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Packages 
Package Description
adapter  
adt  
algorithms  
amira  
anisotropic_diffusion  
bdv  
bdv.cache  
bdv.cache.util  
bdv.export  
bdv.gui  
bdv.ij  
bdv.ij.export  
bdv.ij.export.imgloader  
bdv.ij.export.tiles  
bdv.ij.util  
bdv.img  
bdv.img.cache  
bdv.img.catmaid  
bdv.img.hdf5  
bdv.img.imagestack  
bdv.img.imaris  
bdv.img.openconnectome  
bdv.img.remote  
bdv.img.virtualstack  
bdv.spimdata  
bdv.spimdata.legacy  
bdv.spimdata.tools  
bdv.tools  
bdv.tools.bookmarks  
bdv.tools.boundingbox  
bdv.tools.brightness  
bdv.tools.crop  
bdv.tools.transformation  
bdv.util  
bdv.viewer  
bdv.viewer.animate  
bdv.viewer.overlay  
bdv.viewer.render  
bdv.viewer.state  
bigwarp  
bigwarp.landmarks  
bigwarp.landmarks.actions  
bigwarp.loader  
bigwarp.scripts  
bigwarp.source  
bigwarp.util  
bijnum  
Bug_Submitter  
bunwarpj
Provides the main and utility classes to run the ImageJ/Fiji plugin bUnwarpJ_: consistent and elastic image registration.
bunwarpj.trakem2.transform  
client  
color  
com.sun.source.tree
Provides interfaces to represent source code as abstract syntax trees (AST).
com.sun.source.util
Provides utilities for operations on abstract syntax trees (AST).
com.sun.tools.javac  
com.sun.tools.javac.api  
com.sun.tools.javac.code  
com.sun.tools.javac.comp  
com.sun.tools.javac.file  
com.sun.tools.javac.jvm  
com.sun.tools.javac.main  
com.sun.tools.javac.model  
com.sun.tools.javac.parser  
com.sun.tools.javac.processing  
com.sun.tools.javac.sym  
com.sun.tools.javac.tree  
com.sun.tools.javac.util  
customnode  
customnode.u3d  
delaunay  
distance  
edf  
edfgui  
edu.utexas.archipelago  
edu.utexas.archipelago.image  
edu.utexas.archipelago.plugin  
edu.utexas.archipelago.segmentation  
edu.utexas.clm.archipelago  
edu.utexas.clm.archipelago.compute  
edu.utexas.clm.archipelago.data  
edu.utexas.clm.archipelago.example  
edu.utexas.clm.archipelago.exception  
edu.utexas.clm.archipelago.ijsupport  
edu.utexas.clm.archipelago.ijsupport.bottle  
edu.utexas.clm.archipelago.listen  
edu.utexas.clm.archipelago.network  
edu.utexas.clm.archipelago.network.client  
edu.utexas.clm.archipelago.network.node  
edu.utexas.clm.archipelago.network.server  
edu.utexas.clm.archipelago.network.shell  
edu.utexas.clm.archipelago.network.shell.ssh  
edu.utexas.clm.archipelago.network.translation  
edu.utexas.clm.archipelago.ui  
edu.utexas.clm.archipelago.util  
edu.utexas.clm.crop  
edu.utexas.clm.reconstructreader  
edu.utexas.clm.reconstructreader.reconstruct  
edu.utexas.clm.reconstructreader.trakem2  
emblcmci  
events  
features  
fiji  
fiji.analyze.directionality  
fiji.color  
fiji.debugging  
fiji.denoise  
fiji.drawing  
fiji.expressionparser  
fiji.expressionparser.function  
fiji.features  
fiji.geom  
fiji.gui  
fiji.help  
fiji.packaging  
fiji.patches  
fiji.plugin  
fiji.plugin.timelapsedisplay  
fiji.plugin.trackmate  
fiji.plugin.trackmate.action  
fiji.plugin.trackmate.detection  
fiji.plugin.trackmate.detection.semiauto  
fiji.plugin.trackmate.detection.util  
fiji.plugin.trackmate.features  
fiji.plugin.trackmate.features.edges
Package for the classes that compute scalar features on links between spots (edges), such as instantaneous velocities, etc....
fiji.plugin.trackmate.features.manual  
fiji.plugin.trackmate.features.spot  
fiji.plugin.trackmate.features.track  
fiji.plugin.trackmate.graph
A package containing utility classes for the manipulation and analysis of tracks as JGraphT graphs.
fiji.plugin.trackmate.gui  
fiji.plugin.trackmate.gui.descriptors  
fiji.plugin.trackmate.gui.panels  
fiji.plugin.trackmate.gui.panels.components  
fiji.plugin.trackmate.gui.panels.detector  
fiji.plugin.trackmate.gui.panels.tracker  
fiji.plugin.trackmate.io  
fiji.plugin.trackmate.providers  
fiji.plugin.trackmate.tracking  
fiji.plugin.trackmate.tracking.kalman  
fiji.plugin.trackmate.tracking.kdtree  
fiji.plugin.trackmate.tracking.oldlap  
fiji.plugin.trackmate.tracking.oldlap.costfunction  
fiji.plugin.trackmate.tracking.oldlap.costmatrix  
fiji.plugin.trackmate.tracking.oldlap.hungarian  
fiji.plugin.trackmate.tracking.sparselap  
fiji.plugin.trackmate.tracking.sparselap.costfunction  
fiji.plugin.trackmate.tracking.sparselap.costmatrix  
fiji.plugin.trackmate.tracking.sparselap.linker  
fiji.plugin.trackmate.util  
fiji.plugin.trackmate.visualization  
fiji.plugin.trackmate.visualization.hyperstack  
fiji.plugin.trackmate.visualization.threedviewer  
fiji.plugin.trackmate.visualization.trackscheme  
fiji.plugin.trackmate.visualization.trackscheme.utils  
fiji.plugin.volumeviewer  
fiji.process  
fiji.process3d  
fiji.selection  
fiji.stacks  
fiji.statistics  
fiji.threshold  
fiji.tool  
fiji.updater  
fiji.util  
fiji.util.gui  
fiji.util.node  
FlowJ  
fsalign  
gadgets  
graphcut  
gui  
histogram2  
ij.gui  
ij3d  
ij3d.behaviors  
ij3d.contextmenu  
ij3d.gui  
ij3d.pointlist  
ij3d.segmentation  
ij3d.shapes  
ij3d.shortcuts  
imagej.legacy.plugin  
imageware  
imglib.ops.condition  
imglib.ops.function  
imglib.ops.function.p1  
imglib.ops.function.p2  
imglib.ops.function.pn  
imglib.ops.observer  
imglib.ops.operation  
imglib.ops.operator  
imglib.ops.operator.binary  
imglib.ops.operator.unary  
inference  
ini.trakem2  
ini.trakem2.analysis  
ini.trakem2.display  
ini.trakem2.display.d3d  
ini.trakem2.display.graphics  
ini.trakem2.display.inspect  
ini.trakem2.display.paint  
ini.trakem2.imaging  
ini.trakem2.imaging.filters  
ini.trakem2.io  
ini.trakem2.parallel  
ini.trakem2.persistence  
ini.trakem2.plugin  
ini.trakem2.scripting  
ini.trakem2.tree  
ini.trakem2.utils  
ini.trakem2.vector  
isosurface  
javax.annotation.processing
Facilities for declaring annotation processors and for allowing annotation processors to communicate with an annotation processing tool environment.
javax.lang.model
Classes and hierarchies of packages used to model the Java programming language.
javax.lang.model.element
Interfaces used to model elements of the Java programming language.
javax.lang.model.type
Interfaces used to model Java programming language types.
javax.lang.model.util
Utilities to assist in the processing of program elements and types.
javax.tools
Provides interfaces for tools which can be invoked from a program, for example, compilers.
jitk.spline  
jRenderer3D  
landmarks  
leica  
lenscorrection  
levelsets.algorithm  
levelsets.filter  
levelsets.ij  
lineage  
loci.plugins
Bio-Formats Plugins: a collection of plugins for ImageJ, including the Bio-Formats Importer, Bio-Formats Exporter, Bio-Formats Macro Extensions, Data Browser and Stack Slicer.
loci.plugins.config
Bio-Formats Plugins Configuration plugin for ImageJ.
loci.plugins.in
Bio-Formats Importer plugin for ImageJ.
loci.plugins.macro
Bio-Formats Macro Extensions plugin for ImageJ.
loci.plugins.out
Bio-Formats Exporter plugin for ImageJ.
loci.plugins.prefs
Classes for managing Bio-Formats plugins preferences.
loci.plugins.shortcut
Bio-Formats Plugins Shortcut Window plugin for ImageJ.
loci.plugins.util
Utility classes and methods for the Bio-Formats plugins for ImageJ.
marchingcubes  
math  
math3d  
mmorpho  
mpi.fruitfly.general  
mpi.fruitfly.math  
mpi.fruitfly.math.datastructures  
mpi.fruitfly.registration  
mpicbg.icp  
mpicbg.ij  
mpicbg.ij.clahe  
mpicbg.ij.plugin  
mpicbg.imglib  
mpicbg.imglib.algorithm  
mpicbg.imglib.algorithm.correlation  
mpicbg.imglib.algorithm.extremafinder  
mpicbg.imglib.algorithm.fft  
mpicbg.imglib.algorithm.floydsteinberg  
mpicbg.imglib.algorithm.function  
mpicbg.imglib.algorithm.gauss  
mpicbg.imglib.algorithm.histogram  
mpicbg.imglib.algorithm.histogram.arbitrary  
mpicbg.imglib.algorithm.histogram.discrete  
mpicbg.imglib.algorithm.integral  
mpicbg.imglib.algorithm.kdtree  
mpicbg.imglib.algorithm.kdtree.node  
mpicbg.imglib.algorithm.labeling  
mpicbg.imglib.algorithm.math  
mpicbg.imglib.algorithm.mirror  
mpicbg.imglib.algorithm.pde  
mpicbg.imglib.algorithm.peak  
mpicbg.imglib.algorithm.projection  
mpicbg.imglib.algorithm.roi  
mpicbg.imglib.algorithm.scalespace  
mpicbg.imglib.algorithm.transformation  
mpicbg.imglib.container  
mpicbg.imglib.container.array  
mpicbg.imglib.container.basictypecontainer  
mpicbg.imglib.container.basictypecontainer.array  
mpicbg.imglib.container.cell  
mpicbg.imglib.container.constant  
mpicbg.imglib.container.dynamic  
mpicbg.imglib.container.imageplus  
mpicbg.imglib.container.planar  
mpicbg.imglib.container.shapelist  
mpicbg.imglib.cursor  
mpicbg.imglib.cursor.array  
mpicbg.imglib.cursor.cell  
mpicbg.imglib.cursor.constant  
mpicbg.imglib.cursor.dynamic  
mpicbg.imglib.cursor.imageplus  
mpicbg.imglib.cursor.link  
mpicbg.imglib.cursor.planar  
mpicbg.imglib.cursor.shapelist  
mpicbg.imglib.cursor.special  
mpicbg.imglib.cursor.vector  
mpicbg.imglib.exception  
mpicbg.imglib.function  
mpicbg.imglib.image  
mpicbg.imglib.image.display  
mpicbg.imglib.image.display.imagej  
mpicbg.imglib.interpolation  
mpicbg.imglib.interpolation.dct  
mpicbg.imglib.interpolation.lanczos  
mpicbg.imglib.interpolation.linear  
mpicbg.imglib.interpolation.nearestneighbor  
mpicbg.imglib.io  
mpicbg.imglib.labeling  
mpicbg.imglib.multithreading  
mpicbg.imglib.outofbounds  
mpicbg.imglib.type  
mpicbg.imglib.type.label  
mpicbg.imglib.type.logic  
mpicbg.imglib.type.numeric  
mpicbg.imglib.type.numeric.complex  
mpicbg.imglib.type.numeric.integer  
mpicbg.imglib.type.numeric.real  
mpicbg.imglib.util  
mpicbg.imglib.wrapper  
mpicbg.panorama  
mpicbg.pointdescriptor  
mpicbg.pointdescriptor.exception  
mpicbg.pointdescriptor.matcher  
mpicbg.pointdescriptor.model  
mpicbg.pointdescriptor.similarity  
mpicbg.pointdescriptor.test  
mpicbg.spim  
mpicbg.spim.data  
mpicbg.spim.data.generic  
mpicbg.spim.data.generic.base  
mpicbg.spim.data.generic.sequence  
mpicbg.spim.data.legacy  
mpicbg.spim.data.registration  
mpicbg.spim.data.sequence  
mpicbg.spim.fusion  
mpicbg.spim.fusion.entropy  
mpicbg.spim.io  
mpicbg.spim.mpicbg  
mpicbg.spim.postprocessing.deconvolution  
mpicbg.spim.postprocessing.deconvolution2  
mpicbg.spim.preprocessing  
mpicbg.spim.registration  
mpicbg.spim.registration.bead  
mpicbg.spim.registration.bead.error  
mpicbg.spim.registration.bead.laplace  
mpicbg.spim.registration.detection  
mpicbg.spim.registration.detection.descriptor  
mpicbg.spim.registration.segmentation  
mpicbg.spim.registration.threshold  
mpicbg.spim.segmentation  
mpicbg.spim.simulation  
mpicbg.spim.vis3d  
mpicbg.stitching  
mpicbg.stitching.fusion  
mpicbg.trakem2.align  
mpicbg.trakem2.align.concurrent  
mpicbg.trakem2.transform  
mpicbg.trakem2.util  
mpicbg.util  
myij  
net.imagej.ui.swing.ops  
net.imglib2  
net.imglib2.algorithm.math  
net.imglib2.display  
net.imglib2.img.basictypeaccess.volatiles  
net.imglib2.img.basictypeaccess.volatiles.array  
net.imglib2.interpolation.randomaccess  
net.imglib2.predicate  
net.imglib2.type.volatiles  
nrrd  
octree  
oldsegmenters  
org.imagearchive.lsm.reader  
org.imagearchive.lsm.reader.info  
org.imagearchive.lsm.toolbox  
org.imagearchive.lsm.toolbox.gui  
org.imagearchive.lsm.toolbox.info  
org.imagearchive.lsm.toolbox.info.scaninfo  
org.janelia.intensity  
org.janelia.it.fiji.plugins.h5j  
org.janelia.it.h5j.fiji.adapter  
org.janelia.it.jacs.shared.ffmpeg  
org.janelia.utility.ui  
org.janelia.vaa3d.reader  
org.jfree.chart.annotations  
org.jfree.chart.renderer  
org.jfree.data.statistics  
org.siox  
org.siox.example  
org.siox.util  
orthoslice  
pal.math  
plugin  
process  
process3d  
QuickPALM  
register_virtual_stack  
registration3d  
results  
sc.fiji.analyzeSkeleton  
sc.fiji.balloonSegmentation  
sc.fiji.balloonSegmentation.structure  
sc.fiji.balloonSegmentation.utils  
sc.fiji.colourDeconvolution  
sc.fiji.i5d  
sc.fiji.i5d.cal  
sc.fiji.i5d.gui  
sc.fiji.i5d.plugin  
sc.fiji.i5d.util  
sc.fiji.io  
sc.fiji.io.icns  
sc.fiji.localThickness  
sc.fiji.multiKymograph  
sc.fiji.skeletonize3D  
sc.fiji.timelapse  
script.imglib  
script.imglib.algorithm  
script.imglib.algorithm.fn  
script.imglib.analysis  
script.imglib.color  
script.imglib.color.fn  
script.imglib.math  
script.imglib.math.fn  
selection  
sholl
Implements "Analyze> Sholl>" commands.
sholl.gui
Implements GUI customizations required by the Sholl Analysis plugin.
siox  
snake2D  
spim  
spim.fiji  
spim.fiji.datasetmanager  
spim.fiji.plugin  
spim.fiji.plugin.apply  
spim.fiji.plugin.cluster  
spim.fiji.plugin.fusion  
spim.fiji.plugin.interestpointdetection  
spim.fiji.plugin.interestpointregistration  
spim.fiji.plugin.queryXML  
spim.fiji.plugin.removedetections  
spim.fiji.plugin.resave  
spim.fiji.plugin.thinout  
spim.fiji.plugin.util  
spim.fiji.spimdata  
spim.fiji.spimdata.boundingbox  
spim.fiji.spimdata.explorer  
spim.fiji.spimdata.explorer.interestpoint  
spim.fiji.spimdata.explorer.popup  
spim.fiji.spimdata.explorer.registration  
spim.fiji.spimdata.explorer.util  
spim.fiji.spimdata.imgloaders  
spim.fiji.spimdata.interestpoints  
spim.process.cuda  
spim.process.fusion  
spim.process.fusion.boundingbox  
spim.process.fusion.boundingbox.automatic  
spim.process.fusion.deconvolution  
spim.process.fusion.export  
spim.process.fusion.weightedavg  
spim.process.fusion.weights  
spim.process.interestpointdetection  
spim.process.interestpointregistration  
spim.process.interestpointregistration.centerofmass  
spim.process.interestpointregistration.geometricdescriptor  
spim.process.interestpointregistration.geometrichashing  
spim.process.interestpointregistration.icp  
spim.process.interestpointregistration.optimizationtypes  
spim.process.interestpointregistration.registrationstatistics  
spim.vecmath  
spimopener  
SplineDeformationGenerator  
stacks  
stitching  
stitching.model  
stitching.utils  
surfacemap  
surfaceplot  
textureByRef  
tools  
tracing  
treeline  
util  
util.opencsv  
Utilities  
vib  
vib.app  
vib.app.gui  
vib.app.module  
vib.edge  
vib.oldregistration  
vib.segment  
vib.transforms  
video  
video2  
view4d  
view5d  
voltex  
volume  
volumeCalculator  
VolumeJ  
wavelets  
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