├── .gitignore ├── LICENSE ├── README.md ├── docs ├── Makefile ├── PyLattice_Manual.pdf ├── _build │ ├── doctrees │ │ ├── _themes │ │ │ └── sphinx_rtd_theme │ │ │ │ ├── README.doctree │ │ │ │ ├── docs │ │ │ │ ├── changelog.doctree │ │ │ │ ├── configuring.doctree │ │ │ │ ├── contributing.doctree │ │ │ │ ├── demo │ │ │ │ │ ├── api.doctree │ │ │ │ │ ├── demo.doctree │ │ │ │ │ ├── lists_tables.doctree │ │ │ │ │ ├── long.doctree │ │ │ │ │ └── structure.doctree │ │ │ │ ├── index.doctree │ │ │ │ └── installing.doctree │ │ │ │ └── tests │ │ │ │ └── roots │ │ │ │ ├── test-basic │ │ │ │ ├── bar.doctree │ │ │ │ ├── foo.doctree │ │ │ │ └── index.doctree │ │ │ │ ├── test-empty │ │ │ │ └── index.doctree │ │ │ │ └── test-missing-toctree │ │ │ │ └── index.doctree │ │ ├── debuggingMatlabMac.doctree │ │ ├── environment.pickle │ │ ├── index.doctree │ │ ├── installation.doctree │ │ ├── running.doctree │ │ └── thisIsATest.doctree │ └── html │ │ ├── .buildinfo │ │ ├── .nojekyll │ │ ├── _downloads │ │ └── d8764b51ec10a32a429450528a40eee1 │ │ │ └── yi_jing_01_chien.jpg │ │ ├── _images │ │ ├── pyLattice_logo.png │ │ └── yi_jing_01_chien.jpg │ │ ├── _sources │ │ ├── _themes │ │ │ └── sphinx_rtd_theme │ │ │ │ ├── README.rst.txt │ │ │ │ ├── docs │ │ │ │ ├── changelog.rst.txt │ │ │ │ ├── configuring.rst.txt │ │ │ │ ├── contributing.rst.txt │ │ │ │ ├── demo │ │ │ │ │ ├── api.rst.txt │ │ │ │ │ ├── demo.rst.txt │ │ │ │ │ ├── lists_tables.rst.txt │ │ │ │ │ ├── long.rst.txt │ │ │ │ │ └── structure.rst.txt │ │ │ │ ├── index.rst.txt │ │ │ │ └── installing.rst.txt │ │ │ │ └── tests │ │ │ │ └── roots │ │ │ │ ├── test-basic │ │ │ │ ├── bar.rst.txt │ │ │ │ ├── foo.rst.txt │ │ │ │ └── index.rst.txt │ │ │ │ ├── test-empty │ │ │ │ └── index.rst.txt │ │ │ │ └── test-missing-toctree │ │ │ │ └── index.rst.txt │ │ ├── debuggingMatlabMac.rst.txt │ │ ├── index.rst.txt │ │ ├── installation.rst.txt │ │ ├── running.rst.txt │ │ └── thisIsATest.rst.txt │ │ ├── _static │ │ ├── ajax-loader.gif │ │ ├── alabaster.css │ │ ├── basic.css │ │ ├── comment-bright.png │ │ ├── comment-close.png │ │ ├── comment.png │ │ ├── css │ │ │ ├── badge_only.css │ │ │ ├── fonts │ │ │ │ ├── Roboto-Slab-Bold.woff │ │ │ │ ├── Roboto-Slab-Bold.woff2 │ │ │ │ ├── Roboto-Slab-Regular.woff │ │ │ │ ├── Roboto-Slab-Regular.woff2 │ │ │ │ ├── fontawesome-webfont.eot │ │ │ │ ├── fontawesome-webfont.svg │ │ │ │ ├── fontawesome-webfont.ttf │ │ │ │ ├── fontawesome-webfont.woff │ │ │ │ ├── fontawesome-webfont.woff2 │ │ │ │ ├── lato-bold-italic.woff │ │ │ │ ├── lato-bold-italic.woff2 │ │ │ │ ├── lato-bold.woff │ │ │ │ ├── lato-bold.woff2 │ │ │ │ ├── lato-normal-italic.woff │ │ │ │ ├── lato-normal-italic.woff2 │ │ │ │ ├── lato-normal.woff │ │ │ │ └── lato-normal.woff2 │ │ │ └── theme.css │ │ ├── custom.css │ │ ├── doctools.js │ │ ├── documentation_options.js │ │ ├── down-pressed.png │ │ ├── down.png │ │ ├── file.png │ │ ├── fonts │ │ │ ├── FontAwesome.otf │ │ │ ├── Inconsolata-Bold.ttf │ │ │ ├── Inconsolata-Regular.ttf │ │ │ ├── Inconsolata.ttf │ │ │ ├── Lato-Bold.ttf │ │ │ ├── Lato-Regular.ttf │ │ │ ├── Lato │ │ │ │ ├── lato-bold.eot │ │ │ │ ├── lato-bold.ttf │ │ │ │ ├── lato-bold.woff │ │ │ │ ├── lato-bold.woff2 │ │ │ │ ├── lato-bolditalic.eot │ │ │ │ ├── lato-bolditalic.ttf │ │ │ │ ├── lato-bolditalic.woff │ │ │ │ ├── lato-bolditalic.woff2 │ │ │ │ ├── lato-italic.eot │ │ │ │ ├── lato-italic.ttf │ │ │ │ ├── lato-italic.woff │ │ │ │ ├── lato-italic.woff2 │ │ │ │ ├── lato-regular.eot │ │ │ │ ├── lato-regular.ttf │ │ │ │ ├── lato-regular.woff │ │ │ │ └── lato-regular.woff2 │ │ │ ├── Roboto-Slab-Bold.woff │ │ │ ├── Roboto-Slab-Bold.woff2 │ │ │ ├── Roboto-Slab-Light.woff │ │ │ ├── Roboto-Slab-Light.woff2 │ │ │ ├── Roboto-Slab-Regular.woff │ │ │ ├── Roboto-Slab-Regular.woff2 │ │ │ ├── Roboto-Slab-Thin.woff │ │ │ ├── Roboto-Slab-Thin.woff2 │ │ │ ├── RobotoSlab-Bold.ttf │ │ │ ├── RobotoSlab-Regular.ttf │ │ │ ├── RobotoSlab │ │ │ │ ├── roboto-slab-v7-bold.eot │ │ │ │ ├── roboto-slab-v7-bold.ttf │ │ │ │ ├── roboto-slab-v7-bold.woff │ │ │ │ ├── roboto-slab-v7-bold.woff2 │ │ │ │ ├── roboto-slab-v7-regular.eot │ │ │ │ ├── roboto-slab-v7-regular.ttf │ │ │ │ ├── roboto-slab-v7-regular.woff │ │ │ │ └── roboto-slab-v7-regular.woff2 │ │ │ ├── fontawesome-webfont.eot │ │ │ ├── fontawesome-webfont.svg │ │ │ ├── fontawesome-webfont.ttf │ │ │ ├── fontawesome-webfont.woff │ │ │ ├── fontawesome-webfont.woff2 │ │ │ ├── lato-bold-italic.woff │ │ │ ├── lato-bold-italic.woff2 │ │ │ ├── lato-bold.woff │ │ │ ├── lato-bold.woff2 │ │ │ ├── lato-normal-italic.woff │ │ │ ├── lato-normal-italic.woff2 │ │ │ ├── lato-normal.woff │ │ │ └── lato-normal.woff2 │ │ ├── jquery-3.1.0.js │ │ ├── jquery-3.4.1.js │ │ ├── jquery-3.5.1.js │ │ ├── jquery.js │ │ ├── js │ │ │ ├── badge_only.js │ │ │ ├── html5shiv-printshiv.min.js │ │ │ ├── html5shiv.min.js │ │ │ ├── modernizr.min.js │ │ │ └── theme.js │ │ ├── language_data.js │ │ ├── minus.png │ │ ├── plus.png │ │ ├── pyLattice_logo_small.png │ │ ├── pyLattice_logo_small_100px.png │ │ ├── pyLattice_logo_small_150px.png │ │ ├── pyLattice_logo_small_200px.png │ │ ├── pygments.css │ │ ├── searchtools.js │ │ ├── underscore-1.3.1.js │ │ ├── underscore.js │ │ ├── up-pressed.png │ │ ├── up.png │ │ └── websupport.js │ │ ├── _themes │ │ └── sphinx_rtd_theme │ │ │ ├── README.html │ │ │ ├── docs │ │ │ ├── changelog.html │ │ │ ├── configuring.html │ │ │ ├── contributing.html │ │ │ ├── demo │ │ │ │ ├── api.html │ │ │ │ ├── demo.html │ │ │ │ ├── lists_tables.html │ │ │ │ ├── long.html │ │ │ │ └── structure.html │ │ │ ├── index.html │ │ │ └── installing.html │ │ │ └── tests │ │ │ └── roots │ │ │ ├── test-basic │ │ │ ├── bar.html │ │ │ ├── foo.html │ │ │ └── index.html │ │ │ ├── test-empty │ │ │ └── index.html │ │ │ └── test-missing-toctree │ │ │ └── index.html │ │ ├── debuggingMatlabMac.html │ │ ├── genindex.html │ │ ├── index.html │ │ ├── installation.html │ │ ├── objects.inv │ │ ├── running.html │ │ ├── search.html │ │ ├── searchindex.js │ │ └── thisIsATest.html ├── _static │ ├── pyLattice_logo_small.png │ ├── pyLattice_logo_small_100px.png │ ├── pyLattice_logo_small_150px.png │ └── pyLattice_logo_small_200px.png ├── _themes │ └── sphinx_rtd_theme │ │ ├── .gitattributes │ │ ├── .github │ │ ├── CODE_OF_CONDUCT.md │ │ └── ISSUE_TEMPLATE.md │ │ ├── .gitignore │ │ ├── .readthedocs.yml │ │ ├── .travis.yml │ │ ├── .tx │ │ └── config │ │ ├── Apache-License-2.0.txt │ │ ├── LICENSE │ │ ├── MANIFEST.in │ │ ├── OFL-License.txt │ │ ├── README.rst │ │ ├── babel.cfg │ │ ├── bin │ │ └── preinstall.js │ │ ├── docs │ │ ├── Makefile │ │ ├── changelog.rst │ │ ├── conf.py │ │ ├── configuring.rst │ │ ├── contributing.rst │ │ ├── demo │ │ │ ├── api.rst │ │ │ ├── demo.rst │ │ │ ├── lists_tables.rst │ │ │ ├── long.rst │ │ │ ├── static │ │ │ │ ├── logo-wordmark-light.svg │ │ │ │ ├── screen_desktop.png │ │ │ │ ├── screen_mobile.png │ │ │ │ └── yi_jing_01_chien.jpg │ │ │ ├── structure.rst │ │ │ └── test_py_module │ │ │ │ ├── __init__.py │ │ │ │ └── test.py │ │ ├── index.rst │ │ ├── installing.rst │ │ ├── make.bat │ │ └── requirements.txt │ │ ├── package-lock.json │ │ ├── package.json │ │ ├── setup.cfg │ │ ├── setup.py │ │ ├── sphinx_rtd_theme │ │ ├── __init__.py │ │ ├── breadcrumbs.html │ │ ├── footer.html │ │ ├── layout.html │ │ ├── locale │ │ │ ├── de │ │ │ │ └── LC_MESSAGES │ │ │ │ │ ├── sphinx.mo │ │ │ │ │ └── sphinx.po │ │ │ ├── en │ │ │ │ └── LC_MESSAGES │ │ │ │ │ ├── sphinx.mo │ │ │ │ │ └── sphinx.po │ │ │ ├── es │ │ │ │ └── LC_MESSAGES │ │ │ │ │ ├── sphinx.mo │ │ │ │ │ └── sphinx.po │ │ │ ├── nl │ │ │ │ └── LC_MESSAGES │ │ │ │ │ ├── sphinx.mo │ │ │ │ │ └── sphinx.po │ │ │ ├── ru │ │ │ │ └── LC_MESSAGES │ │ │ │ │ ├── sphinx.mo │ │ │ │ │ └── sphinx.po │ │ │ └── sphinx.pot │ │ ├── search.html │ │ ├── searchbox.html │ │ ├── static │ │ │ ├── css │ │ │ │ ├── badge_only.css │ │ │ │ ├── fonts │ │ │ │ │ ├── Roboto-Slab-Bold.woff │ │ │ │ │ ├── Roboto-Slab-Bold.woff2 │ │ │ │ │ ├── Roboto-Slab-Regular.woff │ │ │ │ │ ├── Roboto-Slab-Regular.woff2 │ │ │ │ │ ├── fontawesome-webfont.eot │ │ │ │ │ ├── fontawesome-webfont.svg │ │ │ │ │ ├── fontawesome-webfont.ttf │ │ │ │ │ ├── fontawesome-webfont.woff │ │ │ │ │ ├── fontawesome-webfont.woff2 │ │ │ │ │ ├── lato-bold-italic.woff │ │ │ │ │ ├── lato-bold-italic.woff2 │ │ │ │ │ ├── lato-bold.woff │ │ │ │ │ ├── lato-bold.woff2 │ │ │ │ │ ├── lato-normal-italic.woff │ │ │ │ │ ├── lato-normal-italic.woff2 │ │ │ │ │ ├── lato-normal.woff │ │ │ │ │ └── lato-normal.woff2 │ │ │ │ └── theme.css │ │ │ └── js │ │ │ │ ├── badge_only.js │ │ │ │ └── theme.js │ │ ├── theme.conf │ │ └── versions.html │ │ ├── src │ │ ├── sass │ │ │ ├── _theme_badge.sass │ │ │ ├── _theme_badge_fa.sass │ │ │ ├── _theme_breadcrumbs.sass │ │ │ ├── _theme_font_awesome_compatibility.sass │ │ │ ├── _theme_font_local.sass │ │ │ ├── _theme_layout.sass │ │ │ ├── _theme_mathjax.sass │ │ │ ├── _theme_rst.sass │ │ │ ├── _theme_variables.sass │ │ │ ├── badge_only.sass │ │ │ └── theme.sass │ │ └── theme.js │ │ ├── tests │ │ ├── __init__.py │ │ ├── roots │ │ │ ├── test-basic │ │ │ │ ├── bar.rst │ │ │ │ ├── conf.py │ │ │ │ ├── foo.rst │ │ │ │ └── index.rst │ │ │ ├── test-empty │ │ │ │ ├── conf.py │ │ │ │ └── index.rst │ │ │ └── test-missing-toctree │ │ │ │ ├── conf.py │ │ │ │ └── index.rst │ │ ├── test_builders.py │ │ └── util.py │ │ ├── tox.ini │ │ ├── webpack.common.js │ │ ├── webpack.dev.js │ │ └── webpack.prod.js ├── conf.py ├── index.rst ├── installation.rst ├── pyLattice_logo.png └── running.rst ├── requirements.txt └── src ├── SwAK_tools └── rotate180 │ └── SwAK_rotate180.ipynb ├── jupyter ├── box.tif ├── box_around_fiji_derived_coords.tif ├── box_mesh.tif ├── detectedPuncta_csv2bild.ipynb ├── detectedPuncta_detectApicalBasalLateralSeparationLine_3D.ipynb ├── detectedPuncta_drawBoxAroundEveryDetectionInFrame.ipynb ├── detectedPuncta_oneFrame_plot.ipynb ├── detectedTracksProcessed_apibasointer_lifetimeCohorts.ipynb ├── detectedTracksProcessed_cropInputMovie_zoomOnTrack_createBox.ipynb ├── detectedTracksProcessed_csv2bild.ipynb ├── detectedTracksProcessed_gatherTrackingStatistics.ipynb ├── detectedTracksProcessed_lifetimeCohorts_fluorescenceIntensity.ipynb ├── detectedTracksProcessed_lifetimeCohorts_travelDistance.ipynb ├── detectedTracksProcessed_plotAll_2DProjections.ipynb ├── detectedTracksProcessed_plotAll_3D.ipynb ├── detectedTracksProcessed_plot_bothChannels.ipynb ├── detectedTracksProcessed_plot_bothChannels_overview.ipynb ├── detectedTracks_analyze.ipynb ├── detectedTracks_csv2bild.ipynb ├── detectedTracks_lifetimeCohorts.ipynb ├── detectedTracks_plot.ipynb ├── illustration_filters.ipynb ├── latticeFrame_showFrame.ipynb ├── latticeMovie_correctBleaching.ipynb ├── latticeMovie_cropRegion.ipynb └── latticeMovie_cropRegion_parallel.ipynb ├── matlab └── trackingModule │ ├── III_onlyTracking.m │ ├── III_tracksRaw2csv.m │ ├── II_stitchMatlabFramesTogether.m │ ├── IV_onlyTrackingProcessing.m │ ├── IV_tracksProcessed2csv.m │ ├── I_onlyDetection_framebyframe_nonParallel.m │ ├── dependencies │ ├── binarySegmentLengths.m │ ├── costMatLinearMotionCloseGaps2.m │ ├── costMatLinearMotionLink2.m │ ├── estimTrackTypeParamLM2.m │ ├── getAveDispEllipseAll2.m │ ├── llsmtools-master │ │ ├── .gitignore │ │ ├── README.md │ │ ├── cmeAnalysis3D │ │ │ ├── cmeAnalysis3D.m │ │ │ ├── cropMovie3D.m │ │ │ ├── deskewData.m │ │ │ ├── getCellVolume.m │ │ │ ├── getCropRegions3D.m │ │ │ ├── getFluorPropStruct.m │ │ │ ├── getLifetimeData.m │ │ │ ├── getVisitorIndex.m │ │ │ ├── loadConditionData.m │ │ │ ├── loadConditionData3D.m │ │ │ ├── loadTrackSettings.m │ │ │ ├── loadTracks.m │ │ │ ├── plotIntensityCohorts.m │ │ │ ├── plotLifetimes.m │ │ │ ├── rotateDetections3D.m │ │ │ ├── rotateTracks3D.m │ │ │ ├── runDetection3D.m │ │ │ ├── runLifetimeAnalysis.m │ │ │ ├── runTrackProcessing3D.m │ │ │ └── runTracking3D.m │ │ ├── graphics │ │ │ ├── loadFigureSettings.m │ │ │ ├── setupFigure.m │ │ │ └── stackviewer.m │ │ ├── iofunc │ │ │ ├── readtiff.m │ │ │ └── writetiff.m │ │ ├── mathfunc │ │ │ ├── KDTreeBallQuery.mexa64 │ │ │ ├── KDTreeBallQuery.mexmaci64 │ │ │ ├── KDTreeBallQuery.mexw64 │ │ │ ├── interpln.m │ │ │ ├── scaleContrast.m │ │ │ └── scaleEDFs.m │ │ ├── pathfunc │ │ │ ├── getCellDir.m │ │ │ ├── getDirFromPath.m │ │ │ ├── getMovieName.m │ │ │ ├── getShortPath.m │ │ │ ├── recursiveDir.m │ │ │ └── sortStringsByToken.m │ │ ├── psdetect3d │ │ │ ├── conv3fast.m │ │ │ ├── conv3fast.mexa64 │ │ │ ├── conv3fast.mexmaci64 │ │ │ ├── conv3fast.mexw64 │ │ │ ├── fitGaussian3D.m │ │ │ ├── fitGaussian3D.mexa64 │ │ │ ├── fitGaussian3D.mexmaci64 │ │ │ ├── fitGaussian3D.mexw64 │ │ │ ├── fitGaussians3D.m │ │ │ ├── locmax3d.m │ │ │ └── pointSourceDetection3D.m │ │ └── transforms │ │ │ ├── deskewFrame3D.m │ │ │ └── rotateFrame3D.m │ ├── locmax1d.m │ └── u-track │ │ ├── GPL-License.txt │ │ ├── Readme_u-track.pdf │ │ └── software │ │ ├── +cached │ │ ├── FileCache.m │ │ ├── FileCacheWithIndexing.m │ │ ├── MatFileCache.m │ │ ├── TestImfinfo.m │ │ ├── TestLoad.m │ │ ├── clear.m │ │ ├── imfinfo.m │ │ ├── load.m │ │ └── save.m │ │ ├── @AnisoGaussianDetectionProcess │ │ └── AnisoGaussianDetectionProcess.m │ │ ├── @BioFormatsReader │ │ ├── BioFormatsReader.m │ │ ├── getDeltaT.m │ │ ├── getXML.m │ │ └── showMetadata.m │ │ ├── @Channel │ │ └── Channel.m │ │ ├── @DataProcessingProcess │ │ └── DataProcessingProcess.m │ │ ├── @DetectionProcess │ │ └── DetectionProcess.m │ │ ├── @HCSReader │ │ └── HCSReader.m │ │ ├── @HistogramDisplay │ │ └── HistogramDisplay.m │ │ ├── @ImageAnalysisProcess │ │ └── ImageAnalysisProcess.m │ │ ├── @ImageDisplay │ │ └── ImageDisplay.m │ │ ├── @ImageOverlayDisplay │ │ └── ImageOverlayDisplay.m │ │ ├── @LineDisplay │ │ └── LineDisplay.m │ │ ├── @MaskIntersectionProcess │ │ └── MaskIntersectionProcess.m │ │ ├── @MaskProcess │ │ └── MaskProcess.m │ │ ├── @MaskProcessingProcess │ │ └── MaskProcessingProcess.m │ │ ├── @MotionAnalysisProcess │ │ └── MotionAnalysisProcess.m │ │ ├── @MovieData │ │ ├── MovieData.m │ │ ├── addAnalysisFolder.m │ │ ├── isequal.m │ │ ├── isequaln.m │ │ └── isequalwithequalnans.m │ │ ├── @MovieDataDisplay │ │ └── MovieDataDisplay.m │ │ ├── @MovieList │ │ ├── MovieList.m │ │ └── addAnalysisFolder.m │ │ ├── @MovieObject │ │ ├── MovieObject.m │ │ ├── addAnalysisFolder.m │ │ └── getOwnerAndProcess.m │ │ ├── @NonSingularProcess │ │ └── NonSingularProcess.m │ │ ├── @NucleiDetectionProcess │ │ └── NucleiDetectionProcess.m │ │ ├── @NucleiTrackingPackage │ │ └── NucleiTrackingPackage.m │ │ ├── @OmeroReader │ │ └── OmeroReader.m │ │ ├── @Package │ │ └── Package.m │ │ ├── @PointSourceDetectionProcess │ │ └── PointSourceDetectionProcess.m │ │ ├── @PointSourceDetectionProcess3D │ │ └── PointSourceDetectionProcess3D.m │ │ ├── @PostTrackingProcess │ │ └── PostTrackingProcess.m │ │ ├── @Process │ │ ├── Process.m │ │ └── getOwnerAndProcess.m │ │ ├── @Reader │ │ └── Reader.m │ │ ├── @SubResolutionProcess │ │ └── SubResolutionProcess.m │ │ ├── @TextDisplay │ │ └── TextDisplay.m │ │ ├── @TiffSeriesReader │ │ └── TiffSeriesReader.m │ │ ├── @TrackingPackage │ │ └── TrackingPackage.m │ │ ├── @TrackingProcess │ │ └── TrackingProcess.m │ │ ├── @TracksDisplay │ │ └── TracksDisplay.m │ │ ├── @UTrackPackage │ │ └── UTrackPackage.m │ │ ├── @UTrackPackage3D │ │ └── UTrackPackage3D.m │ │ ├── CometDetectionProcess.m │ │ ├── CometPostTrackingProcess.m │ │ ├── GaussFitND.m │ │ ├── GaussFitND_gradient.m │ │ ├── GaussListND.m │ │ ├── HCSplatestack.m │ │ ├── MTTracksDisplay.m │ │ ├── MakeQTMovie.m │ │ ├── PlusTipTrackerPackage.m │ │ ├── abstractProcessGUI.fig │ │ ├── abstractProcessGUI.m │ │ ├── addMovieViewerKeyboardShortcuts.m │ │ ├── addROIGUI.fig │ │ ├── addROIGUI.m │ │ ├── all_insequence.m │ │ ├── analyzeMovieMotion.m │ │ ├── anisoGaussian2DSupport.m │ │ ├── anisoGaussianDetectionProcessGUI.fig │ │ ├── anisoGaussianDetectionProcessGUI.m │ │ ├── asymDeterm2D3D.m │ │ ├── barplot2.m │ │ ├── bfImport.m │ │ ├── bioformats │ │ ├── NEWS.rst │ │ ├── bfCheckJavaMemory.m │ │ ├── bfCheckJavaPath.m │ │ ├── bfGetFileExtensions.m │ │ ├── bfGetPlane.m │ │ ├── bfGetReader.m │ │ ├── bfInitLogging.m │ │ ├── bfOpen3DVolume.m │ │ ├── bfUpgradeCheck.m │ │ ├── bfopen.m │ │ ├── bfsave.m │ │ ├── bioformats_package.jar │ │ ├── createMinimalOMEXMLMetadata.m │ │ └── private │ │ │ └── is_octave.m │ │ ├── blobSegmentThreshold.m │ │ ├── calcTrackMoments.m │ │ ├── catStruct.m │ │ ├── centroid2D.m │ │ ├── centroid3D.m │ │ ├── centroidSubResFeatures2D.m │ │ ├── channelGUI.fig │ │ ├── channelGUI.m │ │ ├── checkallChannels_Callback.m │ │ ├── chooseTracks.m │ │ ├── combineGroupListFiles.m │ │ ├── cometDetection.m │ │ ├── cometDetectionProcessGUI.fig │ │ ├── cometDetectionProcessGUI.m │ │ ├── cometPostTrackingProcessGUI.fig │ │ ├── cometPostTrackingProcessGUI.m │ │ ├── convStruct2MatIgnoreMS.m │ │ ├── convStruct2MatNoMS.m │ │ ├── coordAmpMatFromIndicesSparse.m │ │ ├── costMatRandomDirectedSwitchingMotionCloseGaps.m │ │ ├── costMatRandomDirectedSwitchingMotionCloseGapsGUI.fig │ │ ├── costMatRandomDirectedSwitchingMotionCloseGapsGUI.m │ │ ├── costMatRandomDirectedSwitchingMotionLink.m │ │ ├── costMatRandomDirectedSwitchingMotionLinkGUI.fig │ │ ├── costMatRandomDirectedSwitchingMotionLinkGUI.m │ │ ├── costMat_OpeningFcn.m │ │ ├── cropMovie.m │ │ ├── cropMovieGUI.fig │ │ ├── cropMovieGUI.m │ │ ├── cropStack.m │ │ ├── cutFirstHistMode.m │ │ ├── dataPreparationGUI.fig │ │ ├── dataPreparationGUI.m │ │ ├── deleteChannel_Callback.m │ │ ├── detectComets.m │ │ ├── detectComets3D.m │ │ ├── detectMovieAnisoGaussians.m │ │ ├── detectMovieComets.m │ │ ├── detectMovieNuclei.m │ │ ├── detectMoviePointSources.m │ │ ├── detectMoviePointSources3D.m │ │ ├── detectMovieSubResFeatures.m │ │ ├── detectNuclei.m │ │ ├── detectSubResFeatures2D_StandAlone.m │ │ ├── detectSubResFeatures2D_V2.m │ │ ├── discriminationMatrix.m │ │ ├── distribTest.m │ │ ├── doc │ │ ├── AnisoGaussianDetectionProcess.pdf │ │ ├── CometDetectionProcess.pdf │ │ ├── CometPostTrackingProcess.pdf │ │ ├── DetectionProcess.pdf │ │ ├── MotionAnalysisProcess.pdf │ │ ├── NucleiDetectionProcess.pdf │ │ ├── PostTrackingProcess.pdf │ │ ├── SubResolutionProcess.pdf │ │ ├── TrackingPackage.pdf │ │ ├── TrackingProcess.pdf │ │ ├── addROIGUI.pdf │ │ ├── channelGUI.pdf │ │ ├── costMatRandomDirectedSwitchingMotionCloseGapsGUI.pdf │ │ ├── costMatRandomDirectedSwitchingMotionLinkGUI.pdf │ │ ├── dataPreparationGUI.pdf │ │ ├── kalmanInitializationGUI.pdf │ │ ├── movieDataGUI.pdf │ │ ├── movieSelectorGUI.pdf │ │ ├── movieViewer.pdf │ │ ├── overlayFeaturesMovie.pdf │ │ ├── overlayTracksMovieNew.pdf │ │ ├── plotTracks2D.pdf │ │ ├── plusTipCostMatCloseGapsGUI.pdf │ │ └── plusTipCostMatLinearMotionLinkGUI.pdf │ │ ├── estimTrackTypeParamRDS.m │ │ ├── extendedColors.m │ │ ├── extern │ │ ├── connectOmero.m │ │ ├── createMask.m │ │ ├── createObjectDictionary.m │ │ ├── exportImageAsOMETIFF.m │ │ ├── findOmero.m │ │ ├── getAnnotationTypes.m │ │ ├── getAnnotations.m │ │ ├── getDatasetFileAnnotations.m │ │ ├── getDatasets.m │ │ ├── getFileAnnotationContent.m │ │ ├── getFileAnnotations.m │ │ ├── getImageFileAnnotations.m │ │ ├── getImages.m │ │ ├── getObjectAnnotations.m │ │ ├── getObjectTypes.m │ │ ├── getObjects.m │ │ ├── getOmeroJars.m │ │ ├── getProjects.m │ │ ├── linkAnnotation.m │ │ ├── loadOmero.m │ │ ├── omeroVersion.m │ │ ├── rdouble.m │ │ ├── rlong.m │ │ ├── rstring.m │ │ ├── structToHashMap.m │ │ ├── tiffread.m │ │ ├── toJavaList.m │ │ ├── toMatlabList.m │ │ ├── toMatrix.m │ │ ├── updateFileAnnotation.m │ │ ├── updateOriginalFile.m │ │ ├── vline.m │ │ └── writeFileAnnotation.m │ │ ├── filterGauss2D.m │ │ ├── filterGauss3D.m │ │ ├── filterLoG.m │ │ ├── findOverlapPSFs2D.m │ │ ├── findTrackGaps.m │ │ ├── fitGaussianMixtures2D.m │ │ ├── fitGaussianMixtures3D.m │ │ ├── fitGaussians2D.m │ │ ├── fitGaussians3D.m │ │ ├── fitNGaussians2D.m │ │ ├── formatPath.m │ │ ├── fsFigure.m │ │ ├── generateReport.m │ │ ├── getFileStackNames.m │ │ ├── getFilenameBody.m │ │ ├── getFilesep.m │ │ ├── getFluorPropStruct.m │ │ ├── getGaussianPSFsigma.m │ │ ├── getGaussianPSFsigmaFrom3DData.m │ │ ├── getLCCBCopyright.m │ │ ├── getLCCBOmeroNamespace.m │ │ ├── getLensProperties.m │ │ ├── getMultiplicity.m │ │ ├── getNumSegmentsPerTrack.m │ │ ├── getOmeroLists.m │ │ ├── getOmeroMovies.m │ │ ├── getRelocationDirs.m │ │ ├── getSearchRegionRDS.m │ │ ├── getTrackSEL.m │ │ ├── getTrackType.m │ │ ├── getindexstart.m │ │ ├── graphViewer.m │ │ ├── icon_ButtonDownFcn.m │ │ ├── icons │ │ ├── accepted 48 32x32.png │ │ ├── cancel 48 32x32.png │ │ ├── dialog-question-22x22.png │ │ ├── dialog-question-48x48.png │ │ ├── document-open-8.png │ │ └── warning 48 32x32.png │ │ ├── imDir.m │ │ ├── imseriesshow.m │ │ ├── inputParserRetrofit.m │ │ ├── insequence.m │ │ ├── insequence_and_scalar.m │ │ ├── intersectMovieMasks.m │ │ ├── isConcreteClass.m │ │ ├── isProcessOrMovieData.m │ │ ├── isProcessOrMovieObject.m │ │ ├── isSubclass.m │ │ ├── isposint.m │ │ ├── isvalid.m │ │ ├── joinColumns.m │ │ ├── kalmanGainLinearMotion.m │ │ ├── kalmanInitLinearMotion.m │ │ ├── kalmanInitializationGUI.fig │ │ ├── kalmanInitializationGUI.m │ │ ├── kalmanResMemLM.m │ │ ├── kalmanReverseLinearMotion.m │ │ ├── lap.m │ │ ├── lineWithGaps.m │ │ ├── linkFeaturesKalmanSparse.m │ │ ├── loadLCCBIcons.m │ │ ├── locmax2d.m │ │ ├── locmax3d.m │ │ ├── markedWatershed.m │ │ ├── mex │ │ ├── KDTreeBallQuery.m │ │ ├── KDTreeBallQuery.mexa64 │ │ ├── KDTreeBallQuery.mexmaci64 │ │ ├── KDTreeBallQuery.mexw64 │ │ ├── conv3fast.m │ │ ├── conv3fast.mexa64 │ │ ├── conv3fast.mexmaci64 │ │ ├── conv3fast.mexw64 │ │ ├── createDistanceMatrix.dll │ │ ├── createDistanceMatrix.m │ │ ├── createDistanceMatrix.mexa64 │ │ ├── createDistanceMatrix.mexglx │ │ ├── createDistanceMatrix.mexmaci │ │ ├── createDistanceMatrix.mexmaci64 │ │ ├── createDistanceMatrix.mexw64 │ │ ├── fitAnisoGaussian2D.m │ │ ├── fitAnisoGaussian2D.mexa64 │ │ ├── fitAnisoGaussian2D.mexmaci64 │ │ ├── fitAnisoGaussian2D.mexw64 │ │ ├── fitGaussian2D.m │ │ ├── fitGaussian2D.mexa64 │ │ ├── fitGaussian2D.mexmaci64 │ │ ├── fitGaussian2D.mexw64 │ │ ├── fitGaussian3D.m │ │ ├── fitGaussian3D.mexa64 │ │ ├── fitGaussian3D.mexmaci64 │ │ ├── fitGaussian3D.mexw64 │ │ ├── fitGaussianMixture2D.m │ │ ├── fitGaussianMixture2D.mexa64 │ │ ├── fitGaussianMixture2D.mexmaci64 │ │ ├── fitGaussianMixture2D.mexw64 │ │ ├── fitGaussianMixture3D.m │ │ ├── fitGaussianMixture3D.mexa64 │ │ ├── fitGaussianMixture3D.mexmaci64 │ │ ├── fitGaussianMixture3D.mexw64 │ │ ├── mexLap.dll │ │ ├── mexLap.mexa64 │ │ ├── mexLap.mexglx │ │ ├── mexLap.mexmaci │ │ ├── mexLap.mexmaci64 │ │ ├── mexLap.mexw64 │ │ ├── steerableDetector.m │ │ ├── steerableDetector.mexa64 │ │ ├── steerableDetector.mexmaci64 │ │ ├── steerableDetector.mexw64 │ │ ├── vectorialPSF.m │ │ ├── vectorialPSF.mexa64 │ │ ├── vectorialPSF.mexmaci64 │ │ └── vectorialPSF.mexw64 │ │ ├── mkClrDir.m │ │ ├── mmfDistPV.m │ │ ├── mmfInitGuessLowerUpperBounds.m │ │ ├── mockMovieData.m │ │ ├── motionAnalysisProcessGUI.fig │ │ ├── motionAnalysisProcessGUI.m │ │ ├── movieDataGUI.fig │ │ ├── movieDataGUI.m │ │ ├── movieInfrastructure.m │ │ ├── movieSelectorGUI.fig │ │ ├── movieSelectorGUI.m │ │ ├── movieViewer.m │ │ ├── movieViewerOptions.m │ │ ├── msgboxGUI.fig │ │ ├── msgboxGUI.m │ │ ├── naFromLensID.m │ │ ├── name2wavelength.m │ │ ├── normList.m │ │ ├── nucleiDetectionProcessGUI.fig │ │ ├── nucleiDetectionProcessGUI.m │ │ ├── omeroCacheImport.m │ │ ├── omeroDataSelectionGUI.fig │ │ ├── omeroDataSelectionGUI.m │ │ ├── omeroImport.m │ │ ├── omeroLoginGUI.fig │ │ ├── omeroLoginGUI.m │ │ ├── omeroSave.m │ │ ├── optimalHistogram.m │ │ ├── overlayFeaturesMovie.m │ │ ├── overlayTracksMovieNew.m │ │ ├── packageGUI.fig │ │ ├── packageGUI.m │ │ ├── packageGUI_OpeningFcn.m │ │ ├── packageGUI_RefreshFcn.m │ │ ├── packageGUI_RunFcn.m │ │ ├── padarrayXT.m │ │ ├── parseProcessParams.m │ │ ├── permTest.m │ │ ├── perpVector.m │ │ ├── pixPerFrame2umPerMin.m │ │ ├── plotScaleBar.m │ │ ├── plotTimeStamp.m │ │ ├── plotTracks2D.m │ │ ├── plotTracks3D.m │ │ ├── plotTracksDiffAnalysis2D.m │ │ ├── plusTipBreakNonlinearTracks.m │ │ ├── plusTipCostMatCloseGaps.m │ │ ├── plusTipCostMatCloseGapsGUI.fig │ │ ├── plusTipCostMatCloseGapsGUI.m │ │ ├── plusTipCostMatLinearMotionLink.m │ │ ├── plusTipCostMatLinearMotionLinkGUI.fig │ │ ├── plusTipCostMatLinearMotionLinkGUI.m │ │ ├── plusTipDynamParam.m │ │ ├── plusTipExtractGroupData.m │ │ ├── plusTipGetHits.m │ │ ├── plusTipGetSubtrackCoords.m │ │ ├── plusTipGetVelocitiesFromMat.m │ │ ├── plusTipGroupAnalysisGUI.fig │ │ ├── plusTipGroupAnalysisGUI.m │ │ ├── plusTipKalmanGainLinearMotion.m │ │ ├── plusTipKalmanInitLinearMotion.m │ │ ├── plusTipMakeBoxplots.m │ │ ├── plusTipMakeHistograms.m │ │ ├── plusTipMergeSubtracks.m │ │ ├── plusTipPerCellPlot.m │ │ ├── plusTipPoolGroupData.m │ │ ├── plusTipRemBegEnd.m │ │ ├── plusTipTestDistrib.m │ │ ├── plusTipTrackerPackageGUI.m │ │ ├── plusTipWithinGroupComparison.m │ │ ├── pointSourceDetection.m │ │ ├── pointSourceDetection3D.m │ │ ├── pointSourceDetectionProcessGUI.fig │ │ ├── pointSourceDetectionProcessGUI.m │ │ ├── pointSourceDetectionProcessGUI3D.fig │ │ ├── pointSourceDetectionProcessGUI3D.m │ │ ├── postProcessMTTracks.m │ │ ├── postProcessMovieComets.m │ │ ├── prepPerChannelParams.m │ │ ├── processGUI_ApplyFcn.m │ │ ├── processGUI_OpeningFcn.m │ │ ├── progressText.m │ │ ├── projectCoordOntoDir.m │ │ ├── randomColormap.m │ │ ├── readIXMHTDFileM.m │ │ ├── readtiff.m │ │ ├── recycleProcessGUI.fig │ │ ├── recycleProcessGUI.m │ │ ├── relocatePath.m │ │ ├── robustMean.m │ │ ├── rotateXTickLabels.m │ │ ├── roundOddOrEven.m │ │ ├── runProcesses.m │ │ ├── scriptCorrectImageDrift.m │ │ ├── scriptDetectGeneral.m │ │ ├── scriptTrackGeneral.m │ │ ├── sec2struct.m │ │ ├── selectChannel_Callback.m │ │ ├── setErrorbarStyle.m │ │ ├── spatialMovAveBG.m │ │ ├── splitPerChannelParams.m │ │ ├── stackRead.m │ │ ├── stamp3d.m │ │ ├── subResolutionProcessGUI.fig │ │ ├── subResolutionProcessGUI.m │ │ ├── summarizeDiffAnRes.m │ │ ├── swapMaskValues.m │ │ ├── thresholdFluorescenceImage.m │ │ ├── thresholdFluorescenceImageFewBg.m │ │ ├── thresholdOtsu.m │ │ ├── thresholdRosin.m │ │ ├── tif3Dread.m │ │ ├── timeColormap.m │ │ ├── trackCloseGapsKalmanSparse.m │ │ ├── trackDiffusionAnalysis1.m │ │ ├── trackMSSAnalysis.m │ │ ├── trackMovie.m │ │ ├── trackedFeatures.mat │ │ ├── trackingProcessGUI.fig │ │ ├── trackingProcessGUI.m │ │ ├── uTrackPackageGUI.m │ │ ├── uTrackParCluster.m │ │ ├── userfcn_checkAllMovies.m │ │ ├── userfcn_drawIcon.m │ │ ├── userfcn_enable.m │ │ ├── userfcn_lampSwitch.m │ │ ├── userfcn_saveCheckbox.m │ │ ├── wavelength2rgb.m │ │ ├── weightedStats.m │ │ └── whichMatFile.m │ ├── runTrackingModule.m │ └── tools │ ├── estGaussianAmplitude3D.m │ ├── getAllFiles.m │ ├── loadTrackSettingsAguet.m │ ├── loadTrackSettingsJohMergeAguetAndUTrack.m │ ├── loadTrackSettingsJohUTrack.m │ ├── loadTrackSettings_.m │ ├── readParam.m │ └── roundConstr.m ├── python ├── CHANGES.txt ├── README.md ├── build │ └── lib │ │ └── pylattice │ │ ├── __init__.py │ │ ├── classes │ │ ├── Track.py │ │ ├── TrackUnprocessed.py │ │ └── __init__.py │ │ └── functions │ │ ├── DataAnalysis.py │ │ ├── InputProcessing.py │ │ ├── InterfaceChimeraX.py │ │ ├── TiffBoxDrawing.py │ │ ├── TiffProcessing.py │ │ └── __init__.py ├── buildAndUpload.sh ├── dist │ ├── pylattice-0.1.3-py3-none-any.whl │ └── pylattice-0.1.3.tar.gz ├── pylattice.egg-info │ ├── PKG-INFO │ ├── SOURCES.txt │ ├── dependency_links.txt │ └── top_level.txt ├── pylattice │ ├── __init__.py │ ├── classes │ │ ├── .ipynb_checkpoints │ │ │ └── track_test-checkpoint.ipynb │ │ ├── Track.py │ │ ├── TrackUnprocessed.py │ │ ├── Track_test.ipynb │ │ ├── __init__.py │ │ └── __pycache__ │ │ │ └── TrackUnprocessed.cpython-36.pyc │ └── functions │ │ ├── DataAnalysis.py │ │ ├── InputProcessing.py │ │ ├── InterfaceChimeraX.py │ │ ├── ParallelFunctions.py │ │ ├── TiffBoxDrawing.py │ │ ├── TiffProcessing.py │ │ ├── __init__.py │ │ └── __pycache__ │ │ ├── DataAnalysis.cpython-36.pyc │ │ └── TiffBoxDrawing.cpython-36.pyc └── setup.py └── visualization ├── bleachCorrection.py └── tests ├── __pycache__ └── test_bleachCorrection.cpython-37-pytest-5.4.3.pyc └── test_bleachCorrection.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pylattice/pyLattice/HEAD/.gitignore -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pylattice/pyLattice/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pylattice/pyLattice/HEAD/README.md -------------------------------------------------------------------------------- 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