users/Groed/Desktop/Fiji.app/plugins/CorrectBleach_-2.0.2.jar, file:/C:/Users/Groed/Desktop/Fiji.app/plugins/Correct_3D_Drift-1.0.1.jar, file:/C:/Users/Groed/Desktop/Fiji.app/plugins/CPU_Meter-2.0.1.jar, file:/C:/Users/Groed/Desktop/Fiji.app/plugins/Descriptor_based_registration-2.1.2.jar, file:/C:/Users/Groed/Desktop/Fiji.app/plugins/Dichromacy_-2.1.1.jar, file:/C:/Users/Groed/Desktop/Fiji.app/plugins/Directionality_-2.0.2.jar, file:/C:/Users/Groed/Desktop/Fiji.app/plugins/Feature_Detection-2.0.2.jar, file:/C:/Users/Groed/Desktop/Fiji.app/plugins/Fiji_Archipelago-2.0.1.jar, file:/C:/Users/Groed/Desktop/Fiji.app/plugins/Fiji_Developer-2.0.6.jar, file:/C:/Users/Groed/Desktop/Fiji.app/plugins/Fiji_Package_Maker-2.1.1.jar, file:/C:/Users/Groed/Desktop/Fiji.app/plugins/Fiji_Plugins-3.1.1.jar, file:/C:/Users/Groed/Desktop/Fiji.app/plugins/FlowJ_-1.29.3.jar, file:/C:/Users/Groed/Desktop/Fiji.app/plugins/FS_Align_TrakEM2-2.0.2.jar, file:/C:/Users/Groed/Desktop/Fiji.app/plugins/Graph_Cut-1.0.2.jar, file:/C:/Users/Groed/Desktop/Fiji.app/plugins/Gray_Morphology-2.3.4.jar, file:/C:/Users/Groed/Desktop/Fiji.app/plugins/H5J_Loader_Plugin-1.0.6.jar, file:/C:/Users/Groed/Desktop/Fiji.app/plugins/Helmholtz_Analysis-2.0.2.jar, file:/C:/Users/Groed/Desktop/Fiji.app/plugins/IJ_Robot-2.0.1.jar, file:/C:/Users/Groed/Desktop/Fiji.app/plugins/Image_5D-2.0.2.jar, file:/C:/Users/Groed/Desktop/Fiji.app/plugins/Image_Expression_Parser-3.0.1.jar, file:/C:/Users/Groed/Desktop/Fiji.app/plugins/Interactive_3D_Surface_Plot-3.0.0.jar, file:/C:/Users/Groed/Desktop/Fiji.app/plugins/IO_-3.0.3.jar, file:/C:/Users/Groed/Desktop/Fiji.app/plugins/IsoData_Classifier-2.0.1.jar, file:/C:/Users/Groed/Desktop/Fiji.app/plugins/Kuwahara_Filter-2.0.1.jar, file:/C:/Users/Groed/Desktop/Fiji.app/plugins/KymographBuilder-1.2.3.jar, file:/C:/Users/Groed/Desktop/Fiji.app/plugins/Lasso_and_Blow_Tool-2.0.2.jar, file:/C:/Users/Groed/Desktop/Fiji.app/plugins/level_sets-1.0.2.jar, file:/C:/Users/Groed/Desktop/Fiji.app/plugins/Linear_Kuwahara-2.0.1.jar, file:/C:/Users/Groed/Desktop/Fiji.app/plugins/LocalThickness_-4.0.2.jar, file:/C:/Users/Groed/Desktop/Fiji.app/plugins/LSM_Reader-4.1.2.jar, file:/C:/Users/Groed/Desktop/Fiji.app/plugins/LSM_Toolbox-4.1.2.jar, file:/C:/Users/Groed/Desktop/Fiji.app/plugins/Manual_Tracking-2.1.1.jar, file:/C:/Users/Groed/Desktop/Fiji.app/plugins/mpicbg_-1.1.1.jar, file:/C:/Users/Groed/Desktop/Fiji.app/plugins/MTrack2_-2.0.1.jar, file:/C:/Users/Groed/Desktop/Fiji.app/plugins/Multi_Kymograph-3.0.1.jar, file:/C:/Users/Groed/Desktop/Fiji.app/plugins/M_I_P-2.0.1.jar, file:/C:/Users/Groed/Desktop/Fiji.app/plugins/panorama_-3.0.2.jar, file:/C:/Users/Groed/Desktop/Fiji.app/plugins/PIV_analyser-1.1.2.jar, file:/C:/Users/Groed/Desktop/Fiji.app/plugins/QuickPALM_-1.1.2.jar, file:/C:/Users/Groed/Desktop/Fiji.app/plugins/RATS_-2.0.1.jar, file:/C:/Users/Groed/Desktop/Fiji.app/plugins/Reconstruct_Reader-2.0.3.jar, file:/C:/Users/Groed/Desktop/Fiji.app/plugins/register_virtual_stack_slices-3.0.3.jar, file:/C:/Users/Groed/Desktop/Fiji.app/plugins/registration_3d-2.0.1.jar, file:/C:/Users/Groed/Desktop/Fiji.app/plugins/Samples_-2.0.2.jar, file:/C:/Users/Groed/Desktop/Fiji.app/plugins/Series_Labeler-2.0.1.jar, file:/C:/Users/Groed/Desktop/Fiji.app/plugins/Sholl_Analysis-3.7.0.jar, file:/C:/Users/Groed/Desktop/Fiji.app/plugins/Simple_Neurite_Tracer-3.1.5.jar, file:/C:/Users/Groed/Desktop/Fiji.app/plugins/Siox_Segmentation-1.0.5.jar, file:/C:/Users/Groed/Desktop/Fiji.app/plugins/Skeletonize3D_-2.1.1.jar, file:/C:/Users/Groed/Desktop/Fiji.app/plugins/slim_plugin-2.0.0-SNAPSHOT.jar, file:/C:/Users/Groed/Desktop/Fiji.app/plugins/SPIM_Opener-2.0.2.jar, file:/C:/Users/Groed/Desktop/Fiji.app/plugins/SPIM_Registration-5.0.16.jar, file:/C:/Users/Groed/Desktop/Fiji.app/plugins/SplineDeformationGenerator_-2.0.1.jar, file:/C:/Users/Groed/Desktop/Fiji.app/plugins/Stack_Manipulation-2.0.2.jar, file:/C:/Users/Groed/Desktop/Fiji.app/plugins/Statistical_Region_Merging-2.0.1.jar, file:/C:/Users/Groed/Desktop/Fiji.app/plugins/Stitching_-3.1.5.jar, file:/C:/Users/Groed/Desktop/Fiji.app/plugins/Sync_Win-1.7-fiji4.jar, file:/C:/Users/Groed/Desktop/Fiji.app/plugins/Thread_Killer-2.0.1.jar, file:/C:/Users/Groed/Desktop/Fiji.app/plugins/Time_Lapse-2.1.0.jar, file:/C:/Users/Groed/Desktop/Fiji.app/plugins/Time_Stamper-2.0.1.jar, file:/C:/Users/Groed/Desktop/Fiji.app/plugins/ToAST_-25.0.2.jar, file:/C:/Users/Groed/Desktop/Fiji.app/plugins/TopoJ_-2.0.1.jar, file:/C:/Users/Groed/Desktop/Fiji.app/plugins/TrackMate_-3.5.3.jar, file:/C:/Users/Groed/Desktop/Fiji.app/plugins/Trainable_Segmentation-3.2.17.jar, file:/C:/Users/Groed/Desktop/Fiji.app/plugins/TrakEM2_-1.0i.jar, file:/C:/Users/Groed/Desktop/Fiji.app/plugins/TrakEM2_Archipelago-2.0.2.jar, file:/C:/Users/Groed/Desktop/Fiji.app/plugins/trakem2_tps-1.1.3.jar, file:/C:/Users/Groed/Desktop/Fiji.app/plugins/Vaa3d_Reader-2.0.2.jar, file:/C:/Users/Groed/Desktop/Fiji.app/plugins/Vaa3d_Writer-1.0.2.jar, file:/C:/Users/Groed/Desktop/Fiji.app/plugins/VIB_-3.0.2.jar, file:/C:/Users/Groed/Desktop/Fiji.app/plugins/Video_Editing-2.0.1.jar, file:/C:/Users/Groed/Desktop/Fiji.app/plugins/View5D_-1.3.2.jar, file:/C:/Users/Groed/Desktop/Fiji.app/plugins/Volume_Calculator-2.0.2.jar, file:/C:/Users/Groed/Desktop/Fiji.app/plugins/Volume_Viewer-2.01.2.jar, file:/C:/Users/Groed/Desktop/Fiji.app/plugins/z_spacing-1.0.3.jar])
Exception in thread "AWT-EventQueue-0" java.lang.Error: Cannot call invokeAndWait from the event dispatcher thread
	at java.awt.EventQueue.invokeAndWait(EventQueue.java:1301)
	at java.awt.EventQueue.invokeAndWait(EventQueue.java:1294)
	at loci.slim.SLIMProcessor.showFileDialog(SLIMProcessor.java:1561)
	at loci.slim.SLIMProcessor.access$800(SLIMProcessor.java:124)
	at loci.slim.SLIMProcessor$1.openFile(SLIMProcessor.java:706)
	at loci.slim.ui.UserInterfacePanel$1.actionPerformed(UserInterfacePanel.java:443)
	at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2022)
	at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2348)
	at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:402)
	at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259)
	at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:252)
	at java.awt.Component.processMouseEvent(Component.java:6535)
	at javax.swing.JComponent.processMouseEvent(JComponent.java:3324)
	at java.awt.Component.processEvent(Component.java:6300)
	at java.awt.Container.processEvent(Container.java:2236)
	at java.awt.Component.dispatchEventImpl(Component.java:4891)
	at java.awt.Container.dispatchEventImpl(Container.java:2294)
	at java.awt.Component.dispatchEvent(Component.java:4713)
	at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888)
	at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4525)
	at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466)
	at java.awt.Container.dispatchEventImpl(Container.java:2280)
	at java.awt.Window.dispatchEventImpl(Window.java:2750)
	at java.awt.Component.dispatchEvent(Component.java:4713)
	at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758)
	at java.awt.EventQueue.access$500(EventQueue.java:97)
	at java.awt.EventQueue$3.run(EventQueue.java:709)
	at java.awt.EventQueue$3.run(EventQueue.java:703)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86)
	at java.awt.EventQueue$4.run(EventQueue.java:731)
	at java.awt.EventQueue$4.run(EventQueue.java:729)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
	at java.awt.EventQueue.dispatchEvent(EventQueue.java:728)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
	at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
	at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)

When I try to run it using the example macro for batch on the wiki, after fitting one image as directed, I get the following prompt (as you can see slim-curve is running):

From a python script I get the samme error. Any advice on how to get this running is appreciated, maybe I’ve misunderstood the directions or there is a bug here. Or maybe there is something wrong with my files, I am new to lifetime imaging.

In the end I would like to batch process slim-curve along with a weka segmentation.

(Developer tags: @ctrueden, @hinerm, @aksagar )

Fiji, IJ ver 1.51n, java 1.8.0_66 W10 64bit.
EDIT: The plugin was installed via the update site as directed on the wiki.


#2

Thanks for the detailed bug report, @Sverre!

@aksagar Any ideas?


#3

@aksagar is out of town until Monday… he said he’d take a look then @Sverre. :slight_smile:

eta


#4

@sverre You could have a look at http://flimfit.org/ which can handle directories of .sdt images, particularly if you are trying to fit “globally” i.e. assuming that llifetimes are common across all the images.


#5

Hi Imunro and thanks for the suggestion. SPC image can also handle directories but I would prefer to do all my analysis in ImageJ, where I also analyse my sensitized emission data (I’d like to see if I can integrate SLIMCURVE in my FRET analysis script).

Of course a big issue with SPC image is that its proprietary software and you need a license to use it… In this regard flimfit is a much better solution…


#6

Just a thought. Out of curiosity do you know if SPC Image can do “Global” fitting across images.


#7

Not as far as I can tell.


#8

Thanks and good luck.


#9

Hi @Sverre,

Thanks for the detailed bug report. I was out of state and could not reach out to you. I will look into your issue this week and let you know if there is a fix. Batch processing used to work last I remembered. I will try my best to find out the reason it is not working now.
Also, SPCImage can do a batch processing if you absolutely need to use it. You can basically use one IRF to fit across a batch of images and then export them. And as you already have SDT data I am assuming you have the license to use it that comes with SPC hardware.


#10

Any luck @aksagar? If you had some time to look at it.

I am Ok with SPC image thus far, but I would like to transition to IJ at some point.


#11

Hi @Sverre, thanks for your patience and sorry for the delay.

We have finally figured out the issue and released the update. You should Update SLIM-Curve and it should work fine. This version also includes major speed improvement for fitting images. So your analysis speed should be much better.

Thanks a lot for your patience again.


#12

Hi @aksagar, thanks for taking the time! I get a new error now, which could be completely unrelated, I don’t know. I fit file #1 then hit newfile/batch and select a number of similar images, but I always get this Problem writing to file error. Either pixels or the others if I try to deselect export pixels.

This was done manually in the user interface. I updated SLIM curve using the update site.

Sample data for batch.

I found the exception here in the source code, but it doesn’t tell me much. Something is wrong with the path, but as I run it from the UI it should get the right path, no?


#13

Hi @aksagar, @ctrueden.

To finish this thread: The plugin runs fine on a fresh install of Fiji with the SLIM curve update site enabled in W7 and in Ubuntu, batch mode included.

Thanks for your help in resolving this issue.

I have some comments on the plugin but they are not at all urgent - I will post issues on github and you can see to them if or when you find the time :slight_smile: