├── .gitignore ├── README.md ├── README.pdf ├── auxiliaryMethods ├── .gitignore ├── KLEEtoCNN │ ├── changeToLocalTracing.m │ ├── convertKleeTracingToLocalStack.m │ ├── findBBoxKLEE.m │ ├── generateCNNcontrol.m │ ├── generateCNNstacks.m │ ├── getClosedContour.m │ ├── removeSomaStacks.m │ ├── selectFiles.m │ ├── selectFilesHD.m │ ├── viewCNNstacks.m │ └── xyzMaskIntraExtra.m ├── addTree.m ├── bfs.m ├── convertKnossosNmlToHoc.m ├── copyCubeSubset.m ├── distinguishable_colors.m ├── exportSurfaceToAmira.m ├── genpathGit.m ├── license.txt ├── loadClassData.m ├── makeIsosurfaceView.m ├── makeMovie.m ├── makeSegMovie.m ├── makeSegmentList.m ├── mergeTrees.m ├── parseNml.c ├── parseNml_noInVP.c ├── plotIsosurfaces.m ├── plotOriginalData.m ├── readKnossosCube.m ├── readKnossosRoi.m ├── readNml.m ├── removeBbox.m ├── removeEmptySkeletons.m ├── removeGlia.m ├── startCPU.m ├── voxelBasedMetrics │ ├── Rand │ │ ├── fullRand.m │ │ ├── randContingencyTable.cpp │ │ ├── randErr.m │ │ ├── randErrMaskGreaterZero.m │ │ ├── randRMex.c │ │ ├── randRMexMaskGreaterZero.c │ │ └── useRand.m │ └── Warp │ │ ├── useWarp.m │ │ ├── voxelErr.m │ │ ├── warpErr.m │ │ ├── warpMexFull.c │ │ └── warpMexFull.cpp ├── writeKnossosConf.m ├── writeKnossosCube.m ├── writeKnossosRoi.m ├── writeNml.m └── writeNmlOld.m ├── cortex ├── CNN │ ├── .gitignore │ ├── @cnn │ │ ├── bwdPass3D.m │ │ ├── cnn.m │ │ ├── flipdims.m │ │ ├── forWeights.m │ │ ├── fwdPass3D.m │ │ ├── fwdPass3DonKhierachy.m │ │ ├── gradientPass.m │ │ ├── learn.m │ │ ├── loadLastCNN.m │ │ ├── loadResults.m │ │ ├── onlyFwdPass3D.m │ │ ├── plotNetActivities.m │ │ ├── plotNetActivitiesFull.m │ │ └── sgd.m │ ├── @train │ │ ├── expLearn.m │ │ ├── linearLearn.m │ │ └── train.m │ ├── cnnStart.m │ ├── evolution │ │ ├── cnnParameterSelection.m │ │ ├── continueParameterSearch.m │ │ ├── getResults.m │ │ ├── parameterSearch.m │ │ ├── plotError.m │ │ ├── plotErrorBinned.m │ │ ├── plotErrorResorted.m │ │ ├── plotResults.m │ │ ├── removeSomaStacks.m │ │ └── selectBestPerformers.m │ └── normalizeStack.m ├── metrics07x2 │ ├── convertTestSetFromKLEETracingToLabelmatrix.m │ ├── initalizationSchemeStatistics.m │ ├── metricsISBI.bsh │ ├── metricsISBIautomatedTest.bsh │ ├── metricsISBIautomatedTraining.bsh │ ├── testSetMetricsFor07x2.m │ ├── tifWriteForISBI.m │ └── watershedSegMarkersHmin2D.m ├── segmentation │ ├── correctSkeletonsToBBox_v2.m │ ├── equalizeSkeletons.m │ ├── evalParameterSegmentation.m │ ├── evaluateSeg.m │ ├── getParamCombinations.m │ ├── getPathLength.m │ ├── mainSeg.m │ ├── morphScanAndEval.m │ ├── parsave.m │ ├── seg20141017.m │ ├── skeletonPreparations.m │ ├── skeletonStatistics.m │ ├── switchToLocalCoords_v2.m │ ├── visualization │ │ ├── makeErrorMoviesP.m │ │ ├── makeSkeletonMovies.m │ │ ├── visSeg.m │ │ ├── visualizeMeSp.m │ │ ├── visualizeObjHistP.m │ │ ├── visualizeObjectChainsP_leftout.m │ │ ├── visualizeObjectChainsP_merger.m │ │ ├── visualizeObjectChainsP_show.m │ │ ├── visualizeOverview.m │ │ ├── visualizeOverviewComparison.m │ │ ├── visualizeOverviewNew.m │ │ ├── visualizeOverviewNodeSizeControl.m │ │ ├── visualizeOverviewWithThreeLinesAndZeroHits.m │ │ └── visualizeSingle.m │ ├── watershedSeg_v1_cortex.m │ └── watershedSeg_v2_cortex.m ├── setParameterSettings.m ├── setParameterSettingsBig.m ├── startup.m └── wholeDataset │ ├── bigFwdPass.m │ ├── miniSegmentation.m │ ├── minicubeFwdPass.m │ ├── onlyFwdPass3DonKnossosFolder.m │ └── wholeDatasetFwdPass.m ├── initalSettings.m ├── installer.fig ├── installer.m ├── license.txt ├── retina ├── CNN │ ├── @cnn │ │ ├── bwdPass3D.m │ │ ├── cnn.m │ │ ├── flipdims.m │ │ ├── forAll.m │ │ ├── fwdPass3D.m │ │ ├── fwdPass3Dfaster.m │ │ ├── gradientPass.m │ │ ├── learn.m │ │ ├── normalizeStack.m │ │ ├── probMask.m │ │ ├── trainGradient.m │ │ ├── xyMask.m │ │ ├── xyzMask.m │ │ └── xyzMaskIso.m │ ├── @train │ │ ├── train.m │ │ └── updateCasts.m │ ├── bigFwdPass.m │ ├── libJobHandling │ │ ├── getKleeStackList.m │ │ ├── killAllJobs.m │ │ ├── killJob.m │ │ ├── saveJobParamToXls.m │ │ └── submitJob.m │ ├── loadCNNResults.m │ ├── loadSingleCNN.m │ ├── main_legacy.m │ ├── minicubeFwdPass.m │ ├── normalizeStack.m │ └── visualization │ │ ├── plotError.m │ │ ├── plotErrorBinned.m │ │ ├── plotErrorResorted.m │ │ └── plotNetActivities.m ├── segmentation │ ├── correctSkeletonsToBBox.m │ ├── evalParameterSegmentation.m │ ├── evaluateSeg.m │ ├── getPathLength.m │ ├── mainSeg_legacy.m │ ├── morphR.m │ ├── parsave.m │ ├── scanParameterSegmentation.m │ ├── switchToLocalCoords.m │ ├── visualization │ │ ├── autoKLEE_colormap.mat │ │ ├── distinguishable_colors.m │ │ ├── makeErrorMovies.m │ │ ├── makeErrorMoviesP.m │ │ ├── makeErrorStacksP.m │ │ ├── makeOriginalDataMovie.m │ │ ├── makeSkeletonMovies.m │ │ ├── paper_plotRibbonsInGlobalBB.m │ │ ├── visSeg_legacy.m │ │ ├── visualizeMeSp.m │ │ ├── visualizeObjHist.m │ │ ├── visualizeObjHistP.m │ │ ├── visualizeObjectChains.m │ │ ├── visualizeObjectChainsP.m │ │ ├── visualizeObjectChainsP_leftout.m │ │ ├── visualizeObjectChainsP_merger.m │ │ ├── visualizeObjectChainsP_mergerNew.m │ │ ├── visualizeObjectChainsP_show.m │ │ ├── visualizeOverview.m │ │ ├── visualizeOverviewSamplingSeries.m │ │ ├── visualizeOverviewTestComparisonRetinaVsCortex.m │ │ ├── visualizeOverview_2.m │ │ ├── visualizeOverview_4.m │ │ └── visualizeSingle.m │ ├── watershedBasedSeg │ │ ├── binAff.m │ │ ├── sk_mbwshed_3d_2.m │ │ ├── watershedSeg_v1_paper.m │ │ ├── watershedSeg_v2_paper.m │ │ ├── watershed_3D.m │ │ ├── watershed_3D_PP.m │ │ ├── watershed_threeTimes3D.c │ │ └── watershed_threeTimes3D.cpp │ └── wholeDataset │ │ ├── ekSegmentationToJm.m │ │ └── segment_ek_0563ForPaper.m ├── startup.m └── wholeDatasetFwdPass.m └── volumeReconstruction ├── accumulateOverCubeBorders.m ├── contactDetectionCortex.m ├── contactDetectionCortexStart.m ├── contactDetectionRetina.m ├── contactDetectionRetinaStart.m ├── galleryCortex.m ├── galleryCortexStart.m ├── galleryRetina.m ├── 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