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Bugzilla – Bug 698 |
TrakEM2: "Export -> Make Flat Image ..." : GOOD vs Patch.makeFlatImage: BAD |
Last modified: 2014-01-29 13:57:55 CST |
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NOTICE! This is a static HTML version of a legacy Fiji BugZilla bug. The Fiji project now uses GitHub Issues for issue tracking. Please file all new issues there. |
| TrakEM2: "Export -> Make Flat Image ..." : GOOD vs Patch.makeFlatImage: BAD | |
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When I export and downscale an image in TrakEM2, the manual and script approaches do not give me the same result. The manual way looks ok but the script (see below) gives me a bad image quality. Using Patch.makeFlatImage or project.getLoader().makeFlatImage gives the same result. Below is the procedure to replicate the problem. Thanks for your help Thomas Import a picture into a new TrakEM project (the Fiji template 'boats' for example). -- Manual -- Export -> Make Flat Image ... -> Choose a 10% scale factor. The result looks ok. -- Script -- (In the script editor. The TrakEM project should be open) from java.awt import Color project = Project.getProjects().get(0) layerset = project.getRootLayerSet() loader = project.getLoader() for l,layer in enumerate(layerset.getLayers()): IJ.log('Exporting layer ' + str(l)) ip = Patch.makeFlatImage(ImagePlus.GRAY8,layer,layerset.get2DBounds(),0.1,layer.getAll(Patch), Color.black) imp = ImagePlus("Flat_montage", ip) imp.show() The result looks bad. Information about your version of Java: os.arch => amd64 os.name => Windows NT (unknown) os.version => 6.2 java.version => 1.6.0_24 java.vendor => Sun Microsystems Inc. java.runtime.name => Java(TM) SE Runtime Environment java.runtime.version => 1.6.0_24-b07 java.vm.name => Java HotSpot(TM) 64-Bit Server VM java.vm.version => 19.1-b02 java.vm.vendor => Sun Microsystems Inc. java.vm.info => mixed mode java.awt.graphicsenv => sun.awt.Win32GraphicsEnvironment java.specification.name => Java Platform API Specification java.specification.version => 1.6 sun.cpu.endian => little sun.desktop => windows file.separator => \ The up-to-date check says: UP_TO_DATE Information relevant to JAVA_HOME related problems: JAVA_HOME is set to: D:\FIJI-W~2\Fiji.app/java/win64/jdk1.6.0_24//jre ij.dir => D:\FIJI-W~2\Fiji.app Information about the version of each plugin: 2c93d9a6:2d9d2593:be71a9c0 20130807155009 :00efaa6 9770ed7e:40cf929f:0606b3ee 20130520193855 :011890f 13ce586a:be23db6b:315fb93c 20131026202116 :02ea642 426d64f4:be49972e:be49972e 20131026202150 :0307564 8c8f6d33:ac4c137b:ac4c137b 20130729150445 :0326851 dc0a9d07:01345c54:3449bd49 20140110160504 :034fe21 6cfb774f:b8f734bb:b8f734bb 20140110160512 :04478f7 24590873:d3ccdd03:d3ccdd03 20130502153702 :044f3fe 015d8a2e:9cbf5db5:8de91f6b 20130819125438 :04782f0 6738a701:d6932866:d6932866 20130729150437 :04a4a5c 30420365:5a23ed73:5a23ed73 20130502153702 :069ebf3 3f876cb1:205f633a:205f633a 20130502153704 :07e9a49 738cf583:36e9a80a:bca93bda 20140110160453 :087a0a0 09868b51:09868b51:09868b51 20130502153702 :09868b5 b0e5ec4f:f9fb1b1e:7b2063a5 20130729150359 :0a2a17f 0a93f0be:0a93f0be:0a93f0be 20130502153702 :0a93f0b 1cea16c4:5674b1fc:c120c076 20140110160455 :0af0912 cd9eda33:239d2a49:f25c125a 20130502153704 :0b76869 079072d5:3f320e23:0bfab9b2 20130729150410 :0bc2f58 61ab84fd:2a4992aa:2a4992aa 20130729150448 :0bd5f17 283a7027:9263e996:9263e996 20130502153704 :0c2a5e1 72ea2fc2:73af3a23:73af3a23 20130520193955 :0d4057e 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20130502153704 :166036a b2275d1c:f7a5eb30:4918803a 20130502153702 :16bbe0c 68b5039b:0dc5c1a8:4a8bf900 20131026202056 :1728149 174a4b19:174a4b19:174a4b19 20130502153702 :174a4b1 89258d31:f1bb8ccf:cc515ccd 20130807154950 :17c042b 53b934a5:21896ddd:980cba3f 20130729150415 :17eeef0 c0edb63b:3b1f88b2:4ed7ae8c 20130611095235 :18606e8 97d046c8:9467908f:9467908f 20130729150458 :186e052 f0dde207:5b731066:5b731066 20130729150425 :1902ce8 2750162f:ee9e5ec5:ee9e5ec5 20130729150440 :19181db 95a9e32c:c395f259:925450a6 20130729150409 :1941524 1a6345a2:1a6345a2:1a6345a2 20130502153702 :1a6345a 5a40b171:9017d436:63e90571 20130502153704 :1ad3be0 25fdd56a:2545e299:5f7905f1 20140110160430 :1ad6b45 e094b1c1:44ab48c3:5633cb6f 20130502153706 :1b71cda 19335ace:fc1a3d5e:28e1ad96 20130520193951 :1c88458 1cee26bc:1cee26bc:1cee26bc 20130502153702 :1cee26b eadb2593:64b484df:281c847d 20130729150354 :1d44a0d cd63c0bf:92f964a3:92f964a3 20130502153706 :1daf580 981f35fd:f48d5b7d:a7d5f82c 20130502153706 :1dedefe 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20130520193955 :248a32e 357b1056:8156e009:8156e009 20130502153706 :24d47d7 d7c670b5:f555145a:f555145a 20130729150455 :253c6df 6f15ca4d:9a219c5c:48ce3361 20130731154015 :258c223 83895477:0a5b1beb:34181783 20140123181427 :259df97 726af6cb:5ad6878a:5ad6878a 20130502153702 :263158a 265850b3:265850b3:265850b3 20130502153702 :265850b def4038f:787984b3:d558718f 20130502153704 :265cb26 a540e248:2c1035fa:2c1035fa 20130520212906 :27b4abe 0f832edd:81589f14:1651ecce 20131031211217 :27c6f58 97baa7b5:de42e047:de42e047 20130729150426 :27de591 eedac93f:52476ec4:effdb45e 20130807155012 :2837db0 eff3a295:639027a3:639027a3 20130729150452 :295ba57 a1e1676a:1399a949:2fece12c 20130805153412 :2a17560 c716cfad:c357e934:69c529de 20130611095300 :2a26b5e 7caabb2a:c5a9c9bf:c5a9c9bf 20130823141230 :2a72259 d9e0bf3a:1d693ab8:60903c8f 20130502153706 :2b318f7 c92bc1d4:2928de88:ba375fb6 20130503235225 :2bd4340 84c6ebeb:1dc1193a:1dc1193a 20130729150447 :2bda1f6 0e158e32:8cdb360f:8cdb360f 20131026202153 :2bde09b 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20130729150442 :34d0deb 34dfe8f4:34dfe8f4:34dfe8f4 20130502153702 :34dfe8f fc45d44e:027485e0:027485e0 20130902115859 :3582cd5 1910f7d0:35de4ecb:d9674003 20131026202054 :35c256a b6a2df10:9b100a5d:9b100a5d 20131026202145 :369b635 55f79ce5:c3ab5cd0:c3ab5cd0 20130502153702 :36b6b0d 91d6774f:81ee7dda:831d5b93 20130502153708 :36cdef5 74eb0251:4dd61c5a:008da5fc 20130729150343 :37afe6e 76812dce:45409dcf:25d93bd6 20130805153413 :37da6fe 49a38892:86901120:86901120 20050928181902 :3814d5a b851408d:46e4714e:46e4714e 20131026202139 :38b2c2b d3aa0468:2dbaef27:eb94a247 20131026202059 :398ab19 39d4aaaf:39d4aaaf:39d4aaaf 20130502153702 :39d4aaa 9373a092:2bfe6962:310d12cb 20130807154946 :39eba37 27359058:67e005e1:67e005e1 20140120110911 :3aacabe 02bc6560:8b5fc706:7a3e1a44 20140110160437 :3ae2fa1 96ab42df:8aff2407:77ccabc8 20130902115857 :3b5dda7 4b051b74:2a0a96ae:2a0a96ae 20130729150500 :3bac3fb 7a2916d6:39f45f23:f23b1754 20131026202122 :3da60e9 581a3b53:c57906e2:c57906e2 20130729150423 :3e4163b 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20140110160527 :4792fc4 bbaa5d63:c3118719:98177a88 20130807155013 :4893859 b084f173:f2aa5b6f:5e158006 20130502153704 :48b11a3 48b8264d:48b8264d:48b8264d 20130502153702 :48b8264 82470171:71558705:8f68b42c 20130520193854 :48d65ab c46c1146:f92c1a68:9d580ea8 20130502153704 :491c119 1cb0f570:531ace18:32378753 20130502153704 :491e89c 49378a9e:49378a9e:49378a9e 20130502153702 :49378a9 4e413753:44aafb65:9f9ca554 20130502153704 :49fa9fc 3d3036a6:dc5d617c:8c8eb84b 20131026202119 :4a6a7fb 0d1491b2:fd451b31:f1a32dea 20140110160431 :4aaaf83 149624c4:43bb3a7b:43bb3a7b 20130502153702 :4b60e05 a24ce274:37fb74fb:b76d671a 20130502153704 :4c95b69 b0363640:88d2d3c3:88d2d3c3 20130729150453 :4cf5921 b7a44134:037852cf:0246b1cb 20130729150456 :4d3cf93 aa7b2f5e:1e637876:320feebf 20140110160503 :4d4ed5c 4347a907:0a7f6fd2:0a7f6fd2 20130729150503 :4d6319b 4d7eaf23:4d7eaf23:4d7eaf23 20130502153702 :4d7eaf2 4ddf620c:4ddf620c:4ddf620c 20130502153702 :4ddf620 8eecd63b:45f47f5c:45f47f5c 20130729150451 :4ea625b 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20130502153704 :5967b4d c3cdfa73:da9726b8:da9726b8 20130729150452 :59f3629 dead0306:87f2e802:dbab80ab 20130502153702 :5a0c796 ba51e520:cfb31b56:40b8050c 20130502153702 :5a50a9e 8e36ff4d:08337e72:08337e72 20131026202209 :5a6f6f2 80dd7c7b:05441be1:65145dfe 20131026202132 :5b03a32 dd22ba46:669f94f8:7f3c7afe 20140110160512 :5b5857d c668544b:3d92075e:1000a27f 20130502153706 :5b6595f 024477fb:38a320fe:f04f945c 20131026202107 :5b86e1d dbe04762:dec2cbc4:dec2cbc4 20131026202127 :5bd64fb 93f3a920:9318a836:9318a836 20130729150424 :5c7f396 0eb05f4b:a21f73a7:a21f73a7 20130502153706 :5ce5840 82562288:7e94c46c:a49c22f8 20130502153704 :5d6e928 7f225384:a9f2cced:544df635 20140110160526 :5da6834 fcdf8254:1ca2d42b:1ca2d42b 20130520193956 :5dc26c8 bd608d78:7f84137c:02348ce5 20130729150346 :5e0e489 5e32d936:5e32d936:5e32d936 20130502153702 :5e32d93 1680407d:5f2bf066:5f2bf066 20130807155022 :5e73d56 8a2d5aa5:0f8eafea:9c8df86d 20131026202120 :5eff582 96f8f5a6:62d0cdd0:62d0cdd0 20140120110932 :5f45848 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5fb422d7:5bab7768:5bab7768 20130502153702 :ff131d4 a15791e0:723fa207:2510e060 20131026202126 :ffff0cc 7c30c48a 20130503003702 Contents/Info.plist 6b82c620 20130503003702 Contents/Resources/Fiji.icns 992807f6 20130503003702 Contents/Resources/ImageJ.icns 0f7817ae 20130807155008 ImageJ-win64.exe 1faaeed6 20130503003708 images/icon-flat.png a02d5340 20130503003708 images/icon.png c3f8675e 20130503003702 jars/Jama.jar ad44ab73 20130503003702 jars/VIB-lib-2.0.0-SNAPSHOT.jar bd573380 20130503003702 jars/VectorString.jar 8e160955 20130503003702 jars/ant-junit.jar 4124ed0d 20130503003702 jars/ant-launcher.jar b18659ff 20130503003702 jars/ant-nodeps.jar 70c12cd3 20130503003702 jars/ant.jar ff131d48 20130503003702 jars/autocomplete.jar 2daf8bdd 20130503003702 jars/base64-2.3.8.jar 5a0c7964 20130503003702 jars/batik.jar ab79445e 20130503003702 jars/bcmail-jdk14-138.jar d2b52892 20130503003702 jars/bcprov-jdk14-138.jar 5f458483 20140120110932 jars/bio-formats-4.4.10.jar b8d5d243 20131026202207 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jars/ij-launcher-2.0.2.jar 3ae2fa17 20140110160437 jars/ij-legacy-2.0.0-beta-7.6.jar 0af09126 20140110160455 jars/ij-minimaven-2.0.0-beta-7.6.jar 9601a9e5 20140110160442 jars/ij-options-2.0.0-beta-7.6.jar 5479459b 20140110160453 jars/ij-platforms-2.0.0-beta-7.6.jar 9e8320ae 20140110160457 jars/ij-scripting-beanshell-2.0.0-beta-7.6.jar b85472b7 20140110160504 jars/ij-scripting-clojure-2.0.0-beta-7.6.jar cf36bec4 20140110160457 jars/ij-scripting-java-2.0.0-beta-7.6.jar 851a4970 20140110160509 jars/ij-scripting-javascript-2.0.0-beta-7.6.jar 034fe219 20140110160504 jars/ij-scripting-jruby-2.0.0-beta-7.6.jar fc7638b2 20140110160504 jars/ij-scripting-jython-2.0.0-beta-7.6.jar 6be7010c 20140110160501 jars/ij-text-2.0.0-beta-7.6.jar 4aaaf835 20140110160431 jars/ij-tools-2.0.0-beta-7.6.jar d1fb3f0d 20140110160431 jars/ij-ui-2.0.0-beta-7.6.jar e3847e56 20140110160430 jars/ij-ui-common-awt-2.0.0-beta-7.6.jar 087a0a05 20140110160453 jars/ij-ui-swing-2.0.0-beta-7.6.jar dc8bfe05 20140110160456 jars/ij-ui-swing-commands-2.0.0-beta-7.6.jar 920bb88d 20140110160455 jars/ij-ui-swing-script-editor-2.0.0-beta-7.6.jar e5966a31 20140110160430 jars/ij-ui-swing-tools-2.0.0-beta-7.6.jar adc2cad2 20140108135937 jars/ij-ui-swing-updater-2.0.0-beta-7.6.jar ebc9b1da 20140114172246 jars/ij-updater-core-2.0.0-SNAPSHOT.jar 1f0b3f86 20140110160430 jars/ij-updater-ssh-2.0.0-beta-7.6.jar 8a4bbd15 20140110160501 jars/ij-updater-webdav-2.0.0-beta-7.6.jar 1ad6b458 20140110160430 jars/ij-util-awt-2.0.0-beta-7.6.jar 7261bf6a 20140110160442 jars/ij-util-swing-2.0.0-beta-7.6.jar be2287e8 20130503003704 jars/imagescience-2.4.1.jar 780fae40 20130503003704 jars/imageware.jar a24f6a79 20140110160453 jars/imglib2-2.0.0-beta-22.jar 6ddd30d8 20140110160443 jars/imglib2-algorithms-2.0.0-beta-22.jar 5b03a327 20131026202132 jars/imglib2-algorithms-gpl-2.0.0-beta-20.jar 4250a4fd 20131026202132 jars/imglib2-algorithms-legacy-2.0.0-beta-20.jar 78a6628b 20131026202122 jars/imglib2-ij-2.0.0-beta-20.jar 1eb9422e 20131026202114 jars/imglib2-io-2.0.0-beta-20.jar 4d4ed5c1 20140110160503 jars/imglib2-meta-2.0.0-beta-22.jar ce659130 20140110160435 jars/imglib2-ops-2.0.0-beta-22.jar 6eeb7cb2 20131026202126 jars/imglib2-realtransform-2.0.0-beta-20.jar f9f1333a 20130503003704 jars/itext-2.1.5.jar c4258671 20130503003704 jars/itextpdf.jar 0dccf163 20130503003704 jars/jacl.jar 8c636e50 20130503003704 jars/jai_codec.jar 717dd8e0 20130503003704 jars/jai_core.jar e5852db5 20130729150343 jars/jai_imageio-1.0.1.jar dd562d0d 20140110160509 jars/jama-1.0.2.jar e4ac596e 20130503003704 jars/java-cup-0.11a.jar 15f34947 20130503003704 jars/javac.jar fb25609e 20130503003704 jars/javassist-3.16.1-GA.jar ccf6c908 20130503003704 jars/jcommon-1.0.17.jar efe2e903 20131026202124 jars/jdatepicker-1.3.2.jar c295a4c5 20130503003704 jars/jdom-2.0.2.jar 64241209 20130503003704 jars/jdom-contrib.jar 166036ab 20130503003704 jars/jep.jar 55d8499c 20130503003704 jars/jfreechart-1.0.14.jar 0e15c072 20130503003704 jars/jgrapht-0.8.3.jar 0b768690 20130503003704 jars/jgraphx-1.10.4.1.jar 242749dc 20130503003704 jars/jhotdraw-7.6.0.jar 90915f54 20130503003704 jars/jna.jar 1ad3be0d 20130503003704 jars/jpedalSTD.jar da499a7d 20130503003704 jars/jruby.jar 65f86378 20130503003706 jars/js.jar 2ce2c00a 20130503003706 jars/jsch-0.1.49.jar 24d47d70 20130503003706 jars/junit-4.8.1.jar f5968a72 20130503003706 jars/jython.jar 5ce5840c 20130503003706 jars/jzlib.jar 5a6f6f25 20131026202209 jars/legacy-imglib1-2.0.0-SNAPSHOT.jar cc466590 20131026202106 jars/loci-common-4.4.9.jar 35c256ae 20131026202054 jars/log4j-1.2.17.jar d1d9b590 20140110160502 jars/mapdb-0.9.7.jar 1daf5806 20130503003706 jars/markdownj-0.3.0-1.0.2b4.jar e8d453ec 20131026202139 jars/mdbtools-java-4.4.9.jar 70e68706 20131026202126 jars/metakit-4.4.9.jar 7f0caa5d 20130503003706 jars/miglayout-3.7.3.1-swing.jar a11cfc71 20130729150419 jars/mij-1.3.6-fiji2-SNAPSHOT.jar b6bf3817 20140110160509 jars/mines-jtk-20100113.jar 5bd64fbe 20131026202127 jars/mpicbg-0.6.1-SNAPSHOT.jar 8b4b4a32 20131026202217 jars/netcdf-4.0.03.jar f41603bf 20130503003706 jars/object-inspector-0.1.jar 5da6834c 20140110160526 jars/ome-formats-0.3.0.jar 3aacabe8 20140120110911 jars/ome-xml-4.4.10.jar e0088259 20130503003706 jars/pal-optimization.jar 82577709 20130503003706 jars/pentaho-package-manager-1.0.0.jar d5a76672 20131026202131 jars/poi-loci-4.4.9.jar c586a356 20130503003706 jars/postgresql.jar 72184439 20130729150414 jars/rsyntaxtextarea-2.0.4.1.jar ddb25fc7 20140120110914 jars/scifio-0.8.2.jar 4792fc4e 20140110160527 jars/scifio-bf-compat-1.3.2.jar af5808fb 20140110160526 jars/scifio-lifesci-0.2.2.jar a465aafa 20140108135941 jars/scijava-common-2.7.0.jar eedc0cd9 20130503003706 jars/serializer-2.7.1.jar 572a727b 20131026202107 jars/slf4j-api-1.7.2.jar 9ae3dd1b 20131026202105 jars/slf4j-log4j12-1.7.2.jar 1dedefe8 20130503003706 jars/tools-1.4.2.jar 68c26a79 20131026202125 jars/udunits-4.3.18.jar 7d5ba6c5 20130503003708 jars/wavelets.jar fc6c0417 20130503003708 jars/weave_jy2java.jar 9a71e194 20130503003708 jars/weka-dev-3.7.6.jar 36cdef55 20130503003708 jars/xalan-2.7.1.jar da8b05de 20130503003708 jars/xml-apis-1.3.04.jar c432f64b 20130503003708 luts/16_colors.lut 89419f99 20130503003708 luts/5_ramps.lut dc3a1bdd 20130503003708 luts/6_shades.lut 0b3bbb6c 20130503003708 luts/Cyan Hot.lut 655b55e6 20130503003708 luts/Green Fire Blue.lut 2918f6d3 20130503003708 luts/HiLo.lut a3312d3f 20130503003708 luts/ICA.lut db5bf8a4 20130503003708 luts/ICA2.lut 9f7dd167 20130503003708 luts/ICA3.lut 697dd3a4 20130503003708 luts/Magenta Hot.lut 524604de 20130503003708 luts/Orange Hot.lut 9c9a56c2 20130503003708 luts/Rainbow RGB.lut 4e686ec6 20130503003708 luts/Red Hot.lut 2fdb7c96 20130503003708 luts/Thermal.lut 32157491 20130503003708 luts/Yellow Hot.lut a4cec22b 20130503003708 luts/blue_orange_icb.lut c9e396a3 20130503003708 luts/brgbcmyw.lut 60f85e63 20130503003708 luts/cool.lut ba88e5f3 20130503003708 luts/edges.lut 0a4dce83 20130503003708 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scripts/Matlab3DViewerDemo_3.m 53d2da73 20130503003708 scripts/Matlab3DViewerIntroduction.m 4bb342fa 20130503003708 scripts/Miji.m 868cd434 20130503003708 scripts/Miji_Test.m dc94c3a3 20130503003708 scripts/bfopen.m a77cab39 20130808172744 scripts/importTrackMateTracks.mThomas, use the FSLoader instance from the current Project, and the getFlatImage method instead: from ini.trakem2 import Project from ini.trakem2.display import Display, Patch # project = Project.getProjects()[0] # or: project = Display.getFront().getProject() # or: project = ControlWindow.getActive() project = Project.getProjects().get(0) layerset = project.getRootLayerSet() loader = project.getLoader() for index, layer in enumerate(layerset.getLayers()): IJ.log('Exporting layer ' + str(index + 1)) imp = loader.makeFlatImage(layer, layerset.get2DBounds(), 0.1, # your scale of 10% 0xffffffff, # full opacity of all ARGB channels ImagePlus.GRAY8, # image type. Also works with COLOR_RGB Patch, layer.getAll(Patch), True, # quality Color.black, None) # do not highlight any Displayable imp.show() See also: https://github.com/fiji/TrakEM2/blob/master/TrakEM2_/src/main/java/ini/trakem2/persistence/Loader.java#L2701Sorry should have said loader.getFlatImage, not makeFlatImage, in the script above. Complete: from ini.trakem2 import Project from ini.trakem2.display import Display, Patch # project = Project.getProjects()[0] # or: project = Display.getFront().getProject() # or: project = ControlWindow.getActive() project = Project.getProjects().get(0) layerset = project.getRootLayerSet() loader = project.getLoader() for index, layer in enumerate(layerset.getLayers()): IJ.log('Exporting layer ' + str(index + 1)) imp = loader.getFlatImage(layer, layerset.get2DBounds(), 0.1, # your scale of 10% 0xffffffff, # full opacity of all ARGB channels ImagePlus.GRAY8, # image type. Also works with COLOR_RGB Patch, layer.getAll(Patch), True, # quality Color.black, None) # do not highlight any Displayable imp.show()Yes it works (except the typo: 0xffffffff should be 0x7fffffff). Thank you for your help. Thomas Final complete : from ini.trakem2 import Project from ini.trakem2.display import Display, Patch # project = Project.getProjects()[0] # or: project = Display.getFront().getProject() # or: project = ControlWindow.getActive() project = Project.getProjects().get(0) layerset = project.getRootLayerSet() loader = project.getLoader() for index, layer in enumerate(layerset.getLayers()): IJ.log('Exporting layer ' + str(index + 1)) imp = loader.getFlatImage(layer, layerset.get2DBounds(), 0.1, # your scale of 10% 0x7fffffff, # full opacity of all ARGB channels ImagePlus.GRAY8, # image type. Also works with COLOR_RGB Patch, layer.getAll(Patch), True, # quality Color.black, None) # do not highlight any Displayable imp.show()