Eclipse: problem installing dependencies (ij package not found)

Development
,
#1

Windows 8, Java8, Eclipse

I am trying to modify with Eclipse a plugin (bigdataviewer-core, that I have cloned and successfully built) in a freshly downloaded Fiji installation by adding a new file.

I have followed the instructions to Install dependencies (see picture below) but I get
package ij does not exist package ini.trakem2.display does not exist package ini.trakem2.display does not exist package ini.trakem2.persistence does not exist.

Should not these dependencies be given by the existing installation ?
Thanks for your help

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.

#2

At a glance, your configuration looks OK to me, although I personally have never copied dependencies to Eclipse in that way. When you say you “get” those error messages: where do they appear? In the ImageJ Console window? Log window? Somewhere else?

Another question: since all you are trying to do is add one single source file, is there some reason “Option 1” (just overwrite that single JAR file) is not sufficient for your deployment needs? If you did not add a new dependency, then the “Option 2” stuff is overkill for what you are trying to achieve.

#3

Thank you for having a look at my question.

Sorry, that was unclear. When I make “Run as” on the pom.xml of the bigdataviewer-core Eclipse project in which I have only added the file I mentioned, I get the following in the console of Eclipe (there is a character number limit so I removed many lines with “Generating …” and some errors at the end)

[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building BigDataViewer Core 2.1.1-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.3.1:enforce (enforce-rules) @ bigdataviewer-core ---
[INFO] Adding ignorable dependency: null:jcodings:null
[INFO]   Adding ignore: org/jcodings/*
[INFO] Adding ignorable dependency: null:jnr-constants:null
[INFO]   Adding ignore: com/kenai/constantine/*
[INFO]   Adding ignore: jnr/constants/*
[INFO] Adding ignorable dependency: null:jnr-ffi:null
[INFO]   Adding ignore: jnr/ffi/*
[INFO] Adding ignorable dependency: null:VIB-lib:null
[INFO]   Adding ignore: javax/media/j3d/
[INFO] Adding ignorable dependency: null:j3d-core:null
[INFO]   Adding ignore: javax/media/j3d/
[INFO] Adding ignorable dependency: null:joda-time:null
[INFO]   Adding ignore: *
[INFO] Adding ignorable dependency: null:slf4j-log4j12:null
[INFO]   Adding ignore: org/slf4j/impl/*
[INFO] Adding ignorable dependency: batik:batik:null
[INFO]   Adding ignore: *
[INFO] Adding ignorable dependency: jama:jama:null
[INFO]   Adding ignore: Jama/*
[INFO] Adding ignorable dependency: com.sun:tools:null
[INFO]   Adding ignore: *
[INFO] 
[INFO] --- build-helper-maven-plugin:1.9.1:regex-property (sanitize-version) @ bigdataviewer-core ---
[INFO] 
[INFO] --- buildnumber-maven-plugin:1.3:create (default) @ bigdataviewer-core ---
[INFO] Executing: cmd.exe /X /C "git rev-parse --verify HEAD"
[INFO] Working directory: D:\Research\FijiJavaDevel\bigdataviewer-core
[INFO] Storing buildNumber: UNKNOWN at timestamp: 1455837935176
[WARNING] Cannot get the branch information from the git repository: 
Detecting the current branch failed: 'git' is not recognized as an internal or external command,
operable program or batch file.

[INFO] Executing: cmd.exe /X /C "git rev-parse --verify HEAD"
[INFO] Working directory: D:\Research\FijiJavaDevel\bigdataviewer-core
[INFO] Storing buildScmBranch: UNKNOWN_BRANCH
[INFO] 
[INFO] --- scijava-maven-plugin:0.5.0:set-rootdir (set-rootdir) @ bigdataviewer-core ---
[INFO] Setting rootdir: D:\Research\FijiJavaDevel\bigdataviewer-core
[INFO] 
[INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ bigdataviewer-core ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 2 resources
[INFO] 
[INFO] --- maven-compiler-plugin:3.1:compile (default-compile) @ bigdataviewer-core ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ bigdataviewer-core ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory D:\Research\FijiJavaDevel\bigdataviewer-core\src\test\resources
[INFO] 
[INFO] --- maven-compiler-plugin:3.1:testCompile (default-testCompile) @ bigdataviewer-core ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-surefire-plugin:2.17:test (default-test) @ bigdataviewer-core ---
[INFO] 
[INFO] --- maven-jar-plugin:2.5:jar (default-jar) @ bigdataviewer-core ---
[INFO] 
[INFO] --- maven-source-plugin:2.3:jar-no-fork (default) @ bigdataviewer-core ---
[INFO] Building jar: D:\Research\FijiJavaDevel\bigdataviewer-core\target\bigdataviewer-core-2.1.1-SNAPSHOT-sources.jar
[INFO] 
[INFO] --- maven-source-plugin:2.3:jar-no-fork (attach-sources) @ bigdataviewer-core ---
[INFO] 
[INFO] --- maven-javadoc-plugin:2.9.1:jar (attach-javadocs) @ bigdataviewer-core ---
[INFO] 
Loading source files for package bdv...
Loading source files for package bdv.export...
Loading source files for package bdv.img.cache...
Loading source files for package bdv.img.catmaid...
Loading source files for package bdv.img.hdf5...
Loading source files for package bdv.img.imaris...
Loading source files for package bdv.img.openconnectome...
Loading source files for package bdv.img.remote...
Loading source files for package bdv.img.trakem2...
Loading source files for package bdv.spimdata.legacy...
Loading source files for package bdv.spimdata...
Loading source files for package bdv.spimdata.tools...
Loading source files for package bdv.tools.bookmarks...
Loading source files for package bdv.tools.boundingbox...
Loading source files for package bdv.tools.brightness...
Loading source files for package bdv.tools.crop...
Loading source files for package bdv.tools...
Loading source files for package bdv.tools.transformation...
Loading source files for package bdv.util...
Loading source files for package bdv.viewer.animate...
Loading source files for package bdv.viewer...
Loading source files for package bdv.viewer.overlay...
Loading source files for package bdv.viewer.render...
Loading source files for package bdv.viewer.state...
Loading source files for package net.imglib2.display...
Loading source files for package net.imglib2.img.basictypeaccess.volatiles.array...
Loading source files for package net.imglib2.img.basictypeaccess.volatiles...
Loading source files for package net.imglib2.interpolation.randomaccess...
Loading source files for package net.imglib2.type.volatiles...
Constructing Javadoc information...
Standard Doclet version 1.8.0_71
Building tree for all the packages and classes...
Generating D:\Research\FijiJavaDevel\bigdataviewer-core\target\apidocs\bdv\AbstractSpimSource.html...
Generating D:\Research\FijiJavaDevel\bigdataviewer-core\target\apidocs\bdv\AbstractViewerSetupImgLoader.html...
Generating D:\Research\FijiJavaDevel\bigdataviewer-core\target\apidocs\bdv\BigDataViewer.html...
Generating D:\Research\FijiJavaDevel\bigdataviewer-core\target\apidocs\bdv\BigDataViewerActions.html...
Generating D:\Research\FijiJavaDevel\bigdataviewer-core\target\apidocs\bdv\BigDataViewerActions.GoToBookmarkAction.html...
Generating D:\Research\FijiJavaDevel\bigdataviewer-core\target\apidocs\bdv\BigDataViewerActions.GoToBookmarkRotationAction.html...
Generating D:\Research\FijiJavaDevel\bigdataviewer-core\target\apidocs\bdv\BigDataViewerActions.LoadSettingsAction.html...
Generating D:\Research\FijiJavaDevel\bigdataviewer-core\target\apidocs\bdv\BigDataViewerActions.ManualTransformAction.html...
Generating D:\Research\FijiJavaDevel\bigdataviewer-core\target\apidocs\bdv\BigDataViewerActions.SaveSettingsAction.html...
Generating D:\Research\FijiJavaDevel\bigdataviewer-core\target\apidocs\bdv\BigDataViewerActions.SetBookmarkAction.html...
Generating D:\Research\FijiJavaDevel\bigdataviewer-core\target\apidocs\bdv\SpimSource.html...
Generating D:\Research\FijiJavaDevel\bigdataviewer-core\target\apidocs\bdv\ViewerImgLoader.html...
Generating D:\Research\FijiJavaDevel\bigdataviewer-core\target\apidocs\bdv\ViewerSetupImgLoader.html...
Generating D:\Research\FijiJavaDevel\bigdataviewer-core\target\apidocs\bdv\VolatileSpimSource.html...
Generating D:\Research\FijiJavaDevel\bigdataviewer-core\target\apidocs\bdv\export\Downsample.html...
Generating D:\Research\FijiJavaDevel\bigdataviewer-core\target\apidocs\bdv\export\ExportMipmapInfo.html...
Generating D:\Research\FijiJavaDevel\bigdataviewer-core\target\apidocs\bdv\export\ProgressWriter.html...
Generating D:\Research\FijiJavaDevel\bigdataviewer-core\target\apidocs\bdv\export\ProgressWriterConsole.html...
Generating D:\Research\FijiJavaDevel\bigdataviewer-core\target\apidocs\bdv\export\ProposeMipmaps.html...
Generating D:\Research\FijiJavaDevel\bigdataviewer-core\target\apidocs\bdv\export\SubTaskProgressWriter.html...
Generating D:\Research\FijiJavaDevel\bigdataviewer-core\target\apidocs\bdv\export\WriteSequenceToHdf5.html...
Generating D:\Research\FijiJavaDevel\bigdataviewer-core\target\apidocs\bdv\export\WriteSequenceToHdf5.AfterEachPlane.html...
Generating D:\Research\FijiJavaDevel\bigdataviewer-core\target\apidocs\bdv\export\WriteSequenceToHdf5.CellCreatorThread.html...
Generating D:\Research\FijiJavaDevel\bigdataviewer-core\target\apidocs\bdv\export\WriteSequenceToHdf5.DefaultLoopbackHeuristic.html...
Generating D:\Research\FijiJavaDevel\bigdataviewer-core\target\apidocs\bdv\export\WriteSequenceToHdf5.LoopbackHeuristic.html...
Generating D:\Research\FijiJavaDevel\bigdataviewer-core\target\apidocs\bdv\img\cache\BlockingFetchQueues.html...
Generating D:\Research\FijiJavaDevel\bigdataviewer-core\target\apidocs\bdv\img\cache\Cache.html...
Generating D:\Research\FijiJavaDevel\bigdataviewer-core\target\apidocs\bdv\img\cache\Cache.Dummy.html...
Generating D:\Research\FijiJavaDevel\bigdataviewer-core\target\apidocs\bdv\img\cache\CacheArrayLoader.html...
Generating D:\Research\FijiJavaDevel\bigdataviewer-core\target\apidocs\bdv\img\cache\CachedCellImg.html...
Generating D:\Research\FijiJavaDevel\bigdataviewer-core\target\apidocs\bdv\img\cache\CacheHints.html...
Generating D:\Research\FijiJavaDevel\bigdataviewer-core\target\apidocs\bdv\img\cache\CacheIoTiming.html...
Generating D:\Research\FijiJavaDevel\bigdataviewer-core\target\apidocs\bdv\img\cache\CacheIoTiming.IoStatistics.html...

[...]

3 errors
100 warnings
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 21.884 s
[INFO] Finished at: 2016-02-19T00:25:53+01:00
[INFO] Final Memory: 25M/425M
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal org.apache.maven.plugins:maven-javadoc-plugin:2.9.1:jar (attach-javadocs) on project bigdataviewer-core: MavenReportException: Error while creating archive:
[ERROR] Exit code: 1 - D:\Research\FijiJavaDevel\bigdataviewer-core\src\main\java\bdv\img\trakem2\TrakEM2ImageLoader.java:3: error: package ij.measure does not exist
[ERROR] import ij.measure.Calibration;
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\bigdataviewer-core\src\main\java\bdv\img\trakem2\TrakEM2ImageLoader.java:4: error: package ini.trakem2 does not exist
[ERROR] import ini.trakem2.ControlWindow;
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\bigdataviewer-core\src\main\java\bdv\img\trakem2\TrakEM2ImageLoader.java:5: error: package ini.trakem2 does not exist
[ERROR] import ini.trakem2.Project;
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\bigdataviewer-core\src\main\java\bdv\img\trakem2\TrakEM2ImageLoader.java:6: error: package ini.trakem2.display does not exist
[ERROR] import ini.trakem2.display.LayerSet;
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\bigdataviewer-core\src\main\java\bdv\img\trakem2\TrakEM2ImageLoader.java:7: error: package ini.trakem2.persistence does not exist
[ERROR] import ini.trakem2.persistence.Loader;
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\bigdataviewer-core\src\main\java\bdv\img\trakem2\TrakEM2ImageLoader.java:12: error: cannot find symbol
[ERROR] import mpicbg.spim.data.View;
[ERROR] ^
[ERROR] symbol:   class View
[ERROR] location: package mpicbg.spim.data
[ERROR] D:\Research\FijiJavaDevel\bigdataviewer-core\src\main\java\bdv\img\trakem2\TrakEM2ImageLoader.java:24: error: cannot find symbol
[ERROR] import bdv.AbstractViewerImgLoader;
[ERROR] ^
[ERROR] symbol:   class AbstractViewerImgLoader
[ERROR] location: package bdv
[ERROR] D:\Research\FijiJavaDevel\bigdataviewer-core\src\main\java\bdv\img\trakem2\TrakEM2ImageLoader.java:27: error: cannot find symbol
[ERROR] import bdv.img.cache.VolatileGlobalCellCache.LoadingStrategy;
[ERROR] ^
[ERROR] symbol:   class LoadingStrategy
[ERROR] location: class VolatileGlobalCellCache
[ERROR] D:\Research\FijiJavaDevel\bigdataviewer-core\src\main\java\bdv\img\trakem2\TrakEM2ImageLoader.java:31: error: cannot find symbol
[ERROR] public class TrakEM2ImageLoader extends AbstractViewerImgLoader< ARGBType, VolatileARGBType >
[ERROR] ^
[ERROR] symbol: class AbstractViewerImgLoader
[ERROR] D:\Research\FijiJavaDevel\bigdataviewer-core\src\main\java\bdv\img\trakem2\TrakEM2ImageLoader.java:33: error: cannot find symbol
[ERROR] private Project project;
[ERROR] ^
[ERROR] symbol:   class Project
[ERROR] location: class TrakEM2ImageLoader
[ERROR] D:\Research\FijiJavaDevel\bigdataviewer-core\src\main\java\bdv\img\trakem2\TrakEM2ImageLoader.java:34: error: cannot find symbol
[ERROR] private Loader loader;
[ERROR] ^
[ERROR] symbol:   class Loader
[ERROR] location: class TrakEM2ImageLoader
[ERROR] D:\Research\FijiJavaDevel\bigdataviewer-core\src\main\java\bdv\img\trakem2\TrakEM2ImageLoader.java:35: error: cannot find symbol
[ERROR] private LayerSet layerset;
[ERROR] ^
[ERROR] symbol:   class LayerSet
[ERROR] location: class TrakEM2ImageLoader
[ERROR] D:\Research\FijiJavaDevel\bigdataviewer-core\src\main\java\bdv\img\trakem2\TrakEM2ImageLoader.java:56: error: type VolatileGlobalCellCache does not take parameters
[ERROR] private VolatileGlobalCellCache< VolatileIntArray > cache;
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\bigdataviewer-core\src\main\java\bdv\img\trakem2\TrakEM2ImageLoader.java:63: error: cannot find symbol
[ERROR] public void init( final Project project, final int tileWidth, final int tileHeight, final int numScales )
[ERROR] ^
[ERROR] symbol:   class Project
[ERROR] location: class TrakEM2ImageLoader
[ERROR] D:\Research\FijiJavaDevel\bigdataviewer-core\src\main\java\bdv\img\trakem2\TrakEM2ImageLoader.java:142: error: cannot find symbol
[ERROR] public RandomAccessibleInterval< ARGBType > getImage( final View view, final int level )
[ERROR] ^
[ERROR] symbol:   class View
[ERROR] location: class TrakEM2ImageLoader
[ERROR] D:\Research\FijiJavaDevel\bigdataviewer-core\src\main\java\bdv\img\trakem2\TrakEM2ImageLoader.java:151: error: cannot find symbol
[ERROR] public RandomAccessibleInterval< VolatileARGBType > getVolatileImage( final View view, final int level )
[ERROR] ^
[ERROR] symbol:   class View
[ERROR] location: class TrakEM2ImageLoader
[ERROR] D:\Research\FijiJavaDevel\bigdataviewer-core\src\main\java\bdv\img\trakem2\TrakEM2ImageLoader.java:176: error: cannot find symbol
[ERROR] protected < T extends NativeType< T > > CellImg< T, VolatileIntArray, VolatileCell< VolatileIntArray > > prepareCachedImage( final View view, final int level, final LoadingStrategy loadingStrategy )
[ERROR] ^
[ERROR] symbol:   class View
[ERROR] location: class TrakEM2ImageLoader
[ERROR] D:\Research\FijiJavaDevel\bigdataviewer-core\src\main\java\bdv\img\trakem2\TrakEM2ImageLoader.java:176: error: cannot find symbol
[ERROR] protected < T extends NativeType< T > > CellImg< T, VolatileIntArray, VolatileCell< VolatileIntArray > > prepareCachedImage( final View view, final int level, final LoadingStrategy loadingStrategy )
[ERROR] ^
[ERROR] symbol:   class LoadingStrategy
[ERROR] location: class TrakEM2ImageLoader
[ERROR] D:\Research\FijiJavaDevel\bigdataviewer-core\src\main\java\bdv\img\trakem2\TrakEM2ImageLoader.java:188: error: type VolatileGlobalCellCache does not take parameters
[ERROR] public VolatileGlobalCellCache< VolatileIntArray > getCache()
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\bigdataviewer-core\src\main\java\bdv\img\trakem2\TrakEM2VolatileIntArrayLoader.java:3: error: package ij does not exist
[ERROR] import ij.ImagePlus;
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\bigdataviewer-core\src\main\java\bdv\img\trakem2\TrakEM2VolatileIntArrayLoader.java:4: error: package ini.trakem2.display does not exist
[ERROR] import ini.trakem2.display.Displayable;
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\bigdataviewer-core\src\main\java\bdv\img\trakem2\TrakEM2VolatileIntArrayLoader.java:5: error: package ini.trakem2.display does not exist
[ERROR] import ini.trakem2.display.LayerSet;
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\bigdataviewer-core\src\main\java\bdv\img\trakem2\TrakEM2VolatileIntArrayLoader.java:6: error: package ini.trakem2.persistence does not exist
[ERROR] import ini.trakem2.persistence.Loader;
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\bigdataviewer-core\src\main\java\bdv\img\trakem2\TrakEM2VolatileIntArrayLoader.java:20: error: cannot find symbol
[ERROR] final private Loader loader;
[ERROR] ^
[ERROR] symbol:   class Loader
[ERROR] location: class TrakEM2VolatileIntArrayLoader
[ERROR] D:\Research\FijiJavaDevel\bigdataviewer-core\src\main\java\bdv\img\trakem2\TrakEM2VolatileIntArrayLoader.java:22: error: cannot find symbol
[ERROR] final private LayerSet layerset;
[ERROR] ^
[ERROR] symbol:   class LayerSet
[ERROR] location: class TrakEM2VolatileIntArrayLoader
[ERROR] D:\Research\FijiJavaDevel\bigdataviewer-core\src\main\java\bdv\img\trakem2\TrakEM2VolatileIntArrayLoader.java:34: error: cannot find symbol
[ERROR] public TrakEM2VolatileIntArrayLoader( final Loader loader, final LayerSet layerset, final int[] zScales )
[ERROR] ^
[ERROR] symbol:   class Loader
[ERROR] location: class TrakEM2VolatileIntArrayLoader
[ERROR] D:\Research\FijiJavaDevel\bigdataviewer-core\src\main\java\bdv\img\trakem2\TrakEM2VolatileIntArrayLoader.java:34: error: cannot find symbol
[ERROR] public TrakEM2VolatileIntArrayLoader( final Loader loader, final LayerSet layerset, final int[] zScales )
[ERROR] ^
[ERROR] symbol:   class LayerSet
[ERROR] location: class TrakEM2VolatileIntArrayLoader
[ERROR] D:\Research\FijiJavaDevel\bigdataviewer-core\src\main\java\bdv\BigDataViewer.java:694: warning: no @param for filename
[ERROR] public static void view( final String filename, final ProgressWriter progressWriter ) throws SpimDataException
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\bigdataviewer-core\src\main\java\bdv\BigDataViewer.java:694: warning: no @param for progressWriter
[ERROR] public static void view( final String filename, final ProgressWriter progressWriter ) throws SpimDataException
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\bigdataviewer-core\src\main\java\bdv\BigDataViewer.java:694: warning: no @throws for mpicbg.spim.data.SpimDataException
[ERROR] public static void view( final String filename, final ProgressWriter progressWriter ) throws SpimDataException
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\bigdataviewer-core\src\main\java\bdv\BigDataViewer.java:641: warning: no @param for spimData
[ERROR] public BigDataViewer( final AbstractSpimData< ? > spimData, final String windowTitle, final ProgressWriter progressWriter )
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\bigdataviewer-core\src\main\java\bdv\BigDataViewer.java:641: warning: no @param for windowTitle
[ERROR] public BigDataViewer( final AbstractSpimData< ? > spimData, final String windowTitle, final ProgressWriter progressWriter )
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\bigdataviewer-core\src\main\java\bdv\BigDataViewer.java:641: warning: no @param for progressWriter
[ERROR] public BigDataViewer( final AbstractSpimData< ? > spimData, final String windowTitle, final ProgressWriter progressWriter )
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\bigdataviewer-core\src\main\java\bdv\BigDataViewer.java:630: warning: no @param for xmlFilename
[ERROR] public BigDataViewer( final String xmlFilename, final String windowTitle, final ProgressWriter progressWriter ) throws SpimDataException
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\bigdataviewer-core\src\main\java\bdv\BigDataViewer.java:630: warning: no @param for windowTitle
[ERROR] public BigDataViewer( final String xmlFilename, final String windowTitle, final ProgressWriter progressWriter ) throws SpimDataException
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\bigdataviewer-core\src\main\java\bdv\BigDataViewer.java:630: warning: no @param for progressWriter
[ERROR] public BigDataViewer( final String xmlFilename, final String windowTitle, final ProgressWriter progressWriter ) throws SpimDataException
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\bigdataviewer-core\src\main\java\bdv\BigDataViewer.java:630: warning: no @throws for mpicbg.spim.data.SpimDataException
[ERROR] public BigDataViewer( final String xmlFilename, final String windowTitle, final ProgressWriter progressWriter ) throws SpimDataException
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\bigdataviewer-core\src\main\java\bdv\viewer\render\MipmapOrdering.java:50: warning: no @return
[ERROR] public MipmapHints getMipmapHints( AffineTransform3D screenTransform, int timepoint, int previousTimepoint );
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\bigdataviewer-core\src\main\java\bdv\img\hdf5\MipmapInfo.java:77: warning: no @return
[ERROR] public double[][] getResolutions()
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\bigdataviewer-core\src\main\java\bdv\img\hdf5\MipmapInfo.java:87: warning: no @return
[ERROR] public AffineTransform3D[] getTransforms()
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\bigdataviewer-core\src\main\java\bdv\img\hdf5\MipmapInfo.java:95: warning: no @return
[ERROR] public int[][] getSubdivisions()
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\bigdataviewer-core\src\main\java\bdv\img\hdf5\MipmapInfo.java:103: warning: no @return
[ERROR] public int getMaxLevel()
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\bigdataviewer-core\src\main\java\bdv\img\hdf5\MipmapInfo.java:110: warning: no description for @return
[ERROR] * @return
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\bigdataviewer-core\src\main\java\bdv\export\ProposeMipmaps.java:57: warning: no description for @param
[ERROR] * @param seq
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\bigdataviewer-core\src\main\java\bdv\export\ProposeMipmaps.java:73: warning: no description for @param
[ERROR] * @param setup
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\bigdataviewer-core\src\main\java\bdv\export\ProposeMipmaps.java:146: warning: no @param for resolutions
[ERROR] public static String getArrayString( final int[][] resolutions )
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\bigdataviewer-core\src\main\java\bdv\export\ProposeMipmaps.java:146: warning: no @return
[ERROR] public static String getArrayString( final int[][] resolutions )
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\bigdataviewer-core\src\main\java\bdv\export\ProposeMipmaps.java:166: warning: no description for @param
[ERROR] * @param size
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\bigdataviewer-core\src\main\java\bdv\export\WriteSequenceToHdf5.java:972: warning: no @param for seq
[ERROR] public static void writeHdf5File(
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\bigdataviewer-core\src\main\java\bdv\export\WriteSequenceToHdf5.java:972: warning: no @param for perSetupMipmapInfo
[ERROR] public static void writeHdf5File(
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\bigdataviewer-core\src\main\java\bdv\export\WriteSequenceToHdf5.java:972: warning: no @param for deflate
[ERROR] public static void writeHdf5File(
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\bigdataviewer-core\src\main\java\bdv\export\WriteSequenceToHdf5.java:972: warning: no @param for hdf5File
[ERROR] public static void writeHdf5File(
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\bigdataviewer-core\src\main\java\bdv\export\WriteSequenceToHdf5.java:972: warning: no @param for loopbackHeuristic
[ERROR] public static void writeHdf5File(
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\bigdataviewer-core\src\main\java\bdv\export\WriteSequenceToHdf5.java:972: warning: no @param for afterEachPlane
[ERROR] public static void writeHdf5File(
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\bigdataviewer-core\src\main\java\bdv\export\WriteSequenceToHdf5.java:972: warning: no @param for progressWriter
[ERROR] public static void writeHdf5File(
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\bigdataviewer-core\src\main\java\bdv\export\WriteSequenceToHdf5.java:991: warning: no @param for seq
[ERROR] public static void writeHdf5File(
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\bigdataviewer-core\src\main\java\bdv\export\WriteSequenceToHdf5.java:991: warning: no @param for resolutions
[ERROR] public static void writeHdf5File(
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\bigdataviewer-core\src\main\java\bdv\export\WriteSequenceToHdf5.java:991: warning: no @param for subdivisions
[ERROR] public static void writeHdf5File(
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\bigdataviewer-core\src\main\java\bdv\export\WriteSequenceToHdf5.java:991: warning: no @param for deflate
[ERROR] public static void writeHdf5File(
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\bigdataviewer-core\src\main\java\bdv\export\WriteSequenceToHdf5.java:991: warning: no @param for hdf5File
[ERROR] public static void writeHdf5File(
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\bigdataviewer-core\src\main\java\bdv\export\WriteSequenceToHdf5.java:991: warning: no @param for loopbackHeuristic
[ERROR] public static void writeHdf5File(
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\bigdataviewer-core\src\main\java\bdv\export\WriteSequenceToHdf5.java:991: warning: no @param for afterEachPlane
[ERROR] public static void writeHdf5File(
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\bigdataviewer-core\src\main\java\bdv\export\WriteSequenceToHdf5.java:991: warning: no @param for progressWriter
[ERROR] public static void writeHdf5File(
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\bigdataviewer-core\src\main\java\bdv\export\WriteSequenceToHdf5.java:1011: warning: no @param for seq
[ERROR] public static void writeHdf5PartitionFile(
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\bigdataviewer-core\src\main\java\bdv\export\WriteSequenceToHdf5.java:1011: warning: no @param for perSetupMipmapInfo
[ERROR] public static void writeHdf5PartitionFile(
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\bigdataviewer-core\src\main\java\bdv\export\WriteSequenceToHdf5.java:1011: warning: no @param for deflate
[ERROR] public static void writeHdf5PartitionFile(
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\bigdataviewer-core\src\main\java\bdv\export\WriteSequenceToHdf5.java:1011: warning: no @param for partition
[ERROR] public static void writeHdf5PartitionFile(
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\bigdataviewer-core\src\main\java\bdv\export\WriteSequenceToHdf5.java:1011: warning: no @param for loopbackHeuristic
[ERROR] public static void writeHdf5PartitionFile(
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\bigdataviewer-core\src\main\java\bdv\export\WriteSequenceToHdf5.java:1011: warning: no @param for afterEachPlane
[ERROR] public static void writeHdf5PartitionFile(
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\bigdataviewer-core\src\main\java\bdv\export\WriteSequenceToHdf5.java:1011: warning: no @param for progressWriter
[ERROR] public static void writeHdf5PartitionFile(
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\bigdataviewer-core\src\main\java\bdv\export\WriteSequenceToHdf5.java:1030: warning: no @param for img
[ERROR] public static void writeViewToHdf5PartitionFile(
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\bigdataviewer-core\src\main\java\bdv\export\WriteSequenceToHdf5.java:1030: warning: no @param for partition
[ERROR] public static void writeViewToHdf5PartitionFile(
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\bigdataviewer-core\src\main\java\bdv\export\WriteSequenceToHdf5.java:1030: warning: no @param for timepointIdPartition
[ERROR] public static void writeViewToHdf5PartitionFile(
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\bigdataviewer-core\src\main\java\bdv\export\WriteSequenceToHdf5.java:1030: warning: no @param for setupIdPartition
[ERROR] public static void writeViewToHdf5PartitionFile(
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\bigdataviewer-core\src\main\java\bdv\export\WriteSequenceToHdf5.java:1030: warning: no @param for mipmapInfo
[ERROR] public static void writeViewToHdf5PartitionFile(
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\bigdataviewer-core\src\main\java\bdv\export\WriteSequenceToHdf5.java:1030: warning: no @param for writeMipmapInfo
[ERROR] public static void writeViewToHdf5PartitionFile(
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\bigdataviewer-core\src\main\java\bdv\export\WriteSequenceToHdf5.java:1030: warning: no @param for deflate
[ERROR] public static void writeViewToHdf5PartitionFile(
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\bigdataviewer-core\src\main\java\bdv\export\WriteSequenceToHdf5.java:1030: warning: no @param for loopbackHeuristic
[ERROR] public static void writeViewToHdf5PartitionFile(
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\bigdataviewer-core\src\main\java\bdv\export\WriteSequenceToHdf5.java:1030: warning: no @param for afterEachPlane
[ERROR] public static void writeViewToHdf5PartitionFile(
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\bigdataviewer-core\src\main\java\bdv\export\WriteSequenceToHdf5.java:1030: warning: no @param for progressWriter
[ERROR] public static void writeViewToHdf5PartitionFile(
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\bigdataviewer-core\src\main\java\bdv\img\cache\BlockingFetchQueues.java:123: warning: no description for @throws
[ERROR] * @throws InterruptedException
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\bigdataviewer-core\src\main\java\bdv\img\cache\Cache.java:57: warning: no @param for partialBudget
[ERROR] public void initIoTimeBudget( final long[] partialBudget );
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\bigdataviewer-core\src\main\java\bdv\img\cache\Cache.java:63: warning: no @return
[ERROR] public CacheIoTiming getCacheIoTiming();
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\bigdataviewer-core\src\main\java\bdv\img\cache\CacheHints.java:53: warning: no description for @param
[ERROR] * @param loadingStrategy
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\bigdataviewer-core\src\main\java\bdv\img\cache\CacheHints.java:54: warning: no description for @param
[ERROR] * @param queuePriority
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\bigdataviewer-core\src\main\java\bdv\img\cache\CacheHints.java:55: warning: no description for @param
[ERROR] * @param enqueuToFront
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\bigdataviewer-core\src\main\java\bdv\img\cache\VolatileGlobalCellCache.java:269: warning: no @param for ms
[ERROR] public void pauseFetcherThreadsFor( final long ms )
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\bigdataviewer-core\src\main\java\bdv\img\cache\VolatileGlobalCellCache.java:278: warning: no @param for timeMillis
[ERROR] public void pauseFetcherThreadsUntil( final long timeMillis )
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\bigdataviewer-core\src\main\java\bdv\img\cache\VolatileGlobalCellCache.java:339: warning: no description for @param
[ERROR] * @param k

I am not sure about how I should proceed even for your simple “option 1”. I still need to make Eclipse aware of the needed dependencies no ? Or instead, I would have to clone and build on the fly each Fiji repo needed ? Here for example I would start by building trakem2 ? If it works like this, I would then copy and overwrite the compiled JAR to an existing Fiji application ?

On the other hand I wanted for example to play around with bigdataviewer. In general I would like to be able to modify existing plugins and testing them.
Thank you for your help

#4

Did you import the project using File :arrow_forward: Import :arrow_forward: Existing Maven Project? If so, Eclipse infers the dependencies automatically from the pom.xml configuration. This is one of the many beautiful things about Maven.

Ah, thank you for clarifying. So you are actually just trying to run the code from Eclipse—NOT from a full installation of ImageJ or Fiji. In that case, the directions you linked originally are actually irrelevant, since you are not testing from an existing installation, but rather from Eclipse directly. So no need to follow “Option 1” or “Option 2” or any other such instructions.

Rather, each project generally has one or more main methods somewhere intended to allow you to take things for a test drive. In this case you might try the BigDataBrowserPlugin of the bigdataviewer_fiji component.

#5

Thanks.

It was a while ago so I just did it again:

  1. clone bigdataviewer-core
  2. File :arrow_forward: Import :arrow_forward: Existing Maven Project
  3. Run the pom.xml (without linking to an existing application). In the Eclipse console I get
[ERROR] COMPILATION ERROR : 
[INFO] -------------------------------------------------------------
[ERROR] No compiler is provided in this environment. Perhaps you are running on a JRE rather than a JDK?
[INFO] 1 error
[INFO] -------------------------------------------------------------
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 4.935 s
[INFO] Finished at: 2016-02-19T08:51:31+01:00
[INFO] Final Memory: 27M/876M
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:3.1:compile (default-compile) on project bigdataviewer-core: Compilation failure
[ERROR] No compiler is provided in this environment. Perhaps you are running on a JRE rather than a JDK?
[ERROR] -> [Help 1]

  1. I follow the instructions of the validated answer from this thread reporting a similar error

  2. Run the pom.xml:

[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------

  1. In the folder bigdataviewer-core\src\main\java\bdv\img I add a folder called trakem2 containing these two files

  2. I run pom.xml (again without setting the imagej.app.directory)

[INFO] -------------------------------------------------------------
[ERROR] COMPILATION ERROR : 
[INFO] -------------------------------------------------------------
[ERROR] /D:/Research/FijiJavaDevel/bigdataviewer-core/src/main/java/bdv/img/trakem2/TrakEM2VolatileIntArrayLoader.java:[3,10] package ij does not exist
[ERROR] /D:/Research/FijiJavaDevel/bigdataviewer-core/src/main/java/bdv/img/trakem2/TrakEM2VolatileIntArrayLoader.java:[4,27] package ini.trakem2.display does not exist
[ERROR] /D:/Research/FijiJavaDevel/bigdataviewer-core/src/main/java/bdv/img/trakem2/TrakEM2VolatileIntArrayLoader.java:[5,27] package ini.trakem2.display does not exist
[ERROR] /D:/Research/FijiJavaDevel/bigdataviewer-core/src/main/java/bdv/img/trakem2/TrakEM2VolatileIntArrayLoader.java:[6,31] package ini.trakem2.persistence does not exist
[ERROR] /D:/Research/FijiJavaDevel/bigdataviewer-core/src/main/java/bdv/img/trakem2/TrakEM2VolatileIntArrayLoader.java:[20,23] cannot find symbol
  symbol:   class Loader
  location: class bdv.img.trakem2.TrakEM2VolatileIntArrayLoader
[ERROR] /D:/Research/FijiJavaDevel/bigdataviewer-core/src/main/java/bdv/img/trakem2/TrakEM2VolatileIntArrayLoader.java:[22,23] cannot find symbol
  symbol:   class LayerSet
  location: class bdv.img.trakem2.TrakEM2VolatileIntArrayLoader
[ERROR] /D:/Research/FijiJavaDevel/bigdataviewer-core/src/main/java/bdv/img/trakem2/TrakEM2VolatileIntArrayLoader.java:[34,53] cannot find symbol
  symbol:   class Loader
  location: class bdv.img.trakem2.TrakEM2VolatileIntArrayLoader
[ERROR] /D:/Research/FijiJavaDevel/bigdataviewer-core/src/main/java/bdv/img/trakem2/TrakEM2VolatileIntArrayLoader.java:[34,74] cannot find symbol
  symbol:   class LayerSet
  location: class bdv.img.trakem2.TrakEM2VolatileIntArrayLoader
[ERROR] /D:/Research/FijiJavaDevel/bigdataviewer-core/src/main/java/bdv/img/trakem2/TrakEM2ImageLoader.java:[3,18] package ij.measure does not exist
[ERROR] /D:/Research/FijiJavaDevel/bigdataviewer-core/src/main/java/bdv/img/trakem2/TrakEM2ImageLoader.java:[4,19] package ini.trakem2 does not exist
[ERROR] /D:/Research/FijiJavaDevel/bigdataviewer-core/src/main/java/bdv/img/trakem2/TrakEM2ImageLoader.java:[5,19] package ini.trakem2 does not exist
[ERROR] /D:/Research/FijiJavaDevel/bigdataviewer-core/src/main/java/bdv/img/trakem2/TrakEM2ImageLoader.java:[6,27] package ini.trakem2.display does not exist
[ERROR] /D:/Research/FijiJavaDevel/bigdataviewer-core/src/main/java/bdv/img/trakem2/TrakEM2ImageLoader.java:[7,31] package ini.trakem2.persistence does not exist
[ERROR] /D:/Research/FijiJavaDevel/bigdataviewer-core/src/main/java/bdv/img/trakem2/TrakEM2ImageLoader.java:[12,24] cannot find symbol
  symbol:   class View
  1. I specify the dependencies and still get the same error
[INFO] -------------------------------------------------------------
[INFO] -------------------------------------------------------------
[ERROR] COMPILATION ERROR : 
[INFO] -------------------------------------------------------------
[ERROR] /D:/Research/FijiJavaDevel/bigdataviewer-core/src/main/java/bdv/img/trakem2/TrakEM2VolatileIntArrayLoader.java:[3,10] package ij does not exist
[ERROR] /D:/Research/FijiJavaDevel/bigdataviewer-core/src/main/java/bdv/img/trakem2/TrakEM2VolatileIntArrayLoader.java:[4,27] package ini.trakem2.display does not exist
[ERROR] /D:/Research/FijiJavaDevel/bigdataviewer-core/src/main/java/bdv/img/trakem2/TrakEM2VolatileIntArrayLoader.java:[5,27] package ini.trakem2.display does not exist
[ERROR] /D:/Research/FijiJavaDevel/bigdataviewer-core/src/main/java/bdv/img/trakem2/TrakEM2VolatileIntArrayLoader.java:[6,31] package ini.trakem2.persistence does not exist
[ERROR] /D:/Research/FijiJavaDevel/bigdataviewer-core/src/main/java/bdv/img/trakem2/TrakEM2VolatileIntArrayLoader.java:[20,23] cannot find symbol

A screenshot here:

1913×1099 92.1 KB

Am I doing something wrong ?

What you describe probably consists of a few simple steps but it is obscure to me. Maybe I can describe precisely what I want to do: transfer a trakem2 project into bdv following these advices. I imagine that at the end I could have a plugin (I would find it by pressing “l” in Fiji), for example “trakem2 to bdv”, that I would easily run from a python script/plugin with for example a IJ.run(‘trakem2_to_bdv’, some arguments). Or if not directly acessible as a plugin, I would run it with something like this

import trakem2ToBdv
trakem2ToBdv.transfer(someArgs)

in a python script.
Thanks for your help.

P.S.: an example of other things I would like to do (and why I was initially thinking that I would better set up a good Fiji/Eclipse environment) was to use the 2D segmentation of squassh for the [detection step] (http://fiji.sc/How_to_write_your_own_detection_algorithm_for_TrackMate) in Trackmate.

#6

It seems like you are just trying to build the trakem2 branch of the bigdataviewer-core repository?

So then, let’s take Eclipse out of the picture. You could simply build the branch from the command line, then replace the bigdataviewer-core of your Fiji with the new one.

I tried to test this, but ran into problems with the branch:

$ git clone git://github.com/bigdataviewer/bigdataviewer-core
Cloning into 'bigdataviewer-core'...
remote: Counting objects: 15194, done.
remote: Total 15194 (delta 0), reused 0 (delta 0), pack-reused 15194
Receiving objects: 100% (15194/15194), 18.99 MiB | 6.79 MiB/s, done.
Resolving deltas: 100% (8167/8167), done.
Checking connectivity... done.
$ cd bigdataviewer-core
$ git checkout trakem2
Branch trakem2 set up to track remote branch trakem2 from origin.
Switched to a new branch 'trakem2'
$ mvn package
[INFO] Scanning for projects...
...
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
...

So it seems like that branch is non-functional at the moment. I tried rebasing it over origin/master but there are conflicts. @tpietzsch @axtimwalde Any suggestions?

#7

Yes.

Hum, so if my problem was not related to the Eclipse configuration then this is probably the prediction of @axtimwalde:

will need some adjustment to the current API but should still work otherwise.

I am not sure whether I can debug that but at least now I know that I should focus on the code and not on the Eclipse configuration. I will give a try.
Thanks for your help

1 Like
#8

For the record, the problem was that I was actually missing the trakem2 and ij dependencies in the pom.xml file of bigdataviewer-core.

The dependencies now look like below, which allows me to import the desired modules:

	<dependencyManagement>
		<dependencies>
			<dependency>
				<groupId>sc.fiji</groupId>
				<artifactId>pom-trakem2</artifactId>
				<version>${pom-trakem2.version}</version>
				<type>pom</type>
				<scope>import</scope>
			</dependency>
		</dependencies>
	</dependencyManagement>	
	
	<dependencies>
		<dependency>
			<groupId>net.imglib2</groupId>
			<artifactId>imglib2</artifactId>
		</dependency>
		<dependency>
			<groupId>net.imglib2</groupId>
			<artifactId>imglib2-realtransform</artifactId>
		</dependency>
		<dependency>
			<groupId>net.imglib2</groupId>
			<artifactId>imglib2-ui</artifactId>
		</dependency>
		<dependency>
			<groupId>net.imglib2</groupId>
			<artifactId>imglib2-algorithm</artifactId>
		</dependency>
		<dependency>
			<groupId>sc.fiji</groupId>
			<artifactId>spim_data</artifactId>
		</dependency>
		<dependency>
			<groupId>cisd</groupId>
			<artifactId>jhdf5</artifactId>
		</dependency>
		<dependency>
			<groupId>org.jdom</groupId>
			<artifactId>jdom2</artifactId>
		</dependency>
		<dependency>
			<groupId>com.google.code.gson</groupId>
			<artifactId>gson</artifactId>
		</dependency>
		<dependency>
			<groupId>org.scijava</groupId>
			<artifactId>ui-behaviour</artifactId>
			<version>1.0.2</version>
		</dependency>
		<!-- TrakEM2 dependencies -->
		<dependency>
			<groupId>sc.fiji</groupId>
			<artifactId>TrakEM2_</artifactId>
		</dependency>

		<!-- Fiji dependencies -->
		<dependency>
			<groupId>mpicbg</groupId>
			<artifactId>mpicbg</artifactId>
		</dependency>
		<dependency>
			<groupId>sc.fiji</groupId>
			<artifactId>bUnwarpJ_</artifactId>
		</dependency>
		<dependency>
			<groupId>sc.fiji</groupId>
			<artifactId>fiji-lib</artifactId>
		</dependency>
		<dependency>
			<groupId>sc.fiji</groupId>
			<artifactId>mpicbg-trakem2</artifactId>
		</dependency>

		<!-- ImageJ dependencies -->
		<dependency>
			<groupId>net.imagej</groupId>
			<artifactId>ij</artifactId>
		</dependency>
		<dependency>
			<groupId>sc.fiji</groupId>
			<artifactId>IO_</artifactId>
		</dependency>

	</dependencies>
3 Likes