bnoi
diff --git a/‎README.md
+16-13 b/‎README.md
+16-13
diff --git a/‎batchMAAR.py
+4 b/‎batchMAAR.py
+4
diff --git a/‎copyFijiDeps.sh
100644100755 b/‎copyFijiDeps.sh
100644100755
diff --git a/‎copyMMDeps.sh
100644100755
+7-1 b/‎copyMMDeps.sh
100644100755
+7-1
diff --git a/‎doc/BfSeg_manual.md
+23-16 b/‎doc/BfSeg_manual.md
+23-16
diff --git a/‎doc/images/seg_bf.gif
1.15 MB b/‎doc/images/seg_bf.gif
1.15 MB
diff --git a/‎doc/manual.md
+6-8 b/‎doc/manual.md
+6-8
diff --git a/‎jars/Fiji_deps/json-20170516.jar
55.9 KB b/‎jars/Fiji_deps/json-20170516.jar
55.9 KB
diff --git a/‎jars/MM_deps/3D_Viewer-4.0.2.jar
555 KB b/‎jars/MM_deps/3D_Viewer-4.0.2.jar
555 KB
diff --git a/‎jars/MM_deps/JWlz-1.4.0.jar
115 KB b/‎jars/MM_deps/JWlz-1.4.0.jar
115 KB
diff --git a/‎jars/MM_deps/TrackMate_-3.5.3.jar
1.33 MB b/‎jars/MM_deps/TrackMate_-3.5.3.jar
1.33 MB
diff --git a/‎jars/MM_deps/VIB-lib-2.1.2.jar
621 KB b/‎jars/MM_deps/VIB-lib-2.1.2.jar
621 KB
diff --git a/‎jars/MM_deps/batik-awt-util-1.9.jar
411 KB b/‎jars/MM_deps/batik-awt-util-1.9.jar
411 KB
diff --git a/‎jars/MM_deps/batik-constants-1.9.jar
8.05 KB b/‎jars/MM_deps/batik-constants-1.9.jar
8.05 KB
diff --git a/‎jars/MM_deps/batik-css-1.9.jar
317 KB b/‎jars/MM_deps/batik-css-1.9.jar
317 KB
diff --git a/‎jars/MM_deps/batik-dom-1.9.jar
180 KB b/‎jars/MM_deps/batik-dom-1.9.jar
180 KB
diff --git a/‎jars/MM_deps/batik-ext-1.9.jar
12.7 KB b/‎jars/MM_deps/batik-ext-1.9.jar
12.7 KB
diff --git a/‎jars/MM_deps/batik-i18n-1.9.jar
11 KB b/‎jars/MM_deps/batik-i18n-1.9.jar
11 KB
diff --git a/‎jars/MM_deps/batik-svggen-1.9.jar
219 KB b/‎jars/MM_deps/batik-svggen-1.9.jar
219 KB
diff --git a/‎jars/MM_deps/batik-util-1.9.jar
124 KB b/‎jars/MM_deps/batik-util-1.9.jar
124 KB
diff --git a/‎jars/MM_deps/batik-xml-1.9.jar
32.7 KB b/‎jars/MM_deps/batik-xml-1.9.jar
32.7 KB
diff --git a/‎jars/MM_deps/bio-formats_plugins-5.5.2.jar
244 KB b/‎jars/MM_deps/bio-formats_plugins-5.5.2.jar
244 KB
diff --git a/‎jars/MM_deps/bio-formats_plugins-5.5.3.jar
244 KB b/‎jars/MM_deps/bio-formats_plugins-5.5.3.jar
244 KB
diff --git a/‎jars/MM_deps/commons-beanutils-1.9.3.jar
240 KB b/‎jars/MM_deps/commons-beanutils-1.9.3.jar
240 KB
diff --git a/‎jars/MM_deps/commons-collections-3.2.2.jar
575 KB b/‎jars/MM_deps/commons-collections-3.2.2.jar
575 KB
diff --git a/‎jars/MM_deps/commons-io-1.3.1.jar
81.7 KB b/‎jars/MM_deps/commons-io-1.3.1.jar
81.7 KB
diff --git a/‎jars/MM_deps/commons-lang3-3.5.jar
469 KB b/‎jars/MM_deps/commons-lang3-3.5.jar
469 KB
diff --git a/‎jars/MM_deps/commons-logging-1.1.1.jar
59.3 KB b/‎jars/MM_deps/commons-logging-1.1.1.jar
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diff --git a/‎jars/MM_deps/commons-math3-3.4.1.jar
1.94 MB b/‎jars/MM_deps/commons-math3-3.4.1.jar
1.94 MB
diff --git a/‎jars/MM_deps/commons-math3-3.6.1.jar
2.11 MB b/‎jars/MM_deps/commons-math3-3.6.1.jar
2.11 MB
diff --git a/‎jars/MM_deps/ejml-0.24.jar
338 KB b/‎jars/MM_deps/ejml-0.24.jar
338 KB
diff --git a/‎jars/MM_deps/eventbus-1.4.jar
80.8 KB b/‎jars/MM_deps/eventbus-1.4.jar
80.8 KB
diff --git a/‎jars/MM_deps/fiji-lib-2.1.2.jar
90.7 KB b/‎jars/MM_deps/fiji-lib-2.1.2.jar
90.7 KB
diff --git a/‎jars/MM_deps/formats-api-5.5.3.jar
116 KB b/‎jars/MM_deps/formats-api-5.5.3.jar
116 KB
diff --git a/‎jars/MM_deps/formats-bsd-5.5.3.jar
674 KB b/‎jars/MM_deps/formats-bsd-5.5.3.jar
674 KB
diff --git a/‎jars/MM_deps/formats-gpl-5.5.3.jar
1.24 MB b/‎jars/MM_deps/formats-gpl-5.5.3.jar
1.24 MB
diff --git a/‎jars/MM_deps/gentyref-1.1.0.jar
16.5 KB b/‎jars/MM_deps/gentyref-1.1.0.jar
16.5 KB
diff --git a/‎jars/MM_deps/gluegen-rt-2.3.2.jar
338 KB b/‎jars/MM_deps/gluegen-rt-2.3.2.jar
338 KB
diff --git a/‎jars/MM_deps/guava-21.0.jar
2.4 MB b/‎jars/MM_deps/guava-21.0.jar
2.4 MB
diff --git a/‎jars/MM_deps/ij-1.51n.jar
2.08 MB b/‎jars/MM_deps/ij-1.51n.jar
2.08 MB
diff --git a/‎jars/MM_deps/ij1-patcher-0.12.6.jar
152 KB b/‎jars/MM_deps/ij1-patcher-0.12.6.jar
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diff --git a/‎jars/MM_deps/imagej-common-0.24.4.jar
449 KB b/‎jars/MM_deps/imagej-common-0.24.4.jar
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diff --git a/‎jars/MM_deps/imagej-deprecated-0.1.2.jar
693 KB b/‎jars/MM_deps/imagej-deprecated-0.1.2.jar
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diff --git a/‎jars/MM_deps/imglib2-4.2.1.jar
632 KB b/‎jars/MM_deps/imglib2-4.2.1.jar
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diff --git a/‎jars/MM_deps/imglib2-algorithm-0.8.0.jar
459 KB b/‎jars/MM_deps/imglib2-algorithm-0.8.0.jar
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diff --git a/‎jars/MM_deps/imglib2-algorithm-fft-0.1.4.jar
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diff --git a/‎jars/MM_deps/imglib2-algorithm-gpl-0.2.1.jar
152 KB b/‎jars/MM_deps/imglib2-algorithm-gpl-0.2.1.jar
152 KB
diff --git a/‎jars/MM_deps/imglib2-ij-2.0.0-beta-37.jar
34.6 KB b/‎jars/MM_deps/imglib2-ij-2.0.0-beta-37.jar
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diff --git a/‎jars/MM_deps/imglib2-realtransform-2.0.0-beta-37.jar
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81.5 KB
diff --git a/‎jars/MM_deps/imglib2-roi-0.4.6.jar
139 KB b/‎jars/MM_deps/imglib2-roi-0.4.6.jar
139 KB
diff --git a/‎jars/MM_deps/itextpdf-5.5.11.jar
2.2 MB b/‎jars/MM_deps/itextpdf-5.5.11.jar
2.2 MB
diff --git a/‎jars/MM_deps/j3dcore-1.6.0-scijava-2.jar
1.85 MB b/‎jars/MM_deps/j3dcore-1.6.0-scijava-2.jar
1.85 MB
diff --git a/‎jars/MM_deps/j3dutils-1.6.0-scijava-2.jar
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1020 KB
diff --git a/‎jars/MM_deps/jai_imageio-5.5.3.jar
1020 KB b/‎jars/MM_deps/jai_imageio-5.5.3.jar
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diff --git a/‎jars/MM_deps/jama-1.0.3.jar
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diff --git a/‎jars/MM_deps/javassist-3.22.0-CR1.jar
718 KB b/‎jars/MM_deps/javassist-3.22.0-CR1.jar
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diff --git a/‎jars/MM_deps/jcommon-1.0.24.jar
323 KB b/‎jars/MM_deps/jcommon-1.0.24.jar
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diff --git a/‎jars/MM_deps/jdom2-2.0.6.jar
298 KB b/‎jars/MM_deps/jdom2-2.0.6.jar
298 KB
diff --git a/‎jars/MM_deps/jfreechart-1.0.19.jar
1.49 MB b/‎jars/MM_deps/jfreechart-1.0.19.jar
1.49 MB
diff --git a/‎jars/MM_deps/jgoodies-common-1.7.0.jar
33 KB b/‎jars/MM_deps/jgoodies-common-1.7.0.jar
33 KB
diff --git a/‎jars/MM_deps/jgoodies-forms-1.7.2.jar
115 KB b/‎jars/MM_deps/jgoodies-forms-1.7.2.jar
115 KB
diff --git a/‎jars/MM_deps/jgrapht-0.8.3.jar
240 KB b/‎jars/MM_deps/jgrapht-0.8.3.jar
240 KB
diff --git a/‎jars/MM_deps/jgraphx-3.4.1.3.jar
769 KB b/‎jars/MM_deps/jgraphx-3.4.1.3.jar
769 KB
diff --git a/‎jars/MM_deps/jhdf5-14.12.0.jar
9.43 MB b/‎jars/MM_deps/jhdf5-14.12.0.jar
9.43 MB
diff --git a/‎jars/MM_deps/jitk-tps-2.1.1.jar
18.8 KB b/‎jars/MM_deps/jitk-tps-2.1.1.jar
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diff --git a/‎jars/MM_deps/joda-time-2.9.9.jar
619 KB b/‎jars/MM_deps/joda-time-2.9.9.jar
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diff --git a/‎jars/MM_deps/jogl-all-2.3.2.jar
3.26 MB b/‎jars/MM_deps/jogl-all-2.3.2.jar
3.26 MB
diff --git a/‎jars/MM_deps/json-20170516.jar
55.9 KB b/‎jars/MM_deps/json-20170516.jar
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diff --git a/‎jars/MM_deps/jxrlib-all-0.2.1.jar
492 KB b/‎jars/MM_deps/jxrlib-all-0.2.1.jar
492 KB
diff --git a/‎jars/MM_deps/kryo-2.24.0.jar
331 KB b/‎jars/MM_deps/kryo-2.24.0.jar
331 KB
diff --git a/‎jars/MM_deps/log4j-1.2.17.jar
478 KB b/‎jars/MM_deps/log4j-1.2.17.jar
478 KB
diff --git a/‎jars/MM_deps/logback-classic-1.2.3.jar
284 KB b/‎jars/MM_deps/logback-classic-1.2.3.jar
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diff --git a/‎jars/MM_deps/logback-core-1.2.3.jar
461 KB b/‎jars/MM_deps/logback-core-1.2.3.jar
461 KB
diff --git a/‎jars/MM_deps/maars_lib-2.0.0-SNAPSHOT.jar
96.6 KB b/‎jars/MM_deps/maars_lib-2.0.0-SNAPSHOT.jar
96.6 KB
diff --git a/‎jars/MM_deps/metadata-extractor-2.6.2.jar
206 KB b/‎jars/MM_deps/metadata-extractor-2.6.2.jar
206 KB
diff --git a/‎jars/MM_deps/metakit-5.3.0.jar
13.9 KB b/‎jars/MM_deps/metakit-5.3.0.jar
13.9 KB
diff --git a/‎jars/MM_deps/mines-jtk-20151125.jar
1.92 MB b/‎jars/MM_deps/mines-jtk-20151125.jar
1.92 MB
diff --git a/‎jars/MM_deps/minlog-1.2.jar
4.85 KB b/‎jars/MM_deps/minlog-1.2.jar
4.85 KB
diff --git a/‎jars/MM_deps/mpicbg-1.1.1.jar
330 KB b/‎jars/MM_deps/mpicbg-1.1.1.jar
330 KB
diff --git a/‎jars/MM_deps/native-lib-loader-2.1.5.jar
17.5 KB b/‎jars/MM_deps/native-lib-loader-2.1.5.jar
17.5 KB
diff --git a/‎jars/MM_deps/netcdf-4.3.22.jar
4.38 MB b/‎jars/MM_deps/netcdf-4.3.22.jar
4.38 MB
diff --git a/‎jars/MM_deps/objenesis-2.1.jar
40.8 KB b/‎jars/MM_deps/objenesis-2.1.jar
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diff --git a/‎jars/MM_deps/ojalgo-43.0.jar
1.59 MB b/‎jars/MM_deps/ojalgo-43.0.jar
1.59 MB
diff --git a/‎jars/MM_deps/ome-common-5.3.1.jar
123 KB b/‎jars/MM_deps/ome-common-5.3.1.jar
123 KB
diff --git a/‎jars/MM_deps/ome-mdbtools-5.3.0.jar
90.4 KB b/‎jars/MM_deps/ome-mdbtools-5.3.0.jar
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diff --git a/‎jars/MM_deps/ome-poi-5.3.1.jar
929 KB b/‎jars/MM_deps/ome-poi-5.3.1.jar
929 KB
diff --git a/‎jars/MM_deps/ome-xml-5.5.4.jar
638 KB b/‎jars/MM_deps/ome-xml-5.5.4.jar
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diff --git a/‎jars/MM_deps/opencsv-3.9.jar
78.8 KB b/‎jars/MM_deps/opencsv-3.9.jar
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diff --git a/‎jars/MM_deps/pal-optimization-2.0.1.jar
43.4 KB b/‎jars/MM_deps/pal-optimization-2.0.1.jar
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diff --git a/‎jars/MM_deps/parsington-1.0.1.jar
42.7 KB b/‎jars/MM_deps/parsington-1.0.1.jar
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diff --git a/‎jars/MM_deps/perf4j-0.9.13.jar
107 KB b/‎jars/MM_deps/perf4j-0.9.13.jar
107 KB
diff --git a/‎jars/MM_deps/scijava-common-2.64.0.jar
766 KB b/‎jars/MM_deps/scijava-common-2.64.0.jar
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diff --git a/‎jars/MM_deps/slf4j-api-1.7.25.jar
40.2 KB b/‎jars/MM_deps/slf4j-api-1.7.25.jar
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diff --git a/‎jars/MM_deps/specification-5.5.4.jar
637 KB b/‎jars/MM_deps/specification-5.5.4.jar
637 KB
diff --git a/‎jars/MM_deps/trove4j-3.0.3.jar
2.41 MB b/‎jars/MM_deps/trove4j-3.0.3.jar
2.41 MB
diff --git a/‎jars/MM_deps/turbojpeg-5.5.3.jar
1.24 MB b/‎jars/MM_deps/turbojpeg-5.5.3.jar
1.24 MB
diff --git a/‎jars/MM_deps/udunits-4.3.18.jar
124 KB b/‎jars/MM_deps/udunits-4.3.18.jar
124 KB
diff --git a/‎jars/MM_deps/vecmath-1.6.0-scijava-2.jar
160 KB b/‎jars/MM_deps/vecmath-1.6.0-scijava-2.jar
160 KB
diff --git a/‎jars/MM_deps/xercesImpl-2.8.1.jar
1.16 MB b/‎jars/MM_deps/xercesImpl-2.8.1.jar
1.16 MB
diff --git a/‎jars/MM_deps/xml-apis-ext-1.3.04.jar
83.7 KB b/‎jars/MM_deps/xml-apis-ext-1.3.04.jar
83.7 KB
diff --git a/‎jars/MM_deps/xmlgraphics-commons-2.2.jar
631 KB b/‎jars/MM_deps/xmlgraphics-commons-2.2.jar
631 KB
diff --git a/‎jars/MM_deps/xmpcore-5.1.2.jar
115 KB b/‎jars/MM_deps/xmpcore-5.1.2.jar
115 KB
diff --git a/‎jars/maars_bfSeg_2.0.0-SNAPSHOT.jar
-5 Bytes b/‎jars/maars_bfSeg_2.0.0-SNAPSHOT.jar
-5 Bytes
diff --git a/‎jars/maars_lib_2.0.0-SNAPSHOT.jar
-3.74 KB b/‎jars/maars_lib_2.0.0-SNAPSHOT.jar
-3.74 KB
diff --git a/‎jars/maars_otf_2.0.0-SNAPSHOT.jar
10 Bytes b/‎jars/maars_otf_2.0.0-SNAPSHOT.jar
10 Bytes
diff --git a/‎jars/maars_post_2.0.0-SNAPSHOT.jar
152 Bytes b/‎jars/maars_post_2.0.0-SNAPSHOT.jar
152 Bytes
diff --git a/‎maars_lib/src/main/resources/maars_default_config.xml
+3-3 b/‎maars_lib/src/main/resources/maars_default_config.xml
+3-3
@@ -0,0 +1,4 @@
+#@OpService ops
+#@String(choices={"fluoConfigurator", "batchSegmentation", "batchFluoAnalysis"}, style="radioButtonVertical") method
+#@File(label="Select a directory", style="directory") d
+ops.run(method, d.getPath(), "maars_config.xml")
@@ -1,2 +1,8 @@
 #!/usr/bin/env bash
-mvn dependency:copy-dependencies -DoutputDirectory=../jars/MAARS_deps -DexcludeGroupIds=org.micromanager -DexcludeArtifactIds=commons-math3,eventbus,gentyref,jcommon,jfreechart,3D_Viewer,scijava-common
+cd maars_lib
+mvn dependency:copy-dependencies -DoutputDirectory=../jars/MAARS_deps -DexcludeGroupIds=org.micromanager
+cd ../maars_otf
+mvn dependency:copy-dependencies -DoutputDirectory=../jars/MAARS_deps -DexcludeGroupIds=org.micromanager
+cd ../maars_bfSeg
+mvn dependency:copy-dependencies -DoutputDirectory=../jars/MAARS_deps -DexcludeGroupIds=org.micromanager
+cd ..
@@ -3,7 +3,7 @@
     <CALIBRATION>0.1066</CALIBRATION>
     <PATH_TO_POSITION_LIST></PATH_TO_POSITION_LIST>
     <FLUO_ANALYSIS_PARAMETERS>
-        <FLUO_PREFIX></FLUO_PREFIX>
+        <FLUO_PREFIX>FLUO_1</FLUO_PREFIX>
         <PATH_TO_FLUO_ACQ_SETTING>AcqSettings_fluo.txt</PATH_TO_FLUO_ACQ_SETTING>
         <DYNAMIC>true</DYNAMIC>
         <!-- the order is important !!!! -->
@@ -57,13 +57,13 @@
         </DEFAULT_CHANNEL_PARAMATERS>
         <SAVING_PATH></SAVING_PATH>
         <!-- not editable with GUI -->
-        <BATCH_MODE>true</BATCH_MODE>
+        <BATCH_MODE>false</BATCH_MODE>
     </GENERAL_ACQUISITION_PARAMETERS>
     <SEGMENTATION_PARAMETERS>
         <!-- only useful in batch mode -->
         <TOLERANCE>10</TOLERANCE>
         <PATH_TO_BF_ACQ_SETTING>AcqSettings_bf.txt</PATH_TO_BF_ACQ_SETTING>
-        <SEG_PREFIX></SEG_PREFIX>
+        <SEG_PREFIX>BF_1</SEG_PREFIX>
         <SIGMA>3.0</SIGMA>
         <DIRECTION>-1</DIRECTION>
         <FOCUS>17</FOCUS>