nformation about your version of Java: os.arch => x86_64 os.name => Mac OS X os.version => 10.9.2 java.version => 1.6.0_65 java.vendor => Apple Inc. java.runtime.name => Java(TM) SE Runtime Environment java.runtime.version => 1.6.0_65-b14-462-11M4609 java.vm.name => Java HotSpot(TM) 64-Bit Server VM java.vm.version => 20.65-b04-462 java.vm.vendor => Apple Inc. java.vm.info => mixed mode java.awt.graphicsenv => apple.awt.CGraphicsEnvironment java.specification.name => Java Platform API Specification java.specification.version => 1.6 sun.cpu.endian => little sun.desktop => null file.separator => / The up-to-date check says: REMIND_LATER Information relevant to JAVA_HOME related problems: JAVA_HOME is set to: null ij.dir => /Applications/Fiji.app Information about the version of each plugin: 2c93d9a6:2d9d2593:be71a9c0 20140420050128 :00efaa6 426d64f4:be49972e:be49972e 20140420050128 :0307564 6cfb774f:b8f734bb:b8f734bb 20140420050128 :04478f7 6738a701:d6932866:d6932866 20140420050128 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plugins/Samples_-2.0.0-SNAPSHOT.jar 6d88799a 20140420050128 plugins/Script_Editor-2.0.0-SNAPSHOT.jar 578994ca 20140420050128 plugins/Scripts/File/Make_Screencast.bsh c70b2e6f 20140420050128 plugins/Scripts/File/Open_Samples/Adelsons_Squares.ijm 60df5674 20140420050128 plugins/Scripts/File/Open_Samples/Spirals_.ijm a3edd6db 20140420050128 plugins/Scripts/Image/Adjust/Scale_to_DPI.js 209aed52 20140420050128 plugins/Scripts/Image/Color/Set_Color_By_Wavelength.ijm 1de6c712 20140420050128 plugins/Scripts/Image/Hyperstacks/Temporal-Color_Code.ijm af064f17 20140420050128 plugins/Scripts/Plugins/Registration/Correct_3D_drift.py a6e496fc 20140420050128 plugins/Scripts/Plugins/Utilities/Create_Desktop_Icon.bsh b5ee58a2 20140420050128 plugins/Scripts/Plugins/Utilities/Find_Jar_For_Class.bsh fc46bd40 20140420050128 plugins/Scripts/Plugins/Utilities/Record_Desktop.py 9d4d012a 20140420050128 plugins/Scripts/Plugins/Utilities/Record_Window.py 8cb22fe2 20140420050128 plugins/Series_Labeler-2.0.0-SNAPSHOT.jar 7c62b5c5 20140420050128 plugins/SheppLogan_-2.0.0-SNAPSHOT.jar 332f6608 20140420050128 plugins/Sholl_Analysis-3.4.1.jar 95dc5b19 20140420050128 plugins/Simple_Neurite_Tracer-2.0.2-SNAPSHOT.jar 0bd5f179 20140420050128 plugins/Siox_Segmentation-1.0.1-SNAPSHOT.jar 52fecf09 20140420050128 plugins/Skeletonize3D_-1.0.1-SNAPSHOT.jar b0820703 20140420050128 plugins/Snakuscule_-2.0.0-SNAPSHOT.jar 33b6af85 20140420050128 plugins/SplineDeformationGenerator_-2.0.0-SNAPSHOT.jar 27de591e 20140420050128 plugins/StackReg_-2.0.0-SNAPSHOT.jar 736bb192 20140420050128 plugins/Stack_Manipulation-2.0.0-SNAPSHOT.jar 59f36299 20140420050128 plugins/Statistical_Region_Merging-2.0.0-SNAPSHOT.jar 08a4daec 20140420050128 plugins/Stitching_-2.0.0-SNAPSHOT.jar 30100de7 20140420050128 plugins/Sync_Win-1.7-fiji2-SNAPSHOT.jar 685ca9dc 20140420050128 plugins/Thread_Killer-2.0.0-SNAPSHOT.jar 2cee6c37 20140420050128 plugins/Threshold_Colour-2.0.1-SNAPSHOT.jar d822b123 20140420050128 plugins/Time_Stamper-2.0.0-SNAPSHOT.jar 584cb5b9 20140420050128 plugins/ToAST_-25.0.1-SNAPSHOT.jar 4cf59217 20140420050128 plugins/TopoJ_-2.0.0-SNAPSHOT.jar 4de49e00 20140420050128 plugins/TrackMate_-2.2.0.jar f90d5cfd 20140420050128 plugins/Trainable_Segmentation-2.1.0-SNAPSHOT.jar 59124982 20140420050128 plugins/TrakEM2_-1.0b-SNAPSHOT.jar 8e7f3b79 20140420050128 plugins/TransformJ_-2.8.1-SNAPSHOT.jar c4e87a76 20140420050128 plugins/TurboReg_-2.0.0-SNAPSHOT.jar 9558400d 20140420050128 plugins/UnwarpJ_.jar a32dfe46 20140420050128 plugins/Utilities/Close_All_Without_Saving.txt 253c6df4 20140420050128 plugins/VIB_-2.0.0-SNAPSHOT.jar baa78901 20140420050128 plugins/Vaa3d_Reader-2.0.0-SNAPSHOT.jar 81279d21 20140420050128 plugins/Video_Editing-2.0.0-SNAPSHOT.jar 73396eef 20140420050128 plugins/View5D_-1.3.1-SNAPSHOT.jar 980c0ed9 20140420050128 plugins/Volume_Calculator-1.0.1-SNAPSHOT.jar 2ef6f1eb 20140420050128 plugins/Volume_Viewer-2.01.1-SNAPSHOT.jar 2079ca32 20140420050128 plugins/bUnwarpJ_-2.6.1-SNAPSHOT.jar 9467b1a2 20140420050128 plugins/bio-formats_plugins-5.0.1.jar 0307564a 20140420050128 plugins/blockmatching_-2.0.0-SNAPSHOT.jar 659ad6a3 20140420050128 plugins/ij-ImageIO_.jar 82f900ac 20140420050128 plugins/level_sets-1.0.1-SNAPSHOT.jar df2af815 20140420050128 plugins/mpicbg_-0.6.1-SNAPSHOT.jar 5e32d936 20140420050128 plugins/panorama_.jar 96b34801 20140420050128 plugins/readme.txt 4bd07822 20140420050128 plugins/register_virtual_stack_slices-2.0.0-SNAPSHOT.jar 16012d5a 20140420050128 plugins/registration_3d-2.0.0-SNAPSHOT.jar 34b7341d 20140420050128 retro/backport-util-concurrent-3.1.jar 8759ba20 20140420050128 retro/retrotranslator-runtime-1.2.9.jar a6d5a3b2 20140420050128 retro/retrotranslator-transformer-1.2.9.jar d7160d38 20140420050128 scripts/InstallJava3D.m 05a92a3c 20140420050128 scripts/IsJava3DInstalled.m ff34d026 20140420050128 scripts/Matlab3DViewerDemo_1.m 25be149f 20140420050128 scripts/Matlab3DViewerDemo_2.m cb529b6c 20140420050128 scripts/Matlab3DViewerDemo_3.m 53d2da73 20140420050128 scripts/Matlab3DViewerIntroduction.m 4bb342fa 20140420050128 scripts/Miji.m 868cd434 20140420050128 scripts/Miji_Test.m dc94c3a3 20140420050128 scripts/bfopen.m a77cab39 20140420050128 scripts/importTrackMateTracks.m The MACRO that i'm using: run("Median...", "radius=2"); min=newArray(3); max=newArray(3); filter=newArray(3); a=getTitle(); run("HSB Stack"); run("Convert Stack to Images"); selectWindow("Hue"); rename("0"); selectWindow("Saturation"); rename("1"); selectWindow("Brightness"); rename("2"); min[0]=0; max[0]=255; filter[0]="pass"; min[1]=0; max[1]=255; filter[1]="pass"; min[2]=87; max[2]=255; filter[2]="stop"; for (i=0;i<3;i++){ selectWindow(""+i); setThreshold(min[i], max[i]); run("Convert to Mask"); if (filter[i]=="stop") run("Invert"); } imageCalculator("AND create", "0","1"); imageCalculator("AND create", "Result of 0","2"); for (i=0;i<3;i++){ selectWindow(""+i); close(); } selectWindow("Result of 0"); close(); selectWindow("Result of Result of 0"); rename(a); run("Grays");