├── .Rhistory ├── .gitattributes ├── .gitignore ├── AK Test Scripts ├── AutoClusterTest.m ├── Batch_autoclustering_sweepK2_2xCV.m ├── Batch_k20_CV12_AK.m ├── ClusterPlay.m ├── ClusteringDiagram.m ├── ColorBox.m ├── DBSCAN.m ├── DBSCAN_AKmod.m ├── FullFishAnalyze.m ├── LoadFullFish_FULL.m ├── PairwiseCorrelations.m ├── PairwiseDistancesSupplement.m ├── PlotClusterinResult.m ├── TestAutoCluster.m ├── getFullFishData.m ├── main.m └── stim_coefs.m ├── GUI functions ├── AllCentroidRegression.m ├── AllCentroidRegression_SizeThres_direct.m ├── AllCentroidRegression_direct.m ├── AllRegsRegression.m ├── ArtifactAnalysis.m ├── AutoClustering.m ├── CorrPlot.m ├── CorrPlotWeighted.m ├── DisplayMaskNames.m ├── DrawCellsOnAnat.m ├── DrawCellsOnAnatProj.m ├── DrawMasksInRGB.m ├── DrawTiledPics.m ├── DrawTiledPics_clus.m ├── DrawTimeSeries.m ├── DrawTimeSeries_MultiFishCentroid.m ├── FindCellsFromCentroids.m ├── FindCentroid.m ├── FindCentroid_Direct.m ├── GetColormap.m ├── GetMotorRegressor.m ├── GetMotorRegressorFromFictive.m ├── GetRegressor.m ├── GetStimBar.m ├── GetStimRegressor.m ├── GetStimStateBinary.m ├── GetTimeIndexedData.m ├── GetTrialAvrLongTrace.m ├── GrowClustersFromSeedsItr.m ├── HierClus_Direct.m ├── InitializeAppData.m ├── Kmeans_Direct.m ├── LoadCluster_Direct.m ├── LoadCurrentFishForAnatPlot.m ├── LoadFullFish.m ├── MakeCircularMask.m ├── MakeFoxels.m ├── MakeFunctionalMask.m ├── MakeNumberedMenu.m ├── MakeSquareMask.m ├── RankByFFT_Direct.m ├── RankByMotorReg_Direct.m ├── RankBySparseness.m ├── RankByStimLock.m ├── SaveCluster.m ├── SaveCluster_Direct.m ├── SaveVARtoMat.m ├── ScreenCellsWithMasks.m ├── SelectClusterRange.m ├── SortGroupIXbyScore.m ├── SqueezeGroupIX.m ├── StimulusKeyPreprocessing - Copy.m ├── StimulusKeyPreprocessing.m ├── UpdateClustersGUI.m ├── UpdateClustersGUI_Direct.m ├── UpdateTimeIndex.m ├── WriteZstack.m ├── imNormalize99.m ├── modified callbacks │ ├── GetTimeIndexedData.m │ ├── Merge_direct.m │ └── UpdateTimeIndex.m └── push_cIX_gIX.m ├── GUI hack scripts ├── BubblePlot.m └── manualRegressor_regression.m ├── GUI preload processing ├── BasicDrawCellsOnAnatProj.m ├── BasicPlotMaps.m ├── ForZBrain_plotCellXYZ_ref.m ├── Formatting_step1_cleanup_forfish2016.m ├── Formatting_step2_anatOutliers.m ├── Formatting_step3_align.m ├── GetFishFreq.m ├── GetFishRange.m ├── GetFishStimset.m ├── IncludeEyeMotorseedInGUIdata_onetime.m ├── IncludeMotorseedInGUIdata_onetime.m ├── InitializationforGUI_step1.m ├── InitializationforGUI_step2_cellselection.m ├── InitializationforGUI_step3_cellindexing.m ├── ManualInspect.m ├── PCApreprocessing.m ├── PatchFixDatasets.m ├── RunSequence.m ├── ZBrain_importNormCellCord.m ├── old │ ├── Formatting_step1_cleanup.m │ ├── GUIpreload_step1_cleanup.asv │ ├── GUIpreload_step1_cleanup.m │ ├── GUIpreload_step1_cleanup_copy.m │ ├── GUIpreload_step1_cleanup_intermediate.m │ ├── GUIpreload_step25_DiscardFromDirectLoad.m │ ├── GUIpreload_step2_anatOutliers.m │ ├── GUIpreload_step2_detrend.m │ ├── GUIpreload_step3_align.m │ ├── GUIpreload_step3extra_PoolClustersFromAllFish.m │ ├── GUIpreload_step4_discardCells.asv │ ├── GUIpreload_step4_discardCells.m │ └── GUIpreload_step5_initializeSavedCells.m ├── read_LSstack_fast_float.m └── read_LSstack_fast_float_mex64.mexw64 ├── GUI_FishExplorer.m ├── LoadGUI.m ├── README.md ├── README_LICENSE.rtf ├── VAR manipulation ├── CompileVARnames.m ├── CopyCluster.m ├── DeleteCluster.m ├── GetClusterName.m ├── MakeNewClusGroup.m ├── MoveCluster.m ├── RenameClusGroup.m ├── RenameCluster.m ├── SaveVARwithBackup.m └── VAR_Script_template.m ├── arrows.jpg ├── arrows_LR.jpg ├── arrows_wide.jpg ├── demo ├── FuncGUI_with_ZBrain_demo.pdf ├── demo1.gif ├── demo_load_GUI.m ├── demo_script.m └── fish8_Autoclus_randomcolors.png ├── dir setup ├── GetCurrentDataDir.m ├── GetMasterFileDir.m ├── GetOutputDataDir.m └── preprocessing │ ├── GetFishDirectories.m │ └── GetNestedDataDir.m ├── figure scripts ├── (revision) │ ├── hist_stimSpecificBehavior.m │ ├── hist_stimSpecificBehavior_ttest.m │ └── mapComparison_helper │ │ └── getStimSetParams.m ├── AddMasktoAnat.m ├── Batch_negative_motor_regression_test.m ├── Clustering │ ├── Batch cluster processing │ │ ├── Batch_crossval_by_stim_consec_halves.m │ │ ├── Batch_crossval_by_stim_randframes.m │ │ ├── Batch_crossval_by_stim_randframes_matchlength.m │ │ ├── Batch_deArtifact.m │ │ ├── Batch_kmeans20.m │ │ ├── Batch_makeAutoClus.m │ │ └── Batch_template_clustersprocessing.m │ ├── Batch_countABNsize_reg08.m │ ├── Batch_multifish_anatplot_from_VAR.m │ ├── Cluster_4Ddecomp_histogram.m │ ├── ConservedClusterScreen │ │ ├── ConservedCluster_variability.m │ │ ├── Master_ConservedClusterScreen.m │ │ ├── PairwiseClusterScreen.m │ │ └── ScreenGraphNodes.m │ ├── ICA │ │ └── spatial_ICA_wholefish.m │ ├── PCA │ │ └── Cluster_vs_PCA.m │ ├── exampleclusters_scatteredanat_Fish8.tif │ ├── fig3_conservedcluscount.m │ ├── fig4_sweepMasterThres_percentcell.m │ ├── fig4_withinfish_anatspread_D12screen.m │ ├── fig4c_4d_Multifish_clustersize_and_withincluscorr.m │ ├── fig4c_4d_clustersize_and_withincluscorr.m │ ├── fig4e_CV_matrix_plot.m │ ├── fig4f_multiF_hist_cluster_anat_spread.m │ ├── fig4h_ClusterSpread_anat_allfish.m │ ├── fig4m_CVtrianglematrix_Batch_computeCVfromVAR.m │ ├── figS4_CVscreenClusters.m │ ├── sweep cluster thresholds │ │ ├── Batch_autoclustering_sweepMasterThresh_CVhalves_AK.m │ │ ├── Batch_autoclustering_sweepMergeCap_CVhalves_AK.m │ │ ├── Batch_autoclustering_sweepnumK2_CVhalves.m │ │ ├── Batch_autoclustering_sweepnumK2_CVhalves_AK.m │ │ ├── Batch_autoclustering_sweepthres_CVstim.m │ │ └── old │ │ │ ├── SweepClusNumAgainstFxNum.m │ │ │ ├── SweepThresMerge.m │ │ │ └── Sweepfoxels.m │ ├── tSNE │ │ ├── fig4f_tSNE_Unfinished.m │ │ └── test_Plot_tSNE.m │ └── tentative_4D_cumsum_clusters.fig ├── MultiSensoryConvergence │ ├── Batch_PTintOMR_periodic_histograms_barplot.m │ ├── Batch_PTintOMR_periodic_scatterplot_anatmap.m │ ├── Batch_PTintOMR_periodic_subint_scatterplot_anatmap.m │ ├── Batch_PTvsOMR_intunion_stimmaps_4Dscatterplot.m │ ├── Batch_PTvsOMR_regbased_intunion_stimmaps.m │ ├── Batch_multistim_ttest.m │ ├── BestRegressor_allcells_allStimMotorRegs.m │ ├── eye_analysis │ │ ├── PoolEyeTail.m │ │ └── multimotor_eye.m │ ├── figurescriptflow.m │ ├── mapComparison_intersection_between_stim.m │ ├── obsl │ │ ├── fig5_4D_SM_preM_fromBetas.m │ │ └── sandbox_downstreamoffig6a.m │ ├── step1_savemats │ │ ├── Batch_PTintOMR_periodic_save_intersection.m │ │ └── Batch_PTvsOMR_regbased_save_intersection.m │ ├── step2_int_cong_plotstimmaps.m │ └── suppl │ │ ├── Batch_PTintOMR_periodic_marginalthreshold_control_sandbox.m │ │ ├── Batch_PTintOMR_periodic_thresholdsweep_sandbox.m │ │ └── plot_excluded_cells_eg_nose.m ├── Overview │ ├── fig1b_AverageActivityProjections.m │ ├── fig1g_count_by_anat_mask.m │ ├── figS1_mastersweeps_oldversion.m │ └── multifish_PCA.m ├── Regression │ ├── arc code │ │ ├── fig2D_Batch_correlation_2regs.m │ │ └── fig2D_Batch_correlation_2regs_fromVAR.m │ ├── fig2A_correlation_1reg_with_hist.m │ ├── fig2D_Batch_correlation_1reg - Copy.m │ ├── fig2D_Batch_correlation_1reg.m │ ├── fig2D_Batch_correlation_2regs_VARoption.m │ ├── fig2D_Batch_correlation_2regs_VARoption_exportedit.m │ ├── fig2EF_HistogramOfRegs_ReprSim.m │ └── fig2GH_GLM.m ├── SensoryMotor │ ├── arc code │ │ ├── fig3_motormap_trialRes_lrRes_tiffstack.m │ │ ├── fig3e_variance.m │ │ ├── fig4d_bubbleplot_oldversion.m │ │ ├── motormap, tRes versions, comparisons, w Clusters or Autoclus to follow │ │ │ ├── fig3D_normal_vs_tRes__notseed.m │ │ │ ├── fig3_motormap_trialRes.m │ │ │ ├── fig3_motormap_trialRes_030317.m │ │ │ ├── fig3_motormap_trialRes_lrRes.m │ │ │ └── fig3_motormap_trialRes_lrRes_notseed.m │ │ ├── motormap_screen with hindbrain mask │ │ │ └── fig3_motormap.m │ │ ├── multimotor_ori_bubbleplot_etc │ │ │ ├── fig3C_multimotor_bubbleplot2.m │ │ │ ├── fig3C_multimotor_script_022817.m │ │ │ ├── fig3C_multimotor_script_0512_tRes.m │ │ │ ├── fig3C_multimotor_script_5visuals.m │ │ │ └── latest version! │ │ │ │ └── fig3_multimotor_071117.m │ │ ├── orthogonalization │ │ │ ├── fig3C_multimotor.m │ │ │ └── fig4a_lowestpanel_exampletraces.m │ │ └── preMotor_SMT_etc │ │ │ └── fig3_fig6_4Dspace_singlehalf.m │ ├── behavior_tRes_analysis_motorseed_or_fictive │ │ └── fig3_varRatios_for_motor.m │ ├── fig3_2x2motormap_from_scatterplot_setdiff_intersect.m │ ├── fig3_2x2motormap_from_scatterplot_setdiff_intersect_exportedit.m │ ├── fig3_LFwR_3waymap_script.m │ ├── fig3_motormap_setdiff_script.m │ ├── fig3a_illustration.m │ ├── fig3b_stimlock_ranking.m │ ├── helper functions │ │ ├── MotorSourceCorrelation.m │ │ ├── MultiMotorVisuals.m │ │ └── thresY.m │ └── step1_savemats │ │ └── fig3_fig6_4Dspace_savebetas.m ├── arc (summer 2016) │ ├── fig1b_AverageActivityProjections.m │ ├── fig2d_clustersize_plus_withincluscorr.m │ ├── fig2f_tSNE.m │ ├── fig2h_ClusterDistance.m │ ├── fig2i_CV_matrix_plot.m │ ├── fig2j_count_by_anat_mask.m │ ├── fig3_conservedcluscount.m │ ├── fig4a_lowestpanel.m │ ├── fig4d_bubbleplot.m │ ├── fig5a_CV_forstims.m │ ├── fig6f_asymmetry.m │ └── figS1_mastersweeps.m ├── obsl │ └── Batch_k20_CV12.m ├── temp_HBO_4stripes.m ├── temp_manuallyCropRegressors.m ├── template_combineFolders.m └── test_script_regression_thres.m ├── fishoutline.png ├── fishpic.jpg ├── frontload scripts └── makeFishOutline.m ├── helper functions ├── DiagCorr.m ├── SaveFigureHelper.m ├── TEMP_mergingfigures.m ├── combineFiguresLR.m ├── combineFiguresTB.m ├── compareFoldersLR.m ├── compareFoldersTB.m ├── getImageFilesFromFolder.m ├── setDir.m └── subplot_tight.m ├── log.txt ├── misc scripts ├── manual check for all fish │ └── quickManualCheckAllFish.m ├── orthogonalized regression │ └── temp_regstff.m ├── output coords for func stacks │ └── saveCellCoords.m ├── screen clusters with ZBrain masks │ └── ScreenAllfMasksWithzMasks.m └── visualizations │ ├── Plot_Reg_etc.m │ └── video │ └── tiff2dff.m ├── old code ├── Batch_autoclustering.m ├── Batch_k20_CV12_AK.m ├── BootstrapTrial.m ├── CheckClustersStats.m ├── DimReduction_practice.m ├── DirectLoadScript_fromData.m ├── DirectSweepGrowROI.m ├── DustAnalysis.m ├── Flip_fromCONST.m ├── GUI_FishExplorer - Copy.m ├── LoadFishDataWithoutTS.m ├── Misha's p-test code_2feb15 │ ├── Misha's p-test code_2feb15.zip │ ├── load_data_00.m │ ├── process_p_values_00.m │ └── visualize_results_00.m ├── README.html ├── README.md ├── Run_autoclus_ButtonsScript_obsolete.m ├── SaveAllCentroids.m ├── TwoFoldCV.m ├── Yu Hu's code │ ├── pca_pruning_linkage │ │ ├── PCA_MP_fit.m │ │ ├── cgkMp_rx_qx_prune.m │ │ ├── cgk_isolated_prune_dist.m │ │ ├── cgk_norm_prune.m │ │ ├── cgk_tf_select.m │ │ ├── estimate_MP2.m │ │ ├── normM.m │ │ ├── push_cgk.m │ │ ├── push_cgk_k10.m │ │ └── step_prune_script.m │ ├── plot_ROI_3D │ │ └── plot_ROI_3D │ │ │ ├── caller_plot_cluster_3D.m │ │ │ ├── data │ │ │ ├── boundary_k_s0.7.mat │ │ │ └── xyz_ls.mat │ │ │ ├── gen_boundary.m │ │ │ ├── plot_3D_shape.m │ │ │ └── plot_ROI_3D.m │ └── set_matching_figure.m ├── cell_location_formatting.m ├── first version │ ├── AccessLocalFunctions.m │ ├── BasicPlotMaps.m │ ├── Conv_test.m │ ├── DA_2_Solution.m │ ├── DrawClusters.m │ ├── DrawClustersOnMap_LSh.m │ ├── FFT_test.m │ ├── GUI_FishExplorer.m │ ├── GetMotorRegressor.m │ ├── GetPhotoTrans.m │ ├── GetStimBar.m │ ├── GetStimRegressor.m │ ├── Load_LSh_step1_cleanup.m │ ├── Load_LSh_step2_detrend.m │ ├── Load_LSh_step3_align.m │ ├── Load_LSh_step4_loadGUI.m │ ├── Modeling001.m │ ├── PlotBy16StimsFromGUI.m │ ├── Plotting.m │ ├── Plotting_withinM.m │ ├── PoolClustersFromAllFish.m │ ├── SortMbystim.m │ ├── imNormalize99.m │ ├── push_cIX_gIX.m │ └── read_LSstack_fast_float.m ├── manual_DirecetCorrections.m ├── obsl │ ├── Batch_poolBasicInfoToMat.m │ ├── DrawMasksInRGB_winnertakeall_notused.m │ ├── LoadFileFromParts.m │ ├── PartitionForFastSaveLoad.m │ ├── RedBlueFrameTurnCorrection_onetimeuse.m │ └── SaveFileInPartsAppendv6.m ├── older versions │ ├── GRfS_Core1_ds.m │ ├── GrowClustersFromSeedsItr_mindist.m │ ├── GrowClustersFromSeedsItr_mindist_dislike.m │ ├── GrowClustersFromSeedsItr_old0511.m │ └── GrowClustersFromSeeds_2P.m ├── poolCellXYZ_forZBrainRegistration.m ├── temp_correction.m ├── test_GLM_script_pickregressors.m ├── test_LDA_example.m ├── test_Multi_regression_obsl.m ├── test_Plot_tSNE.m ├── test_fft.m └── test_manual_correlation.m ├── ref functions ├── Gram-Schmidt Process │ ├── Gram_Schmidt_Process.m │ ├── basis_col.m │ ├── basis_row.m │ ├── is_orthogonal_matrix.m │ ├── is_orthogonal_set.m │ ├── is_orthonormal_set.m │ ├── is_symmetric_matrix.m │ ├── normalise.m │ └── ref.m ├── HotellingT2 │ ├── HotellingT2.m │ ├── MBoxtest.m │ ├── READMEhT2.txt │ ├── T2Hot1.m │ ├── T2Hot2d.m │ ├── T2Hot2ihe.m │ ├── T2Hot2ihe_Direct.m │ └── T2Hot2iho.m ├── bluewhitered.m ├── munkres.m ├── pca_ica │ ├── PCA.m │ ├── PlayAudio.m │ ├── audio │ │ ├── README │ │ ├── source1.wav │ │ ├── source2.wav │ │ ├── source3.wav │ │ ├── source4.wav │ │ ├── source5.wav │ │ ├── source6.wav │ │ ├── source7.wav │ │ ├── source8.wav │ │ ├── source9.wav │ │ ├── voice1.mat │ │ └── voice2.mat │ ├── centerRows.m │ ├── demo_PCA1.m │ ├── demo_PCA2.m │ ├── fastICA.m │ ├── kICA.m │ ├── loadAudio.m │ ├── mvg.m │ ├── normalizeAudio.m │ ├── randomMixingMatrix.m │ ├── screenshot.png │ ├── visualizeAudio.m │ └── whitenRows.m └── smooth.m ├── script functions ├── Add2DcolorbarToAnat.m ├── AddColorbarToAnat.m ├── AverageAnatPlot.m ├── CheckIfLoadFish.m ├── ChooseTopPercentOfFish.m ├── ClusterDistanceD12.m ├── ClusterDistanceTestD12.m ├── ComparefMasks.m ├── ConvertCorrToBestRegRows.m ├── CropFullAnat.m ├── DivideCellsbyHemisphere.m ├── DrawCellsOnAnatProj_MultipleFish.m ├── DrawCustomColorbar.m ├── DrawMasksIn1D.m ├── DrawRainbowHistogram.m ├── FindClustermeans.m ├── FindMergeThresFromPDist.m ├── GetClusterIDs.m ├── GetColorIndexFromScore.m ├── GetNormCellCord.m ├── GetStimRange.m ├── GetStimRegressorByID.m ├── GetTimeIndex_Direct.m ├── GetTimeIndexedData_Default_Direct.m ├── GrowClustersFromSeedsItr2.m ├── HungarianCV.m ├── ImageToRGB.m ├── KmeansSubdivide.m ├── LoadSingleFishDefault.m ├── Make1DColormap.m ├── Make4color2Dcolormap.m ├── MakeDiagonal2Dcolormap.m ├── MakeDiagonal3Dcolormap.m ├── MakeTwoTailedColormap.m ├── MapXYto2Dcolormap.m ├── MapXYto3Dcolormap.m ├── MapXto1Dcolormap.m ├── ResetDisplayParams.m ├── SaveAllCentroids.m ├── SaveImToTiffStack.m ├── SetGroupIXorder.m ├── ShiftBaselinePosSignal.m ├── UpdateClustersViewGUI.m ├── UpdateIndices_Manual.m ├── kmeansPlot.m ├── kmeansPlot_old.m └── older version (not obsl) │ └── GetDefaultClustersFromLoad.m └── unused analyses ├── (figS3) motorseed comparison ├── motorseed_vs_not_comparison_hist.m └── motorseed_vs_not_comparison_hist.png ├── Connectivity └── test_script_connectivity.m ├── GLM ├── GLM_CV_allfish_script.m ├── GLM_CV_cluster_vs_cell_comprison_script.m ├── GLM_allcells_CV.m ├── 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