├── BILCO ├── BILCO.m ├── BILCOMex.cpp ├── BILCOMex.mexa64 ├── BILCOMex.mexmaca64 ├── BILCOMex.mexmaci64 ├── BILCOMex.mexw64 ├── DTW_Edge_input.cpp ├── DTW_Edge_input.mexa64 ├── DTW_Edge_input.mexmaca64 ├── DTW_Edge_input.mexmaci64 ├── DTW_Edge_input.mexw64 ├── midPoint2path.m └── types_BILCO.h ├── CFU_Viewer_Standalone.m ├── CFU_cmd_batch.m ├── LICENSE ├── MATLAB toolbox requirements.txt ├── README.md ├── aqua_cmd_batch.m ├── aqua_gui.m ├── cfg ├── DefaultFolder.mat ├── F0_biasMatrix.mat ├── Order_mus_sigmas.mat ├── batch.csv ├── parameters.csv ├── parameters_for_batch.csv ├── random_Seed.mat ├── smoCorr.mat ├── userColors.csv ├── userFeatures.csv └── userFeatures2.csv ├── frequency.m ├── img ├── Fig_pipeline.png ├── features.png ├── gui_CFU.png ├── gui_event.png ├── logo1.png ├── pipeline.png └── poster_related │ ├── Draw.m │ ├── Draw_raw.m │ ├── Draw_raw_CFU_show.m │ ├── Draw_raw_ac.m │ ├── Draw_raw_seeds.m │ ├── Draw_raw_signal.m │ ├── Draw_raw_spatial_splitting.m │ ├── Draw_raw_standard_deviation_map.m │ ├── Draw_raw_temporal_splitting.m │ ├── Draw_raw_watersheds.m │ ├── Example_dat.mat │ ├── Picture1.png │ ├── Picture2.png │ └── mask.mat ├── multi_session_CFU_comparison.m ├── multi_session_FOV_registration.m ├── src ├── +act │ ├── acDetect.m │ └── bw2Reg.m ├── +burst │ ├── correctBoundaryStd.m │ └── prep1.m ├── +cfu │ ├── CFU_minMeasure.m │ ├── CFU_tmp_function.m │ ├── CFUdetectScript.m │ ├── addCFU.m │ ├── adjDS.m │ ├── allAllFav.m │ ├── calAllDependency.m │ ├── calAllDependencyScript.m │ ├── calDependency.m │ ├── calDependencySimple.m │ ├── changeBackGroundColor.m │ ├── click.m │ ├── closeMe.m │ ├── curveRefresh.m │ ├── delayMode.m │ ├── deleteCFU.m │ ├── favCFUSelect.m │ ├── findRootLabel.m │ ├── getCfuOpts.m │ ├── getRisingTime.m │ ├── groupCFU.m │ ├── groupCFUscript.m │ ├── hierarchicalClusteringMinMeasure.m │ ├── loadCFUData.m │ ├── myBinomialCDF.m │ ├── output.m │ ├── pickCFU.m │ ├── returnMajorGUI.m │ ├── saveWaves.m │ ├── select3D.m │ ├── selectGroup.m │ ├── showSelectCurves.m │ ├── sliceMov3D.m │ ├── sliceView.m │ ├── solveK1d.m │ ├── updateCamera.m │ ├── updtCFUTable.m │ ├── updtGrpTable.m │ ├── updtTable.m │ ├── view3D.m │ ├── winSzAdjust.m │ └── workSpace.m ├── +evt │ ├── 560_res.mat │ ├── addToRisingMap.m │ ├── delayMap2evt.m │ ├── evtRecon.asv │ ├── evtRecon.m │ ├── se2evt.m │ ├── se2evtTop.m │ ├── spgtw.m │ └── warpRef2Tst.m ├── +fea │ ├── evt2lmkProp.m │ ├── evt2lmkProp1.m │ ├── evt2lmkProp1Wrap.m │ ├── evt2lmkProp2.m │ ├── evt2lmkProp2Wrap.m │ ├── extendEventTimeRangeByCurve.m │ ├── getBasicFeatures.m │ ├── getCurveStat.m │ ├── getDistRegionBorderMIMO.m │ ├── getEvtNetworkFeatures.m │ ├── getFeatureTable00.m │ ├── getFeaturesPropTop.m │ ├── getFeaturesTop.m │ ├── getNetworkFeatures.m │ ├── getPropagationCentroidQuad.m │ ├── getPropagationCentroidQuad3D.m │ ├── outputCurves.m │ ├── outputRegions.m │ ├── outputRisingMap.m │ └── reconstructDatR.m ├── +glo │ └── removeDetected.m ├── +img │ ├── getEventBorder.m │ └── imputeMov.m ├── +io │ ├── loadVideo.m │ ├── readSingleFrameMaskTif.m │ ├── readTiffSeq.m │ ├── readTiffSeq_backup.m │ └── writeTiffSeq.m ├── +multiAlign │ ├── maximalRectangle.m │ └── warp.m ├── +plt │ ├── addLabels.m │ ├── regionMapWithData.m │ └── regionMapWithData_newColor.m ├── +pre │ ├── avgDatNoiseEst.m │ ├── baselineLinearEstimate.m │ ├── baselineRemoveAndNoiseEstimation.m │ ├── bleach_correct.m │ ├── bleach_correct2.m │ ├── fit_F0_var.m │ ├── noise_estimation_function.m │ ├── obtainBias.m │ └── truncated_kept_var.m ├── +reg │ ├── calCC.m │ └── regCrossCorrelation.m ├── +se │ ├── GrowOneRound.m │ ├── Individual_Order_Analysis_spa_temp.m │ ├── avgDist.m │ ├── calOrderScore.m │ ├── calTScore.m │ ├── checkHasSeed.m │ ├── correctVar.m │ ├── createMergingInfo.m │ ├── curveSignificance.m │ ├── curveSignificance2.m │ ├── curveSignificance3.m │ ├── curveTestForMajority.m │ ├── dirGenerate.m │ ├── eventCurveSignificance.m │ ├── eventCurveSignificance3.m │ ├── findNeighbor.m │ ├── getGroupStd.m │ ├── getIhwThisPart.m │ ├── getInitIhwInSplit.m │ ├── getIoU.m │ ├── getLocalDifSquare.m │ ├── getLocalDifSquare2.m │ ├── getMajoritySpa.m │ ├── getMajorityTem.m │ ├── getMajority_Ac.m │ ├── getRefineSpaMajority_Ac.m │ ├── getSeedScore.m │ ├── getSeedScore2.m │ ├── getSeedScore_DS.m │ ├── getSeedScore_DS2.m │ ├── getSeedScore_DS3.m │ ├── getSeedScore_DS4.m │ ├── getSeedScore_DS5.m │ ├── growSpa.m │ ├── growWatershedResultSpatial.m │ ├── ksegments_orderstatistics_fin.m │ ├── majorCurveFilter.m │ ├── majorCurveFilter2.m │ ├── markerControlledSplitting_Ac.m │ ├── markerControlledSplitting_AfterSpaGrow.m │ ├── markerControlledSplitting_Principal.m │ ├── mergingRefineByInfo.m │ ├── mergingSEbyInfo.m │ ├── mergingSEbyInfo_UpdateSpa.m │ ├── myResize.m │ ├── neighbor_Individual_spa_temp.m │ ├── normalizeAndResize.m │ ├── ordStatApproxKsecWith0s.m │ ├── ordStatSmallSampleWith0s.m │ ├── pixResize_half_spa_temp.m │ ├── refineEvtsByInfo2.m │ ├── refineEvtsCorrectByInfo.m │ ├── refineShape.m │ ├── seDetection.m │ ├── seed2Majoirty.m │ ├── seedDetect.m │ ├── seedDetect2.m │ ├── seedDetect2_DS.m │ ├── seedDetect2_DS_accelerate.m │ ├── segmentation_MSF2.m │ ├── spaGrow.m │ ├── splitEvt_Ac.m │ └── updateMergingInfo.m ├── +ui │ ├── +com │ │ ├── ableGlo.m │ │ ├── ableSpa.m │ │ ├── ableTemp.m │ │ ├── addCon.m │ │ ├── addConLayer.m │ │ ├── addCon_dat.m │ │ ├── addCon_proj.m │ │ ├── addCon_tools.m │ │ ├── addCon_wkfl.m │ │ ├── addDetectTab.m │ │ ├── advFilters.m │ │ ├── cfuCon.m │ │ └── uiUpdateFor3D.m │ ├── +detect │ │ ├── CFURunGui.m │ │ ├── actRun.m │ │ ├── evtRun.m │ │ ├── feaRun.m │ │ ├── filterInit.m │ │ ├── filterUpdt.m │ │ ├── flow.m │ │ ├── flow2.m │ │ ├── getFeatureTable.m │ │ ├── getPolyInfo.m │ │ ├── gloRun.m │ │ ├── loadOpt.m │ │ ├── phaseRun.m │ │ ├── postRun.m │ │ ├── preProcessRun.m │ │ ├── saveOpt.m │ │ ├── updtFeature.m │ │ └── updtFeatureRegionLandmarkNetworkShow.m │ ├── +evt │ │ ├── addOne.m │ │ ├── addOne2.m │ │ ├── curveRefresh.m │ │ ├── evtMngrDeleteSel.m │ │ ├── evtMngrRefresh.m │ │ ├── evtMngrSelAll.m │ │ ├── evtMngrSelectOne.m │ │ ├── evtMngrShowCurve.m │ │ ├── saveCurveFig.m │ │ ├── saveWaves.m │ │ └── showDetails.m │ ├── +mov │ │ ├── addPatchLineText.m │ │ ├── changeBackGroundColor.m │ │ ├── clearBuilderMask.m │ │ ├── dragReg.m │ │ ├── drawReg.m │ │ ├── drawReg2.m │ │ ├── featurePlot.m │ │ ├── findKeyPress.m │ │ ├── jumpTo.m │ │ ├── movAddAll.m │ │ ├── movClick.m │ │ ├── movClick2.m │ │ ├── movGauss.m │ │ ├── movPan.m │ │ ├── movSideBySide.m │ │ ├── movViewSel.m │ │ ├── movZoom.m │ │ ├── mypostcallback.m │ │ ├── pauseMov.m │ │ ├── playMov.m │ │ ├── regionSL.m │ │ ├── select3D.m │ │ ├── showRisingMap.m │ │ ├── sliceMov3D.m │ │ ├── sliceView.m │ │ ├── stepOne.m │ │ ├── thrAdjust.m │ │ ├── updateCamera.m │ │ ├── updateSlice.m │ │ ├── updtCursorFunMov.m │ │ ├── updtCursorFunMov2.m │ │ └── updtMovInfo.m │ ├── +msk │ │ ├── addCon_datMsk.m │ │ ├── addCon_toolsMsk.m │ │ ├── addCon_wkflMsk.m │ │ ├── adjDS.m │ │ ├── adjMov.m │ │ ├── changeBackGroundColor.m │ │ ├── mskBuilderOpen.m │ │ ├── mskLstViewer.m │ │ ├── readMsk.m │ │ ├── readSingleFrameMsk.m │ │ ├── saveMsk.m │ │ ├── updtMskSld.m │ │ └── viewImgMsk.m │ ├── +over │ │ ├── addBd.m │ │ ├── adjDS.m │ │ ├── adjMov.m │ │ ├── adjTrans3D.m │ │ ├── channelOpt.m │ │ ├── chgOv.m │ │ ├── getColMap.m │ │ ├── getColorCode.m │ │ ├── getOv.m │ │ ├── getOvCurFrame.m │ │ ├── getOvCurFrame3D.m │ │ ├── getVal.m │ │ ├── reMapCol.m │ │ ├── updateOvFtMenu.m │ │ ├── updtColMap.m │ │ └── updtEvtOvShowLst.m │ ├── +proj │ │ ├── AveragePlusOverlay.m │ │ ├── back2welcome.m │ │ ├── closeMe.m │ │ ├── csv2struct.m │ │ ├── exportVar2Base.m │ │ ├── getInputFile.m │ │ ├── getInputFile1.m │ │ ├── getInputFile2.m │ │ ├── getOutputFolder.m │ │ ├── initStates.m │ │ ├── loadExp.m │ │ ├── newProj.m │ │ ├── prep.m │ │ ├── prepInitUI.m │ │ ├── prepInitUIStruct.m │ │ ├── saveExp.m │ │ ├── struct2csv.m │ │ ├── updtPreset.m │ │ └── welcome.m │ ├── movStep.m │ ├── updtCFUcurve.m │ └── 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