| adapter |
|
| adt |
|
| ai |
|
| amira |
|
| anisotropic_diffusion |
|
| bdv |
|
| bdv.cache |
|
| bdv.export |
|
| bdv.export.n5 |
|
| 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.n5 |
|
| 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.ui |
|
| bdv.ui.convertersetupeditor |
|
| bdv.ui.rangeslider |
|
| bdv.ui.sourcegrouptree |
|
| bdv.ui.sourcetable |
|
| bdv.ui.splitpanel |
|
| bdv.ui.viewermodepanel |
|
| bdv.util |
|
| bdv.util.volatiles |
|
| bdv.viewer |
|
| bdv.viewer.animate |
|
| bdv.viewer.overlay |
|
| bdv.viewer.render |
|
| bdv.viewer.render.awt |
|
| bdv.viewer.state |
|
| bigwarp |
|
| bigwarp.landmarks |
|
| bigwarp.landmarks.actions |
|
| bigwarp.loader |
|
| bigwarp.metadata |
|
| bigwarp.scripts |
|
| bigwarp.source |
|
| bigwarp.transforms |
|
| bigwarp.util |
|
| 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 |
|
| customnode |
|
| customnode.u3d |
|
| delaunay |
|
| distance |
|
| 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.help |
|
| fiji.packaging |
|
| fiji.plugin |
|
| fiji.plugin.timelapsedisplay |
|
| fiji.plugin.trackmate |
|
| fiji.plugin.trackmate.action |
|
| fiji.plugin.trackmate.action.fit |
|
| 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.components |
|
| fiji.plugin.trackmate.gui.components.detector |
|
| fiji.plugin.trackmate.gui.components.tracker |
|
| fiji.plugin.trackmate.gui.displaysettings |
|
| fiji.plugin.trackmate.gui.wizard |
|
| fiji.plugin.trackmate.gui.wizard.descriptors |
|
| 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.overlap |
|
| 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.table |
|
| fiji.plugin.trackmate.visualization.trackscheme |
|
| fiji.plugin.trackmate.visualization.trackscheme.utils |
|
| fiji.plugin.volumeviewer |
|
| fiji.process |
|
| fiji.process3d |
|
| fiji.scripting |
|
| fiji.selection |
|
| fiji.stacks |
|
| fiji.statistics |
|
| fiji.threshold |
|
| fiji.tool |
|
| fiji.util |
|
| fiji.util.gui |
|
| fiji.util.node |
|
| fsalign |
|
| graphcut |
|
| gui |
|
| histogram2 |
|
| hr.irb.fastRandomForest |
|
| ij.gui |
|
| ij3d |
|
| ij3d.behaviors |
|
| ij3d.contextmenu |
|
| ij3d.gui |
|
| ij3d.pointlist |
|
| ij3d.segmentation |
|
| ij3d.shapes |
|
| ij3d.shortcuts |
|
| 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 |
|
| 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 |
Mathematical utilies for java.
|
| math3d |
|
| mmorpho |
|
| mpi.fruitfly.general |
|
| mpi.fruitfly.math |
|
| mpi.fruitfly.math.datastructures |
|
| mpi.fruitfly.registration |
|
| mpicbg.icp |
|
| mpicbg.ij |
|
| mpicbg.ij.blockmatching |
|
| mpicbg.ij.clahe |
|
| mpicbg.ij.integral |
|
| mpicbg.ij.plugin |
|
| mpicbg.ij.stack |
|
| mpicbg.ij.util |
|
| mpicbg.ij.visualization |
|
| mpicbg.imagefeatures |
|
| 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.models |
|
| 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 |
|
| net.imagej.ui.swing.ops |
|
| net.imglib2 |
|
| net.imglib2.algorithm.math |
|
| net.imglib2.display |
|
| net.imglib2.iterator |
|
| net.imglib2.predicate |
|
| net.imglib2.realtransform |
|
| 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.thickness |
|
| org.janelia.thickness.inference |
|
| org.janelia.thickness.inference.fits |
|
| org.janelia.thickness.inference.visitor |
|
| org.janelia.thickness.lut |
|
| org.janelia.thickness.plugin |
|
| org.janelia.thickness.trakem2 |
|
| org.janelia.utility |
|
| org.janelia.utility.arrays |
|
| org.janelia.utility.parse |
|
| org.janelia.utility.ui |
|
| org.janelia.vaa3d.reader |
|
| org.siox |
|
| org.siox.example |
|
| org.siox.util |
|
| orthoslice |
|
| pal.math |
|
| plugin |
|
| process |
|
| process3d |
|
| QuickPALM |
|
| register_virtual_stack |
|
| registration3d |
|
| sc.fiji.analyzeSkeleton |
|
| sc.fiji.analyzeSkeleton.ita |
|
| sc.fiji.balloonSegmentation |
|
| sc.fiji.balloonSegmentation.structure |
|
| sc.fiji.balloonSegmentation.utils |
|
| sc.fiji.cellCounter |
|
| sc.fiji.coloc |
|
| sc.fiji.coloc.algorithms |
|
| sc.fiji.coloc.gadgets |
|
| sc.fiji.coloc.results |
|
| sc.fiji.colourDeconvolution |
|
| sc.fiji.hdf5 |
|
| 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.omevisual |
|
| sc.fiji.omevisual.gui |
|
| sc.fiji.omevisual.gui.model |
|
| sc.fiji.omevisual.gui.view |
|
| sc.fiji.skeletonize3D |
|
| sc.fiji.snt |
SNT core classes
|
| sc.fiji.snt.analysis |
|
| sc.fiji.snt.analysis.graph |
Classes for handling neuronal reconstructions as graphs
|
| sc.fiji.snt.analysis.sholl |
Sholl analysis of Images, pre-sampled data and Trees. |
| sc.fiji.snt.analysis.sholl.gui |
GUI customizations (image overlays, plots, etc.) required for Sholl Analysis.
|
| sc.fiji.snt.analysis.sholl.math |
Statistical analysis of Sholl data
|
| sc.fiji.snt.analysis.sholl.parsers |
Parsers to retrieve Profiles from multiple sources (2D/3D images, reconstructions, and tables)
|
| sc.fiji.snt.annotation |
Classes handling neuropil annotations and atlases metadata.
|
| sc.fiji.snt.event |
Utilities for TrakEM2 interaction
|
| sc.fiji.snt.filter |
|
| sc.fiji.snt.gui |
Customizations and commands for SNT's GUI.
|
| sc.fiji.snt.gui.cmds |
Scijava-based GUIs for SNT built-in commands.
|
| sc.fiji.snt.hyperpanes |
Classes implementing SNT's XY, ZY, and XZ canvases.
|
| sc.fiji.snt.io |
Classes for importing reconstructions into SNT.
|
| sc.fiji.snt.plugin |
SNT add-ons as IJ2 commands
|
| sc.fiji.snt.plugin.ij1 |
|
| sc.fiji.snt.tracing |
|
| sc.fiji.snt.tracing.artist |
|
| sc.fiji.snt.tracing.cost |
|
| sc.fiji.snt.tracing.heuristic |
|
| sc.fiji.snt.tracing.image |
|
| sc.fiji.snt.util |
Miscellaneous SNT utilities, including classes defining reconstruction nodes.
|
| sc.fiji.snt.viewer |
Visualization of reconstructions
|
| sc.fiji.snt.viewer.geditor |
|
| 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 |
|
| siox |
|
| spim |
|
| 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 |
|
| surfaceplot |
|
| textureByRef |
|
| tools |
|
| trainableSegmentation |
|
| trainableSegmentation.filters |
|
| trainableSegmentation.metrics |
|
| trainableSegmentation.unsupervised |
|
| trainableSegmentation.utils |
|
| 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 |
|
| volumeCalculator |
|