Index

_

__init__() (neuralib.atlas.brainrender.core.BrainRenderCLI method) (neuralib.atlas.brainrender.probe.ProbeRenderCLI method) (neuralib.atlas.brainrender.probe.ProbeShank method), [1] (neuralib.atlas.brainrender.roi.RoiRenderCLI method) (neuralib.atlas.ccf.dataframe.RoiClassifierDataFrame method), [1] (neuralib.atlas.ccf.dataframe.RoiNormalizedDataFrame method), [1] (neuralib.atlas.ccf.dataframe.RoiSubregionDataFrame method), [1] (neuralib.atlas.ccf.matrix.CCFTransMatrix method), [1] (neuralib.atlas.util.SourceCoordinates method) (neuralib.atlas.view.AbstractSliceView method), [1] (neuralib.atlas.view.SlicePlane method), [1] (neuralib.cellpose.core.CellposeSegmentation method), [1] (neuralib.dashboard.base.BokehServer method), [1] (neuralib.dashboard.base.View method) (neuralib.dashboard.base.ViewComponent method) (neuralib.dashboard.examples.view_all.AllView method), [1] (neuralib.dashboard.examples.view_animal.AnimalView method), [1] (neuralib.dashboard.examples.view_figure.AnimalFigureView method), [1] (neuralib.dashboard.tool.TimeoutUpdateValue method), [1] (neuralib.dashboard.util.ColorBarView method), [1] (neuralib.dashboard.util.MsgLog method), [1] (neuralib.dashboard.view_brain.AbstractBrainView method), [1] (neuralib.dashboard.view_brain.AtlasBrainView method), [1] (neuralib.dashboard.view_brain.BrainView method), [1] (neuralib.dashboard.view_brain.TiffBrainView method), [1] (neuralib.deeplabcut.core.DeepLabCutDataFrame method), [1] (neuralib.deeplabcut.core.DeepLabCutMeta method) (neuralib.deeplabcut.core.DeepLabCutModelConfig method) (neuralib.deeplabcut.core.JointDataFrame method), [1] (neuralib.facemap.core.FaceMapResult method), [1] (neuralib.facemap.core.KeyPointDataFrame method), [1] (neuralib.facemap.core.KeyPointsMeta method) (neuralib.facemap.core.PupilDict method) (neuralib.facemap.core.RoiDict method) (neuralib.facemap.core.SVDVariables method) (neuralib.imglib.array.ImageArrayWrapper method) (neuralib.imglib.labeller.SequenceLabeller method), [1] (neuralib.io.json.JsonEncodeHandler method) (neuralib.io.pyh5.H5pyData method), [1] (neuralib.locomotion.position.CircularPosition method) (neuralib.locomotion.spatial.PlaceFieldResult method) (neuralib.locomotion.spatial.SpatialInfoResult method) (neuralib.morpho.swc.SwcFile method), [1] (neuralib.morpho.swc.SwcNode method) (neuralib.persistence.cli_persistence.PersistenceOptions method) (neuralib.persistence.persistence.AutoIncFieldNotResolvedError method) (neuralib.persistence.persistence.GzipHandler method), [1] (neuralib.persistence.persistence.PersistenceHandler method) (neuralib.persistence.persistence.PickleHandler method), [1] (neuralib.persistence.validator.ETLConcatable method) (neuralib.plot.colormap.DiscreteColorMapper method), [1] (neuralib.plot.tools.AnchoredScaleBar method), [1] (neuralib.plot.tools.AxesExtendHelper method), [1] (neuralib.plot.venn.VennDiagram method), [1] (neuralib.plot.venn.VennHandler method) (neuralib.rastermap.core.RasterMapResult method), [1] (neuralib.rastermap.core.RasterOptions method) (neuralib.rastermap.core.UserCluster method) (neuralib.rastermap.plot.Covariant method) (neuralib.rastermap.plot.RasterMapPlot method), [1] (neuralib.registration.coordinates.CellularCoordinates method), [1] (neuralib.registration.coordinates.FieldOfView method), [1] (neuralib.scan.core.AbstractScanner method), [1] (neuralib.scan.czi.CziScanner method), [1] (neuralib.scan.lsm.TiffScanner method), [1] (neuralib.scanbox.core.SBXInfo method), [1] (neuralib.scanbox.core.SBXInfo.AgcInfo method) (neuralib.scanbox.core.SBXInfo.CalibrationInfo method) (neuralib.scanbox.core.SBXInfo.ConfigInfo method) (neuralib.scanbox.core.SBXInfo.KnobbyInfo method) (neuralib.scanbox.core.SBXInfo.KnobbyPosInfo method) (neuralib.scanbox.core.SBXInfo.ObjectiveInfo method) (neuralib.scanbox.view.ScanBoxView method), [1] (neuralib.scanbox.view.ScanBoxViewOptions method) (neuralib.spikes.cascade.CascadeModelConfig method) (neuralib.spikes.cascade.CascadeSpikePrediction method), [1] (neuralib.stardist.base.AbstractSegmentationOptions method) (neuralib.stardist.core.StarDistSegmentation method), [1] (neuralib.stardist.run_2d.StarDist2DOptions method) (neuralib.suite2p.core.Suite2pGUIOptions method) (neuralib.suite2p.core.Suite2PResult method), [1] (neuralib.suite2p.core.Suite2pRoiStat method) (neuralib.suite2p.signals.DFFSignal method) (neuralib.tools.gspread.GoogleSpreadSheet method), [1] (neuralib.tools.gspread.GoogleWorkSheet method), [1] (neuralib.util.dataframe.DataFrameWrapper method) (neuralib.util.profile.profile_test method), [1] (neuralib.widefield.align.NapariAlignmentOptions method) (neuralib.widefield.ccf.DorsalCCF method), [1] (neuralib.widefield.ccf.RegionLabel method) (neuralib.widefield.fft.SequenceFFT method), [1] (neuralib.widefield.fft_view.WideFieldFFTViewOption method) (neuralib.widefield.preproc.BaselineInfo method) (neuralib.widefield.preproc.DataInfo method) (neuralib.widefield.preproc.InputArguments method) (neuralib.widefield.preproc.MotionCorrInfo method) (neuralib.widefield.preproc.PreprocessMeta method) (neuralib.widefield.preproc.PreprocessOptions method), [1] (neuralib.widefield.preproc.ProcessedInfo method) (neuralib.widefield.svd.SequenceSingularVector method) (neuralib.widefield.transform.RegistrationApp method), [1] (neuralib.widefield.transform.RegistrationOptions method)

__new__() (neuralib.atlas.util.SourceCoordinates static method) (neuralib.atlas.view.AbstractSliceView static method) (neuralib.imglib.array.ImageArrayWrapper static method) (neuralib.locomotion.position.CircularPosition static method) (neuralib.locomotion.spatial.PlaceFieldResult static method) (neuralib.locomotion.spatial.SpatialInfoResult static method) (neuralib.morpho.swc.SwcNode static method) (neuralib.plot.venn.VennHandler static method) (neuralib.rastermap.plot.Covariant static method) (neuralib.suite2p.signals.DFFSignal static method) (neuralib.widefield.ccf.RegionLabel static method) (neuralib.widefield.svd.SequenceSingularVector static method)

A

a (neuralib.scanbox.core.SBXInfo.KnobbyPosInfo attribute) abort_bit (neuralib.scanbox.core.SBXInfo attribute) AbstractBrainView (class in neuralib.dashboard.view_brain) AbstractScanner (class in neuralib.scan.core) AbstractSegmentationOptions (class in neuralib.stardist.base) AbstractSliceView (class in neuralib.atlas.view) acronym (neuralib.widefield.ccf.RegionLabel attribute) act (neuralib.locomotion.spatial.PlaceFieldResult attribute) activity (neuralib.locomotion.spatial.SpatialInfoResult attribute) add_html_format() (in module neuralib.dashboard.util) add_intersection() (neuralib.plot.venn.VennDiagram method) add_total() (neuralib.plot.venn.VennDiagram method) affine_transform() (in module neuralib.imglib.transform) agc (neuralib.scanbox.core.SBXInfo.ConfigInfo attribute) agc_prctile (neuralib.scanbox.core.SBXInfo.AgcInfo attribute) al (neuralib.registration.coordinates.FieldOfView property) align_by_chan (neuralib.suite2p.core.Suite2pGUIOptions attribute) all_joints (neuralib.deeplabcut.core.DeepLabCutModelConfig attribute) all_joints_names (neuralib.deeplabcut.core.DeepLabCutModelConfig attribute) ALLEN_CCF_10um_BREGMA (in module neuralib.atlas.util) ALLEN_FAMILY_TYPE (in module neuralib.atlas.map) allen_id (neuralib.widefield.ccf.RegionLabel attribute) allen_rgb (neuralib.widefield.ccf.RegionLabel attribute) allen_to_brainrender_coord() (in module neuralib.atlas.util) allow_overlap (neuralib.suite2p.core.Suite2pGUIOptions attribute) AllView (class in neuralib.dashboard.examples.view_all) am (neuralib.registration.coordinates.FieldOfView property) anatomical_only (neuralib.suite2p.core.Suite2pGUIOptions attribute) AnchoredScaleBar (class in neuralib.plot.tools) AnimalFigureView (class in neuralib.dashboard.examples.view_figure) AnimalView (class in neuralib.dashboard.examples.view_animal) annotation (neuralib.atlas.brainrender.core.BrainRenderCLI attribute) ap (neuralib.atlas.util.SourceCoordinates property) (neuralib.registration.coordinates.CellularCoordinates attribute) ap_distance (neuralib.registration.coordinates.FieldOfView property) apply_transform() (neuralib.widefield.transform.RegistrationApp method) apply_transformation() (in module neuralib.imglib.transform) area (neuralib.facemap.core.PupilDict attribute) area_line (neuralib.scanbox.core.SBXInfo attribute)

area_smooth (neuralib.facemap.core.PupilDict attribute) array() (in module neuralib.io.pyh5) array2str() (in module neuralib.typing.func) ArrayLike (in module neuralib.typing.alias) ArrayLikeStr (in module neuralib.typing.alias) as_colormap() (neuralib.widefield.fft.SequenceFFT method) as_coords_array() (in module neuralib.atlas.util) as_dict() (in module neuralib.persistence.persistence) as_segment() (in module neuralib.util.segments) as_theoretical() (neuralib.atlas.brainrender.probe.ProbeShank method) asdict() (neuralib.rastermap.core.RasterMapResult method) (neuralib.scanbox.core.SBXInfo method) aspect (neuralib.suite2p.core.Suite2pGUIOptions attribute) aspect_ratio (neuralib.suite2p.core.Suite2pRoiStat attribute) assert_polars_equal_verbose() (in module neuralib.util.dataframe) ATLAS_CACHE_DIRECTORY (in module neuralib.io.core) ATLAS_NAME (in module neuralib.atlas.data) AtlasBrainView (class in neuralib.dashboard.view_brain) attr() (in module neuralib.io.pyh5) attributes_validate() (in module neuralib.persistence.validator) auto_generated_content() (in module neuralib.persistence.persistence) autoinc_field() (in module neuralib.persistence.persistence) AutoIncFieldNotResolvedError available_model_yaml (neuralib.spikes.cascade.CascadeSpikePrediction property) avgframe (neuralib.facemap.core.SVDVariables attribute) avgframe_reshape (neuralib.facemap.core.SVDVariables attribute) avgmotion (neuralib.facemap.core.SVDVariables attribute) avgmotion_reshape (neuralib.facemap.core.SVDVariables attribute) ax (neuralib.atlas.view.SlicePlane attribute) ax_merge() (in module neuralib.plot.figure) ax_set_default_style() (in module neuralib.plot.figure) ax_x (neuralib.plot.tools.AxesExtendHelper attribute) ax_y (neuralib.plot.tools.AxesExtendHelper attribute) axdir (neuralib.facemap.core.PupilDict attribute) AxesArray (in module neuralib.typing.alias) AxesExtendHelper (class in neuralib.plot.tools) axlen (neuralib.facemap.core.PupilDict attribute) axvline_histplot() (in module neuralib.plot.plot) ay (neuralib.atlas.view.SlicePlane attribute)

B

background (neuralib.atlas.brainrender.core.BrainRenderCLI attribute) badframes (neuralib.suite2p.core.Suite2pGUIOptions attribute) ballmotion (neuralib.scanbox.core.SBXInfo attribute) baseline (neuralib.locomotion.spatial.PlaceFieldResult attribute) (neuralib.suite2p.core.Suite2pGUIOptions attribute) baseline_fluctuation (neuralib.suite2p.signals.DFFSignal property) BaselineInfo (class in neuralib.widefield.preproc) batch_mode (neuralib.stardist.base.AbstractSegmentationOptions property) batch_size (neuralib.deeplabcut.core.DeepLabCutMeta attribute) (neuralib.deeplabcut.core.DeepLabCutModelConfig attribute) (neuralib.facemap.core.KeyPointsMeta attribute) (neuralib.spikes.cascade.CascadeModelConfig attribute) (neuralib.suite2p.core.Suite2pGUIOptions attribute) bbox (neuralib.facemap.core.KeyPointsMeta attribute) before_frac (neuralib.spikes.cascade.CascadeModelConfig attribute) bidi_corrected (neuralib.suite2p.core.Suite2pGUIOptions attribute) bidiphase (neuralib.suite2p.core.Suite2pGUIOptions attribute) bin_size (neuralib.locomotion.spatial.PlaceFieldResult attribute)

binarize() (neuralib.imglib.array.ImageArrayWrapper method) binsize (neuralib.rastermap.core.UserCluster attribute) blink (neuralib.facemap.core.SVDVariables attribute) block_size (neuralib.suite2p.core.Suite2pGUIOptions attribute) bodyparts (neuralib.facemap.core.KeyPointsMeta attribute) BokehServer (class in neuralib.dashboard.base) brain_image (neuralib.dashboard.view_brain.AbstractBrainView property) (neuralib.dashboard.view_brain.AtlasBrainView property) (neuralib.dashboard.view_brain.BrainView property) (neuralib.dashboard.view_brain.TiffBrainView property) brain_slice() (neuralib.dashboard.view_brain.AtlasBrainView method) BrainRenderCLI (class in neuralib.atlas.brainrender.core) BrainView (class in neuralib.dashboard.view_brain) bregma (neuralib.atlas.view.AbstractSliceView property) bruker (neuralib.suite2p.core.Suite2pGUIOptions attribute) build_annotation_leaf_map() (in module neuralib.atlas.data) build_goto_link() (neuralib.dashboard.examples.view_all.AllView method) bytesPerBuffer (neuralib.scanbox.core.SBXInfo attribute)

C

calc_signal_baseline() (in module neuralib.suite2p.signals) CALCIUM_TYPE (in module neuralib.suite2p.core) calculate_dff() (neuralib.widefield.preproc.PreprocessOptions method) calibration (neuralib.scanbox.core.SBXInfo attribute) callback() (neuralib.dashboard.tool.TimeoutUpdateValue method) camera_angle (neuralib.atlas.brainrender.core.BrainRenderCLI attribute) canny_filter() (neuralib.imglib.array.ImageArrayWrapper method) CASCADE_MODEL_CACHE_DIRECTORY (in module neuralib.io.core) CASCADE_MODEL_TYPE (in module neuralib.spikes.cascade) cascade_predict() (in module neuralib.spikes.cascade) CascadeModelConfig (class in neuralib.spikes.cascade) CascadeSpikePrediction (class in neuralib.spikes.cascade) causal_kernel (neuralib.spikes.cascade.CascadeModelConfig attribute) CCFTransMatrix (class in neuralib.atlas.ccf.matrix) cell_prob (neuralib.suite2p.core.Suite2PResult property) cell_prob_thres (neuralib.suite2p.core.Suite2PResult attribute) cellpose_point_roi_helper() (in module neuralib.cellpose.core) CellposeSegmentation (class in neuralib.cellpose.core) CellularCoordinates (class in neuralib.registration.coordinates) chan2_thres (neuralib.suite2p.core.Suite2pGUIOptions attribute) chan_choose (neuralib.cellpose.core.CellposeSegmentation property) chance_level (neuralib.plot.venn.VennHandler property) change_html_format() (in module neuralib.dashboard.util) channel (neuralib.scanbox.view.ScanBoxViewOptions attribute) channel_counts (neuralib.atlas.ccf.dataframe.RoiClassifierDataFrame property) channels (neuralib.atlas.ccf.dataframe.RoiClassifierDataFrame property) (neuralib.scanbox.core.SBXInfo attribute) check_mps_available() (in module neuralib.util.gpu) check_note_changes() (neuralib.imglib.labeller.SequenceLabeller method) check_nvidia_cuda_available() (in module neuralib.util.gpu) chunk_size (neuralib.widefield.preproc.InputArguments attribute) (neuralib.widefield.preproc.PreprocessOptions attribute) CircularPosition (class in neuralib.locomotion.position) classified_column (neuralib.atlas.ccf.dataframe.RoiNormalizedDataFrame property) classifier_file (neuralib.atlas.brainrender.roi.RoiRenderCLI attribute) classifier_path (neuralib.suite2p.core.Suite2pGUIOptions attribute) clean_all_cache_dataset() (in module neuralib.io.dataset) clear() (neuralib.tools.gspread.GoogleWorkSheet method) (neuralib.util.dataframe.DataFrameWrapper method) clear_all_points() (neuralib.widefield.transform.RegistrationApp method) clear_note() (neuralib.imglib.labeller.SequenceLabeller method) clone() (neuralib.util.dataframe.DataFrameWrapper method) close() (neuralib.scan.core.AbstractScanner method) (neuralib.scan.czi.CziScanner method) (neuralib.scan.lsm.TiffScanner method) cls_hasattr() (in module neuralib.util.utils)

color (neuralib.facemap.core.RoiDict attribute) (neuralib.rastermap.core.UserCluster attribute) (neuralib.widefield.align.NapariAlignmentOptions attribute) ColorBarView (class in neuralib.dashboard.util) columns (neuralib.util.dataframe.DataFrameWrapper property) com (neuralib.facemap.core.PupilDict attribute) com_smooth (neuralib.facemap.core.PupilDict attribute) combined (neuralib.suite2p.core.Suite2pGUIOptions attribute) compact (neuralib.suite2p.core.Suite2pRoiStat attribute) component (neuralib.widefield.fft.SequenceFFT property) compute_cache() (neuralib.persistence.cli_persistence.PersistenceOptions method) compute_motion_transforms() (neuralib.widefield.preproc.PreprocessOptions method) compute_singular_vector() (in module neuralib.widefield.svd) concat_etl() (neuralib.persistence.validator.ETLConcatable method) config (neuralib.scanbox.core.SBXInfo attribute) config_file (neuralib.spikes.cascade.CascadeSpikePrediction property) connected (neuralib.suite2p.core.Suite2pGUIOptions attribute) consistent_config (neuralib.scan.czi.CziScanner property) content (neuralib.dashboard.examples.view_all.AllView attribute) (neuralib.dashboard.examples.view_animal.AnimalView attribute) content_date (neuralib.dashboard.examples.view_figure.AnimalFigureView attribute) content_title (neuralib.dashboard.examples.view_figure.AnimalFigureView attribute) convert_to_boundary() (neuralib.widefield.transform.RegistrationApp method) coor_on() (neuralib.atlas.view.AbstractSliceView method) coord_abs (neuralib.scanbox.core.SBXInfo.ConfigInfo attribute) coord_rel (neuralib.scanbox.core.SBXInfo.ConfigInfo attribute) coordinate_space (neuralib.atlas.brainrender.core.BrainRenderCLI attribute) coordinates (neuralib.atlas.util.SourceCoordinates attribute) cords (neuralib.stardist.core.StarDistSegmentation property) corners (neuralib.registration.coordinates.FieldOfView attribute) corrXY (neuralib.suite2p.core.Suite2pGUIOptions attribute) corrXY1 (neuralib.suite2p.core.Suite2pGUIOptions attribute) Covariant (class in neuralib.rastermap.plot) create_date_validate() (in module neuralib.persistence.validator) create_fn() (in module neuralib.util.func) crop_pad (neuralib.deeplabcut.core.DeepLabCutModelConfig attribute) cropping (neuralib.deeplabcut.core.DeepLabCutMeta attribute) cropping_parameters (neuralib.deeplabcut.core.DeepLabCutMeta attribute) csv_header() (in module neuralib.io.csv_header) current_animal (neuralib.dashboard.examples.view_animal.AnimalView property) (neuralib.dashboard.examples.view_figure.AnimalFigureView property) current_figure (neuralib.dashboard.examples.view_figure.AnimalFigureView property) current_frame_index (neuralib.imglib.labeller.SequenceLabeller property) czi_file (neuralib.scan.czi.CziScanner property) czi_file() (in module neuralib.scan.czi) CziScanner (class in neuralib.scan.czi)

D

d (neuralib.locomotion.position.CircularPosition attribute) data_brain_slice (neuralib.dashboard.view_brain.AbstractBrainView attribute) data_info (neuralib.widefield.preproc.PreprocessMeta attribute) data_path (neuralib.suite2p.core.Suite2pGUIOptions attribute) DATA_TYPE (in module neuralib.rastermap.run) DataFrame (in module neuralib.typing.alias) dataframe() (neuralib.atlas.ccf.dataframe.RoiClassifierDataFrame method) (neuralib.atlas.ccf.dataframe.RoiNormalizedDataFrame method) (neuralib.atlas.ccf.dataframe.RoiSubregionDataFrame method) (neuralib.deeplabcut.core.DeepLabCutDataFrame method) (neuralib.deeplabcut.core.JointDataFrame method) (neuralib.facemap.core.KeyPointDataFrame method) (neuralib.util.dataframe.DataFrameWrapper method) DataFrameWrapper (class in neuralib.util.dataframe) DataIndex (in module neuralib.tools.gspread) DataInfo (class in neuralib.widefield.preproc) dataset (neuralib.deeplabcut.core.DeepLabCutModelConfig attribute) dataset_type (neuralib.deeplabcut.core.DeepLabCutModelConfig attribute) date_proc (neuralib.suite2p.core.Suite2pGUIOptions attribute) DeepLabCutDataFrame (class in neuralib.deeplabcut.core) DeepLabCutMeta (class in neuralib.deeplabcut.core) DeepLabCutModelConfig (class in neuralib.deeplabcut.core) default() (neuralib.io.json.JsonEncodeHandler method) DEFAULT_COLORS (neuralib.plot.venn.VennDiagram attribute) DEFAULT_FAMILY_DICT (in module neuralib.atlas.map) default_filtered (neuralib.deeplabcut.core.DeepLabCutDataFrame property) DEFAULT_REGION_COLORS (neuralib.atlas.brainrender.core.BrainRenderCLI attribute) DEFAULT_ROI_COLORS (neuralib.atlas.brainrender.roi.RoiRenderCLI attribute) delete_bin (neuralib.suite2p.core.Suite2pGUIOptions attribute) delta (neuralib.scanbox.core.SBXInfo.CalibrationInfo attribute) delta_xy (neuralib.atlas.ccf.matrix.CCFTransMatrix property) denoise (neuralib.suite2p.core.Suite2pGUIOptions attribute) denoise() (neuralib.imglib.array.ImageArrayWrapper method) dense_expansion (neuralib.spikes.cascade.CascadeModelConfig attribute) deprecated_aliases() (in module neuralib.util.deprecation) deprecated_class() (in module neuralib.util.deprecation) deprecated_func() (in module neuralib.util.deprecation) DESCRIPTION (neuralib.atlas.brainrender.core.BrainRenderCLI attribute) (neuralib.atlas.brainrender.probe.ProbeRenderCLI attribute) (neuralib.atlas.brainrender.roi.RoiRenderCLI attribute) (neuralib.scanbox.view.ScanBoxViewOptions attribute) (neuralib.stardist.base.AbstractSegmentationOptions attribute) (neuralib.stardist.run_2d.StarDist2DOptions attribute) (neuralib.widefield.align.NapariAlignmentOptions attribute) (neuralib.widefield.fft_view.WideFieldFFTViewOption attribute) (neuralib.widefield.preproc.PreprocessOptions attribute) (neuralib.widefield.transform.RegistrationOptions attribute)

deterministic (neuralib.deeplabcut.core.DeepLabCutModelConfig attribute) dff (neuralib.suite2p.signals.DFFSignal attribute) dff_baseline (neuralib.suite2p.signals.DFFSignal property) dff_signal() (in module neuralib.suite2p.signals) DFFSignal (class in neuralib.suite2p.signals) dh (neuralib.atlas.view.SlicePlane attribute) diag_heatmap() (in module neuralib.plot.plot) diag_histplot() (in module neuralib.plot.plot) diameter (neuralib.cellpose.core.CellposeSegmentation property) (neuralib.suite2p.core.Suite2pGUIOptions attribute) dimcode (neuralib.scan.core.AbstractScanner property) (neuralib.scan.czi.CziScanner property) (neuralib.scan.lsm.TiffScanner property) direction_2d() (in module neuralib.locomotion.position) directory (neuralib.scanbox.view.ScanBoxViewOptions attribute) (neuralib.stardist.base.AbstractSegmentationOptions attribute) (neuralib.suite2p.core.Suite2PResult attribute) (neuralib.widefield.preproc.PreprocessOptions attribute) directory_suffix (neuralib.stardist.base.AbstractSegmentationOptions attribute) DiscreteColorMapper (class in neuralib.plot.colormap) do_bidiphase (neuralib.suite2p.core.Suite2pGUIOptions attribute) do_registration (neuralib.suite2p.core.Suite2pGUIOptions attribute) document (neuralib.dashboard.base.View attribute) dorsal_map_path (neuralib.widefield.align.NapariAlignmentOptions attribute) DorsalCCF (class in neuralib.widefield.ccf) dotplot() (in module neuralib.plot.plot) download_with_tqdm() (in module neuralib.util.tqdm) drop() (neuralib.util.dataframe.DataFrameWrapper method) drop_nulls() (neuralib.util.dataframe.DataFrameWrapper method) dtype (neuralib.rastermap.plot.Covariant attribute) dv (neuralib.atlas.util.SourceCoordinates property) dw (neuralib.atlas.view.SlicePlane attribute) dye_label_only (neuralib.atlas.brainrender.probe.ProbeRenderCLI attribute)

E

ellipse (neuralib.facemap.core.RoiDict attribute) embedding (neuralib.rastermap.core.RasterMapResult attribute) empty_cache() (neuralib.persistence.cli_persistence.PersistenceOptions method) enable (neuralib.scanbox.core.SBXInfo.AgcInfo attribute) end (neuralib.locomotion.spatial.PlaceFieldResult attribute) end_time (neuralib.rastermap.core.RasterOptions attribute) enhance_blood_vessels() (in module neuralib.imglib.norm) enhance_contrast() (neuralib.imglib.array.ImageArrayWrapper method) enqueue_message() (neuralib.imglib.labeller.SequenceLabeller method)

ensemble_size (neuralib.spikes.cascade.CascadeModelConfig attribute) ensure_dir() (in module neuralib.util.utils) ensure_persistence_class() (in module neuralib.persistence.persistence) error_set (neuralib.dashboard.util.MsgLog attribute) ETLConcatable (class in neuralib.persistence.validator) eval() (neuralib.stardist.base.AbstractSegmentationOptions method) (neuralib.stardist.run_2d.StarDist2DOptions method) EX_GROUP_SOURCE (neuralib.stardist.base.AbstractSegmentationOptions attribute) export() (neuralib.atlas.brainrender.core.BrainRenderCLI class method)

F

f (neuralib.suite2p.signals.DFFSignal attribute) f0 (neuralib.suite2p.signals.DFFSignal attribute) f0_baseline (neuralib.widefield.preproc.PreprocessMeta attribute) f_neu (neuralib.suite2p.core.Suite2PResult attribute) f_raw (neuralib.suite2p.core.Suite2PResult attribute) FaceMapResult (class in neuralib.facemap.core) fast_disk (neuralib.suite2p.core.Suite2pGUIOptions attribute) fcorr (neuralib.suite2p.signals.DFFSignal attribute) fg_fraction (neuralib.deeplabcut.core.DeepLabCutModelConfig attribute) field() (in module neuralib.persistence.persistence) FieldOfView (class in neuralib.registration.coordinates) Figure() (in module neuralib.dashboard.base) FIGURE_TYPE (neuralib.dashboard.examples.view_figure.AnimalFigureView attribute) file (neuralib.atlas.brainrender.probe.ProbeRenderCLI attribute) (neuralib.atlas.brainrender.roi.RoiRenderCLI attribute) (neuralib.io.pyh5.H5pyData property) (neuralib.stardist.base.AbstractSegmentationOptions attribute) (neuralib.widefield.fft_view.WideFieldFFTViewOption attribute) (neuralib.widefield.preproc.PreprocessOptions attribute) file_mode (neuralib.stardist.base.AbstractSegmentationOptions property) file_type (neuralib.scan.lsm.TiffScanner property) filelist (neuralib.suite2p.core.Suite2pGUIOptions attribute) filename (neuralib.cellpose.core.CellposeSegmentation property) (neuralib.rastermap.core.RasterMapResult attribute) (neuralib.stardist.core.StarDistSegmentation property) filename() (in module neuralib.persistence.persistence) (neuralib.persistence.persistence.GzipHandler method) (neuralib.persistence.persistence.PersistenceHandler method) (neuralib.persistence.persistence.PickleHandler method) filenames (neuralib.facemap.core.SVDVariables attribute) filepath (neuralib.scan.core.AbstractScanner property) filepath() (neuralib.persistence.persistence.PersistenceHandler method) fill_nan() (neuralib.util.dataframe.DataFrameWrapper method) fill_null() (neuralib.util.dataframe.DataFrameWrapper method) filter() (neuralib.util.dataframe.DataFrameWrapper method) filter_areas() (neuralib.atlas.ccf.dataframe.RoiNormalizedDataFrame method) filter_capital_name() (neuralib.atlas.ccf.dataframe.RoiClassifierDataFrame method) filter_injection_site() (neuralib.atlas.ccf.dataframe.RoiClassifierDataFrame method) filter_matched() (in module neuralib.util.utils)

filter_numbers (neuralib.spikes.cascade.CascadeModelConfig attribute) filter_overlap() (neuralib.atlas.ccf.dataframe.RoiSubregionDataFrame method) filter_sizes (neuralib.spikes.cascade.CascadeModelConfig attribute) filter_sources() (neuralib.atlas.ccf.dataframe.RoiNormalizedDataFrame method) find_cache() (neuralib.persistence.cli_persistence.PersistenceOptions method) flatten_arraylike() (in module neuralib.typing.func) fliplr() (neuralib.imglib.array.ImageArrayWrapper method) flipud() (neuralib.imglib.array.ImageArrayWrapper method) flows (neuralib.cellpose.core.CellposeSegmentation property) fneu (neuralib.suite2p.signals.DFFSignal attribute) footprint (neuralib.suite2p.core.Suite2pRoiStat attribute) force_compute (neuralib.widefield.preproc.InputArguments attribute) (neuralib.widefield.preproc.PreprocessOptions attribute) force_refImg (neuralib.suite2p.core.Suite2pGUIOptions attribute) force_sktiff (neuralib.suite2p.core.Suite2pGUIOptions attribute) foreach_identifier() (neuralib.morpho.swc.SwcFile method) foreach_line() (neuralib.morpho.swc.SwcFile method) foreach_map() (in module neuralib.util.segments) foreach_node() (neuralib.morpho.swc.SwcFile method) foreach_process_image() (neuralib.stardist.base.AbstractSegmentationOptions method) fov_distance (neuralib.scanbox.core.SBXInfo property) fov_mm (neuralib.widefield.ccf.DorsalCCF property) fprint() (in module neuralib.util.verbose) fps (neuralib.deeplabcut.core.DeepLabCutDataFrame property) (neuralib.deeplabcut.core.DeepLabCutMeta attribute) frame_dimensions (neuralib.deeplabcut.core.DeepLabCutMeta attribute) frame_shape (neuralib.widefield.preproc.DataInfo attribute) frame_times (neuralib.scanbox.core.SBXInfo.ConfigInfo attribute) frames (neuralib.scanbox.core.SBXInfo.ConfigInfo attribute) (neuralib.scanbox.view.ScanBoxViewOptions attribute) frames_include (neuralib.suite2p.core.Suite2pGUIOptions attribute) from_array() (neuralib.widefield.ccf.DorsalCCF class method) from_dict() (in module neuralib.persistence.persistence) from_directory() (neuralib.facemap.core.FaceMapResult class method) from_json() (neuralib.widefield.ccf.DorsalCCF class method) (neuralib.widefield.ccf.RegionLabel class method) fs (neuralib.suite2p.core.Suite2pGUIOptions attribute) (neuralib.suite2p.core.Suite2PResult property) fullSVD (neuralib.facemap.core.SVDVariables attribute) functional_chan (neuralib.suite2p.core.Suite2pGUIOptions attribute)

G

gain_resonant_mult (neuralib.scanbox.core.SBXInfo.CalibrationInfo attribute) gaussian_blur() (neuralib.imglib.array.ImageArrayWrapper method) gen_offset_matrix() (neuralib.dashboard.view_brain.AtlasBrainView method) get() (neuralib.facemap.core.FaceMapResult method) get_annotation_ids() (in module neuralib.atlas.data) get_arg() (neuralib.dashboard.base.View method) get_atlas_brain_globe() (neuralib.atlas.brainrender.core.BrainRenderCLI method) get_available_models() (neuralib.spikes.cascade.CascadeSpikePrediction method) get_blink() (neuralib.facemap.core.FaceMapResult method) get_cell() (neuralib.tools.gspread.GoogleWorkSheet method) get_cellular_coordinate() (in module neuralib.registration.coordinates) get_chance_level() (neuralib.plot.venn.VennDiagram method) get_channel_names() (neuralib.scan.core.AbstractScanner method) (neuralib.scan.czi.CziScanner method) (neuralib.scan.lsm.TiffScanner method) get_channel_source_dict() (neuralib.atlas.ccf.dataframe.RoiClassifierDataFrame method) get_children() (in module neuralib.atlas.data) get_classified_column() (neuralib.atlas.ccf.dataframe.RoiClassifierDataFrame method) get_code() (neuralib.scan.czi.CziScanner method) get_color() (in module neuralib.atlas.brainrender.util) get_config() (neuralib.spikes.cascade.CascadeSpikePrediction method) get_customized_cmap() (in module neuralib.plot.colormap) get_dorsal_cortex() (in module neuralib.atlas.data) get_field_of_view() (in module neuralib.registration.coordinates) get_freq_map() (neuralib.widefield.fft.SequenceFFT method) get_func_default() (in module neuralib.util.func) get_intensity() (neuralib.widefield.fft.SequenceFFT method) get_intersection() (neuralib.plot.venn.VennDiagram method) get_joint() (neuralib.deeplabcut.core.DeepLabCutDataFrame method) get_leaf_in_annotation() (in module neuralib.atlas.data) get_margin_merge_level() (in module neuralib.atlas.util) get_neuron_id_mapping() (neuralib.suite2p.core.Suite2PResult method) get_neuron_signal() (in module neuralib.suite2p.signals) get_options_and_cache() (in module neuralib.persistence.cli_persistence) get_percentile_value() (in module neuralib.imglib.norm) get_phase() (neuralib.widefield.fft.SequenceFFT method) get_pupil() (neuralib.facemap.core.FaceMapResult method) get_pupil_area() (neuralib.facemap.core.FaceMapResult method) get_pupil_center_of_mass() (neuralib.facemap.core.FaceMapResult method) get_pupil_location_movement() (neuralib.facemap.core.FaceMapResult method) get_pure_fraction() (neuralib.plot.venn.VennHandler method) get_pure_number() (neuralib.plot.venn.VennHandler method)

get_range_value() (neuralib.tools.gspread.GoogleWorkSheet method) get_rois_pixels() (neuralib.suite2p.core.Suite2PResult method) get_s2p_coords() (in module neuralib.suite2p.core) get_slice_plane() (neuralib.atlas.ccf.matrix.CCFTransMatrix method) get_slice_view() (in module neuralib.atlas.view) get_soma_pixel() (in module neuralib.suite2p.plot) get_tile_info() (neuralib.scan.czi.CziScanner method) get_worksheet() (neuralib.tools.gspread.GoogleSpreadSheet method) gif_show() (in module neuralib.imglib.io) global_scale (neuralib.deeplabcut.core.DeepLabCutModelConfig attribute) go_to() (neuralib.imglib.labeller.SequenceLabeller method) google_drive_file() (in module neuralib.io.dataset) google_drive_folder() (in module neuralib.io.dataset) GoogleSpreadSheet (class in neuralib.tools.gspread) GoogleWorkSheet (class in neuralib.tools.gspread) goto_begin() (neuralib.imglib.labeller.SequenceLabeller method) goto_btn (neuralib.dashboard.examples.view_all.AllView attribute) goto_end() (neuralib.imglib.labeller.SequenceLabeller method) gpu_available() (in module neuralib.util.gpu) gpu_used (neuralib.widefield.preproc.ProcessedInfo attribute) grey2rgb() (in module neuralib.imglib.color) grid_subplots() (in module neuralib.plot.plot) grid_upsample (neuralib.rastermap.core.RasterOptions attribute) grid_x (neuralib.atlas.view.AbstractSliceView attribute) (neuralib.dashboard.view_brain.AtlasBrainView attribute) grid_y (neuralib.atlas.view.AbstractSliceView attribute) (neuralib.dashboard.view_brain.AtlasBrainView attribute) group() (in module neuralib.io.pyh5) GROUP_ACCEL (neuralib.widefield.preproc.PreprocessOptions attribute) group_by() (neuralib.util.dataframe.DataFrameWrapper method) GROUP_CACHE (neuralib.persistence.cli_persistence.PersistenceOptions attribute) GROUP_IO (neuralib.stardist.base.AbstractSegmentationOptions attribute) (neuralib.widefield.preproc.PreprocessOptions attribute) GROUP_OPTIONAL (neuralib.atlas.brainrender.core.BrainRenderCLI attribute) GROUP_OUTPUT (neuralib.atlas.brainrender.core.BrainRenderCLI attribute) GROUP_PROBE (neuralib.atlas.brainrender.probe.ProbeRenderCLI attribute) GROUP_PROC (neuralib.widefield.preproc.PreprocessOptions attribute) GROUP_REGION (neuralib.atlas.brainrender.core.BrainRenderCLI attribute) GROUP_ROIS (neuralib.atlas.brainrender.roi.RoiRenderCLI attribute) GROUP_ROIS_LOAD (neuralib.atlas.brainrender.roi.RoiRenderCLI attribute) GROUP_SETTINGS (neuralib.atlas.brainrender.core.BrainRenderCLI attribute) grouped_iter() (in module neuralib.util.segments) GzipHandler (class in neuralib.persistence.persistence)

H

h5py (neuralib.suite2p.core.Suite2pGUIOptions attribute) h5py_key (neuralib.suite2p.core.Suite2pGUIOptions attribute) H5pyData (class in neuralib.io.pyh5) handle_command() (neuralib.imglib.labeller.SequenceLabeller method) handle_invalid_value() (in module neuralib.imglib.norm) handle_keycode() (neuralib.imglib.labeller.SequenceLabeller method) has_chan2 (neuralib.suite2p.core.Suite2PResult property) has_cupy (neuralib.widefield.preproc.ProcessedInfo attribute) has_gap() (in module neuralib.util.segments) has_numba (neuralib.widefield.preproc.ProcessedInfo attribute) has_worksheet() (neuralib.tools.gspread.GoogleSpreadSheet method) head() (neuralib.util.dataframe.DataFrameWrapper method) headers (neuralib.tools.gspread.GoogleWorkSheet property) height (neuralib.atlas.view.AbstractSliceView property) (neuralib.cellpose.core.CellposeSegmentation property) (neuralib.dashboard.view_brain.AbstractBrainView property) (neuralib.dashboard.view_brain.AtlasBrainView property) (neuralib.imglib.array.ImageArrayWrapper property) (neuralib.scanbox.view.ScanBoxView property) (neuralib.stardist.core.StarDistSegmentation property) (neuralib.widefield.fft.SequenceFFT property)

height_mm (neuralib.atlas.view.AbstractSliceView property) height_n (neuralib.dashboard.view_brain.AtlasBrainView property) helper_with_index_column() (in module neuralib.util.dataframe) hemisphere (neuralib.atlas.brainrender.core.BrainRenderCLI attribute) (neuralib.widefield.ccf.DorsalCCF property) HEMISPHERE_TYPE (in module neuralib.atlas.typing) (in module neuralib.widefield.ccf) high_pass (neuralib.suite2p.core.Suite2pGUIOptions attribute) host_name (neuralib.scanbox.core.SBXInfo.ConfigInfo attribute)

I

identifier (neuralib.morpho.swc.SwcNode attribute) identifier_name (neuralib.morpho.swc.SwcNode property) ids (neuralib.rastermap.core.UserCluster attribute) ihop (neuralib.suite2p.core.Suite2pGUIOptions attribute) ij_roi_output() (neuralib.stardist.base.AbstractSegmentationOptions method) image (neuralib.atlas.view.SlicePlane property) (neuralib.scan.lsm.TiffScanner property) image_array() (in module neuralib.imglib.array) image_height (neuralib.suite2p.core.Suite2PResult property) (neuralib.widefield.preproc.DataInfo attribute) image_mean (neuralib.suite2p.core.Suite2PResult property) image_mean_ch2 (neuralib.suite2p.core.Suite2PResult property) image_shape (neuralib.widefield.ccf.DorsalCCF property) image_size (neuralib.facemap.core.KeyPointsMeta attribute) image_width (neuralib.suite2p.core.Suite2PResult property) (neuralib.widefield.preproc.DataInfo attribute) ImageArrayWrapper (class in neuralib.imglib.array) implant_depth (neuralib.atlas.brainrender.probe.ProbeRenderCLI attribute) indicator_tau (neuralib.suite2p.core.Suite2PResult property) inference_speed (neuralib.facemap.core.KeyPointsMeta attribute) info (neuralib.scanbox.view.ScanBoxView attribute) init_weights (neuralib.deeplabcut.core.DeepLabCutModelConfig attribute) inner_neuropil_radius (neuralib.suite2p.core.Suite2pGUIOptions attribute) input_arguments (neuralib.widefield.preproc.PreprocessMeta attribute) input_format (neuralib.suite2p.core.Suite2pGUIOptions attribute) input_source (neuralib.widefield.preproc.InputArguments attribute) InputArguments (class in neuralib.widefield.preproc) insert() (neuralib.dashboard.util.ColorBarView method) insert_colorbar() (in module neuralib.plot.colormap) insert_cyclic_colorbar() (in module neuralib.plot.colormap) insert_latex_equation() (in module neuralib.plot.tools) INSTANCE (neuralib.dashboard.base.BokehServer attribute) intermediate_supervision (neuralib.deeplabcut.core.DeepLabCutModelConfig attribute)

intermediate_supervision_layer (neuralib.deeplabcut.core.DeepLabCutModelConfig attribute) interp() (neuralib.atlas.brainrender.probe.ProbeShank method) interp1d_nan() (in module neuralib.util.interp) interp_activity() (neuralib.rastermap.plot.Covariant method) interp_gap2d() (in module neuralib.locomotion.position) interp_pos1d() (in module neuralib.locomotion.position) interp_time() (neuralib.locomotion.position.CircularPosition method) interp_timestamp() (in module neuralib.util.interp) intersections (neuralib.plot.venn.VennDiagram property) invalid_cache (neuralib.persistence.cli_persistence.PersistenceOptions attribute) invalid_existed_result (neuralib.stardist.base.AbstractSegmentationOptions attribute) inverse_lut (neuralib.atlas.brainrender.roi.RoiRenderCLI attribute) invert_axes() (neuralib.registration.coordinates.FieldOfView method) iROI (neuralib.facemap.core.RoiDict attribute) is_apical_dendrite (neuralib.morpho.swc.SwcNode property) is_axon (neuralib.morpho.swc.SwcNode property) is_basal_dendrite (neuralib.morpho.swc.SwcNode property) is_custom (neuralib.morpho.swc.SwcNode property) is_dendrite (neuralib.morpho.swc.SwcNode property) is_iterable() (in module neuralib.typing.func) is_manual (neuralib.cellpose.core.CellposeSegmentation property) is_mosaic (neuralib.scan.czi.CziScanner property) is_namedtuple() (in module neuralib.typing.func) is_numeric_arraylike() (in module neuralib.typing.func) is_overlapped_channel (neuralib.atlas.ccf.dataframe.RoiClassifierDataFrame property) is_soma (neuralib.morpho.swc.SwcNode property) is_sorted() (in module neuralib.util.segments) is_undefined (neuralib.morpho.swc.SwcNode property) iscell (neuralib.suite2p.core.Suite2PResult attribute) isort (neuralib.rastermap.core.RasterMapResult attribute) iter_source_coordinates() (in module neuralib.atlas.util) iteration (neuralib.deeplabcut.core.DeepLabCutMeta attribute) ivid (neuralib.facemap.core.RoiDict attribute)

J

join() (neuralib.util.dataframe.DataFrameWrapper method) joinn() (in module neuralib.util.utils) JointDataFrame (class in neuralib.deeplabcut.core)

joints (neuralib.deeplabcut.core.DeepLabCutDataFrame property) JsonEncodeHandler (class in neuralib.io.json) jump_mask2d() (in module neuralib.locomotion.epoch)

K

keep_movie_raw (neuralib.suite2p.core.Suite2pGUIOptions attribute) KeyPointDataFrame (class in neuralib.facemap.core) keypoints (neuralib.facemap.core.FaceMapResult property)

KeyPointsMeta (class in neuralib.facemap.core) keys_with_value() (in module neuralib.util.utils) knobby (neuralib.scanbox.core.SBXInfo.ConfigInfo attribute)

L

label (neuralib.widefield.ccf.RegionLabel attribute) labels (neuralib.plot.venn.VennDiagram property) (neuralib.stardist.core.StarDistSegmentation property) lam (neuralib.suite2p.core.Suite2pRoiStat attribute) lam_percentile (neuralib.suite2p.core.Suite2pGUIOptions attribute) laser_power (neuralib.scanbox.core.SBXInfo.ConfigInfo attribute) laser_power_perc (neuralib.scanbox.core.SBXInfo.ConfigInfo attribute) launch_napari() (neuralib.stardist.base.AbstractSegmentationOptions method) (neuralib.stardist.run_2d.StarDist2DOptions method) lazy() (neuralib.util.dataframe.DataFrameWrapper method) lazy_load_widefield() (in module neuralib.widefield.data) left_center (neuralib.widefield.ccf.RegionLabel attribute) left_vector (neuralib.widefield.svd.SequenceSingularVector attribute) left_x (neuralib.widefield.ccf.RegionLabel attribute) left_y (neuralib.widefield.ccf.RegionLabel attribute) limit() (neuralib.util.dataframe.DataFrameWrapper method) lines (neuralib.scanbox.core.SBXInfo.ConfigInfo attribute) list_renders() (neuralib.dashboard.base.ViewComponent method) load() (in module neuralib.persistence.persistence) (neuralib.cellpose.core.CellposeSegmentation class method) (neuralib.morpho.swc.SwcFile class method) (neuralib.rastermap.core.RasterMapResult class method) (neuralib.scanbox.core.SBXInfo class method) (neuralib.stardist.core.StarDistSegmentation class method) (neuralib.suite2p.core.Suite2PResult class method) (neuralib.widefield.preproc.PreprocessOptions method) load_all() (neuralib.persistence.persistence.PersistenceHandler method) load_bg_structure_tree() (in module neuralib.atlas.data) load_bg_volumes() (in module neuralib.atlas.data) load_cache() (neuralib.persistence.cli_persistence.PersistenceOptions method) load_cellatlas() (in module neuralib.atlas.cellatlas.core) load_csv() (neuralib.atlas.brainrender.probe.ProbeShank class method) load_dorsal_map() (neuralib.widefield.transform.RegistrationApp method) load_ephys_data() (in module neuralib.io.dataset) load_ephys_meta() (in module neuralib.io.dataset) load_example_czi() (in module neuralib.io.dataset) load_example_dlc_csv() (in module neuralib.io.dataset) load_example_dlc_h5() (in module neuralib.io.dataset) load_example_dorsal_cortex() (in module neuralib.io.dataset) load_example_facemap_keypoints() (in module neuralib.io.dataset) load_example_facemap_pupil() (in module neuralib.io.dataset) load_example_lsm() (in module neuralib.io.dataset)

load_example_rastermap_2p_cache() (in module neuralib.io.dataset) load_example_rastermap_2p_result() (in module neuralib.io.dataset) load_example_retinotopic_data() (in module neuralib.io.dataset) load_example_rois() (in module neuralib.io.dataset) load_example_rois_dir() (in module neuralib.io.dataset) load_example_rois_image() (in module neuralib.io.dataset) load_example_scanbox() (in module neuralib.io.dataset) load_example_suite2p_result() (in module neuralib.io.dataset) load_from_dir() (neuralib.imglib.labeller.SequenceLabeller class method) load_json() (in module neuralib.io.json) load_note() (neuralib.imglib.labeller.SequenceLabeller method) load_npx2_reconstruction() (in module neuralib.io.dataset) load_numpy() (neuralib.atlas.brainrender.probe.ProbeShank class method) load_persistence() (neuralib.persistence.persistence.PersistenceHandler method) load_preprocess_meta() (in module neuralib.widefield.preproc) load_sequence() (in module neuralib.imglib.io) load_sequences() (neuralib.imglib.labeller.SequenceLabeller class method) load_total_neuron_number() (neuralib.suite2p.core.Suite2PResult class method) load_transform_matrix() (in module neuralib.atlas.ccf.matrix) load_widefield() (neuralib.widefield.transform.RegistrationApp method) local_maxima() (neuralib.imglib.array.ImageArrayWrapper method) locality (neuralib.rastermap.core.RasterOptions attribute) location_refinement (neuralib.deeplabcut.core.DeepLabCutModelConfig attribute) locref_huber_loss (neuralib.deeplabcut.core.DeepLabCutModelConfig attribute) locref_loss_weight (neuralib.deeplabcut.core.DeepLabCutModelConfig attribute) locref_stdev (neuralib.deeplabcut.core.DeepLabCutModelConfig attribute) log() (neuralib.widefield.transform.RegistrationApp method) log_dir (neuralib.deeplabcut.core.DeepLabCutModelConfig attribute) logger (neuralib.atlas.brainrender.core.BrainRenderCLI attribute) LOGGING_IO_LEVEL (in module neuralib.util.logging) look_one_level_down (neuralib.suite2p.core.Suite2pGUIOptions attribute) loss_function (neuralib.spikes.cascade.CascadeModelConfig attribute) lsm_file() (in module neuralib.scan.lsm) Lx (neuralib.facemap.core.SVDVariables attribute) (neuralib.suite2p.core.Suite2pGUIOptions attribute) LXbin (neuralib.facemap.core.SVDVariables attribute) Lxbin (neuralib.facemap.core.SVDVariables attribute) Lxc (neuralib.suite2p.core.Suite2pGUIOptions attribute) Ly (neuralib.facemap.core.SVDVariables attribute) (neuralib.suite2p.core.Suite2pGUIOptions attribute) LYbin (neuralib.facemap.core.SVDVariables attribute) Lybin (neuralib.facemap.core.SVDVariables attribute) Lyc (neuralib.suite2p.core.Suite2pGUIOptions attribute)

M

magidx (neuralib.scanbox.core.SBXInfo property) magnification (neuralib.scanbox.core.SBXInfo.ConfigInfo attribute) magnification_list (neuralib.scanbox.core.SBXInfo.ConfigInfo attribute) main() (neuralib.imglib.labeller.SequenceLabeller method) map_brainrender() (neuralib.atlas.brainrender.probe.ProbeShank method) mask_probability() (neuralib.stardist.core.StarDistSegmentation method) masking_time() (neuralib.rastermap.plot.Covariant method) masks (neuralib.cellpose.core.CellposeSegmentation property) matrix (neuralib.atlas.ccf.matrix.CCFTransMatrix attribute) matrix_info() (neuralib.atlas.ccf.matrix.CCFTransMatrix method) max_intersection_areas (neuralib.plot.venn.VennDiagram property) max_iterations (neuralib.suite2p.core.Suite2pGUIOptions attribute) max_overlap (neuralib.suite2p.core.Suite2pGUIOptions attribute) max_proj (neuralib.suite2p.core.Suite2pGUIOptions attribute) max_projection_axis (neuralib.atlas.view.AbstractSliceView property) max_shift (neuralib.widefield.preproc.InputArguments attribute) (neuralib.widefield.preproc.PreprocessOptions attribute) maxregshift (neuralib.suite2p.core.Suite2pGUIOptions attribute) maxregshiftNR (neuralib.suite2p.core.Suite2pGUIOptions attribute) mean_pixel (neuralib.deeplabcut.core.DeepLabCutModelConfig attribute) mean_time (neuralib.rastermap.core.RasterOptions attribute) meanImg (neuralib.suite2p.core.Suite2pGUIOptions attribute) meanImg_chan2 (neuralib.suite2p.core.Suite2pGUIOptions attribute) meanImgE (neuralib.suite2p.core.Suite2pGUIOptions attribute) med (neuralib.suite2p.core.Suite2pRoiStat attribute) merge_until_level() (in module neuralib.atlas.map) mesoscan (neuralib.suite2p.core.Suite2pGUIOptions attribute) messages (neuralib.scanbox.core.SBXInfo attribute) meta (neuralib.deeplabcut.core.DeepLabCutDataFrame property) (neuralib.scanbox.view.ScanBoxView property) metadata (neuralib.scan.core.AbstractScanner property) min_neuropil_pixels (neuralib.suite2p.core.Suite2pGUIOptions attribute) mirror (neuralib.deeplabcut.core.DeepLabCutModelConfig attribute) mkdir_version() (in module neuralib.io.output) ml (neuralib.atlas.util.SourceCoordinates property) (neuralib.registration.coordinates.CellularCoordinates attribute) ml_distance (neuralib.registration.coordinates.FieldOfView property) model (neuralib.stardist.base.AbstractSegmentationOptions attribute) (neuralib.stardist.core.StarDistSegmentation property) (neuralib.stardist.run_2d.StarDist2DOptions attribute) model_config (neuralib.deeplabcut.core.DeepLabCutDataFrame property) (neuralib.deeplabcut.core.DeepLabCutMeta attribute) model_dir (neuralib.spikes.cascade.CascadeSpikePrediction property) model_link (neuralib.spikes.cascade.CascadeSpikePrediction property) model_name (neuralib.spikes.cascade.CascadeModelConfig attribute) module neuralib neuralib.atlas neuralib.atlas.brainrender neuralib.atlas.ccf neuralib.atlas.cellatlas neuralib.cellpose neuralib.dashboard neuralib.dashboard.examples neuralib.decoding neuralib.deeplabcut neuralib.facemap neuralib.imglib neuralib.io neuralib.locomotion neuralib.morpho neuralib.persistence neuralib.plot neuralib.rastermap neuralib.registration neuralib.scan neuralib.scanbox neuralib.spikes neuralib.stardist neuralib.suite2p neuralib.tools neuralib.typing neuralib.util neuralib.widefield

motion (neuralib.facemap.core.SVDVariables attribute) motion_correction (neuralib.widefield.preproc.InputArguments attribute) (neuralib.widefield.preproc.PreprocessMeta attribute) (neuralib.widefield.preproc.PreprocessOptions attribute) MotionCorrInfo (class in neuralib.widefield.preproc) motMask (neuralib.facemap.core.SVDVariables attribute) motMask_reshape (neuralib.facemap.core.SVDVariables attribute) motSv (neuralib.facemap.core.SVDVariables attribute) motSVD (neuralib.facemap.core.SVDVariables attribute) move_bin (neuralib.suite2p.core.Suite2pGUIOptions attribute) movMask (neuralib.facemap.core.SVDVariables attribute) movMask_reshape (neuralib.facemap.core.SVDVariables attribute) movSv (neuralib.facemap.core.SVDVariables attribute) movSVD (neuralib.facemap.core.SVDVariables attribute) mrs (neuralib.suite2p.core.Suite2pRoiStat attribute) mrs0 (neuralib.suite2p.core.Suite2pRoiStat attribute) MsgLog (class in neuralib.dashboard.util) multiplane_parallel (neuralib.suite2p.core.Suite2pGUIOptions attribute)

N

n (neuralib.morpho.swc.SwcNode attribute) n_ap (neuralib.atlas.view.AbstractSliceView property) (neuralib.dashboard.view_brain.AtlasBrainView property) n_channels (neuralib.atlas.ccf.dataframe.RoiClassifierDataFrame property) (neuralib.scanbox.view.ScanBoxView property) n_clusters (neuralib.rastermap.core.RasterMapResult property) (neuralib.rastermap.core.RasterOptions attribute) n_dv (neuralib.atlas.view.AbstractSliceView property) (neuralib.dashboard.view_brain.AtlasBrainView property) n_frame (neuralib.dashboard.view_brain.AtlasBrainView property) (neuralib.suite2p.core.Suite2PResult property) n_frames (neuralib.imglib.labeller.SequenceLabeller property) (neuralib.scanbox.view.ScanBoxView property) (neuralib.widefield.fft.SequenceFFT property) n_jobs (neuralib.widefield.preproc.InputArguments attribute) (neuralib.widefield.preproc.PreprocessOptions attribute) n_keyframes (neuralib.widefield.preproc.BaselineInfo attribute) n_ml (neuralib.atlas.view.AbstractSliceView property) (neuralib.dashboard.view_brain.AtlasBrainView property) n_neurons (neuralib.suite2p.core.Suite2PResult property) n_PCs (neuralib.rastermap.core.RasterOptions attribute) n_pf (neuralib.locomotion.spatial.PlaceFieldResult property) n_plane (neuralib.suite2p.core.Suite2PResult property) n_planes (neuralib.atlas.view.AbstractSliceView property) (neuralib.scanbox.view.ScanBoxView property) n_red_neuron (neuralib.suite2p.core.Suite2PResult property) n_samples (neuralib.rastermap.core.RasterMapResult property) n_scenes (neuralib.scan.core.AbstractScanner property) (neuralib.scan.czi.CziScanner property) (neuralib.scan.lsm.TiffScanner property) n_segmentation (neuralib.cellpose.core.CellposeSegmentation property) (neuralib.stardist.core.StarDistSegmentation property) n_shanks (neuralib.atlas.brainrender.probe.ProbeShank property) n_sources (neuralib.atlas.ccf.dataframe.RoiClassifierDataFrame property) n_splits (neuralib.rastermap.core.RasterOptions attribute) n_subregion (neuralib.atlas.ccf.dataframe.RoiSubregionDataFrame property) n_tif_files (neuralib.widefield.preproc.DataInfo attribute) name (neuralib.rastermap.plot.Covariant attribute) (neuralib.scanbox.core.SBXInfo.ObjectiveInfo attribute) (neuralib.widefield.ccf.RegionLabel attribute) nan_masks (neuralib.cellpose.core.CellposeSegmentation property) nan_outlines (neuralib.cellpose.core.CellposeSegmentation property) napari_view (neuralib.stardist.base.AbstractSegmentationOptions attribute) NapariAlignmentOptions (class in neuralib.widefield.align) nbinned (neuralib.suite2p.core.Suite2pGUIOptions attribute) nblocks (neuralib.suite2p.core.Suite2pGUIOptions attribute) nchan (neuralib.scanbox.core.SBXInfo attribute) nchannels (neuralib.suite2p.core.Suite2pGUIOptions attribute) net_type (neuralib.deeplabcut.core.DeepLabCutModelConfig attribute) neucoeff (neuralib.suite2p.core.Suite2pGUIOptions attribute) (neuralib.suite2p.core.Suite2PResult property) neuralib module neuralib.atlas module neuralib.atlas.brainrender module neuralib.atlas.ccf module neuralib.atlas.cellatlas module neuralib.cellpose module neuralib.dashboard module neuralib.dashboard.examples module neuralib.decoding module neuralib.deeplabcut module

neuralib.facemap module neuralib.imglib module neuralib.io module neuralib.locomotion module neuralib.morpho module neuralib.persistence module neuralib.plot module neuralib.rastermap module neuralib.registration module neuralib.scan module neuralib.scanbox module neuralib.spikes module neuralib.stardist module neuralib.suite2p module neuralib.tools module neuralib.typing module neuralib.util module neuralib.widefield module NEUROLIB_CACHE_DIRECTORY (in module neuralib.io.core) NEUROLIB_DATASET_DIRECTORY (in module neuralib.io.core) neuron_idx (neuralib.registration.coordinates.CellularCoordinates attribute) neuropil_extract (neuralib.suite2p.core.Suite2pGUIOptions attribute) next_frame() (neuralib.widefield.transform.RegistrationApp method) nframes (neuralib.deeplabcut.core.DeepLabCutDataFrame property) (neuralib.deeplabcut.core.DeepLabCutMeta attribute) (neuralib.suite2p.core.Suite2pGUIOptions attribute) nframes_per_folder (neuralib.suite2p.core.Suite2pGUIOptions attribute) nimg_init (neuralib.suite2p.core.Suite2pGUIOptions attribute) no_normalize (neuralib.stardist.base.AbstractSegmentationOptions attribute) no_root (neuralib.atlas.brainrender.core.BrainRenderCLI attribute) node (neuralib.morpho.swc.SwcFile attribute) noise_levels (neuralib.spikes.cascade.CascadeModelConfig attribute) nonrigid (neuralib.suite2p.core.Suite2pGUIOptions attribute) nonrigid_x_offsets (neuralib.suite2p.core.Suite2PResult property) nonrigid_xy_offsets (neuralib.suite2p.core.Suite2PResult property) nonrigid_y_offsets (neuralib.suite2p.core.Suite2PResult property) norm_frames (neuralib.suite2p.core.Suite2pGUIOptions attribute) normalize_sequences() (in module neuralib.imglib.norm) normalize_signal() (in module neuralib.suite2p.signals) normalize_signal_factor() (in module neuralib.suite2p.signals) normalized (neuralib.atlas.ccf.dataframe.RoiNormalizedDataFrame property) normalized_unit (neuralib.atlas.ccf.dataframe.RoiNormalizedDataFrame property) npix (neuralib.suite2p.core.Suite2pRoiStat attribute) npix_norm (neuralib.suite2p.core.Suite2pRoiStat attribute) npix_norm_no_crop (neuralib.suite2p.core.Suite2pRoiStat attribute) npix_soma (neuralib.suite2p.core.Suite2pRoiStat attribute) nplanes (neuralib.suite2p.core.Suite2pGUIOptions attribute) nr_of_epochs (neuralib.spikes.cascade.CascadeModelConfig attribute) NRsm (neuralib.suite2p.core.Suite2pGUIOptions attribute) num_joints (neuralib.deeplabcut.core.DeepLabCutModelConfig attribute) NUM_MERGE_LAYER (in module neuralib.atlas.map) num_outputs (neuralib.deeplabcut.core.DeepLabCutModelConfig attribute)

O

oasis_dcnv() (in module neuralib.spikes.oasis) oasis_matrix (in module neuralib.spikes.oasis) objective (neuralib.scanbox.core.SBXInfo attribute) (neuralib.scanbox.core.SBXInfo.ConfigInfo attribute) objective_type (neuralib.scanbox.core.SBXInfo.ConfigInfo attribute) occupancy (neuralib.locomotion.spatial.SpatialInfoResult attribute) of() (neuralib.tools.gspread.GoogleWorkSheet class method) offset (neuralib.dashboard.view_brain.AtlasBrainView property) (neuralib.dashboard.view_brain.TiffBrainView property) offset() (neuralib.atlas.view.AbstractSliceView method) offset_h (neuralib.dashboard.view_brain.AtlasBrainView property) offset_matrix (neuralib.dashboard.view_brain.AtlasBrainView property) offset_w (neuralib.dashboard.view_brain.AtlasBrainView property) on_figure_type() (neuralib.dashboard.examples.view_animal.AnimalView method) on_hemisphere_changed() (neuralib.widefield.transform.RegistrationApp method) on_message() (neuralib.dashboard.base.View method) (neuralib.dashboard.util.MsgLog method) on_point_clicked() (neuralib.widefield.transform.RegistrationApp method)

on_select_animal() (neuralib.dashboard.examples.view_all.AllView method) on_select_date() (neuralib.dashboard.examples.view_all.AllView method) oneP_reg (neuralib.suite2p.core.Suite2pGUIOptions attribute) only_source (neuralib.atlas.brainrender.roi.RoiRenderCLI attribute) ops (neuralib.rastermap.core.RasterMapResult attribute) (neuralib.suite2p.core.Suite2PResult attribute) ops_path (neuralib.suite2p.core.Suite2pGUIOptions attribute) optimizer (neuralib.deeplabcut.core.DeepLabCutModelConfig attribute) (neuralib.spikes.cascade.CascadeModelConfig attribute) opto2pow (neuralib.scanbox.core.SBXInfo attribute) otparam (neuralib.scanbox.core.SBXInfo attribute) otwave (neuralib.scanbox.core.SBXInfo attribute) otwave_um (neuralib.scanbox.core.SBXInfo attribute) otwavestyle (neuralib.scanbox.core.SBXInfo attribute) outlines (neuralib.cellpose.core.CellposeSegmentation property) output (neuralib.atlas.brainrender.core.BrainRenderCLI attribute) output_dir (neuralib.widefield.preproc.InputArguments attribute) (neuralib.widefield.preproc.PreprocessOptions property) overlap (neuralib.suite2p.core.Suite2pRoiStat attribute)

P

p (neuralib.locomotion.position.CircularPosition attribute) pad_fft (neuralib.suite2p.core.Suite2pGUIOptions attribute) page() (neuralib.dashboard.base.BokehServer method) pairwise_huber_loss (neuralib.deeplabcut.core.DeepLabCutModelConfig attribute) pairwise_predict (neuralib.deeplabcut.core.DeepLabCutModelConfig attribute) parent (neuralib.morpho.swc.SwcNode attribute) parents (neuralib.morpho.swc.SwcFile property) partaffinityfield_predict (neuralib.deeplabcut.core.DeepLabCutModelConfig attribute) partition_by() (neuralib.util.dataframe.DataFrameWrapper method) PathLike (in module neuralib.typing.alias) PathLikeType (in module neuralib.typing.alias) pause_video() (neuralib.widefield.transform.RegistrationApp method) percentile (neuralib.widefield.preproc.BaselineInfo attribute) (neuralib.widefield.preproc.InputArguments attribute) (neuralib.widefield.preproc.PreprocessOptions attribute) peri_onset_1d() (in module neuralib.plot.psth) perpendicular (neuralib.registration.coordinates.FieldOfView attribute) persistence_class (neuralib.persistence.cli_persistence.PersistenceOptions property) (neuralib.persistence.persistence.GzipHandler property) (neuralib.persistence.persistence.PersistenceHandler property) (neuralib.persistence.persistence.PickleHandler property) persistence_class() (in module neuralib.persistence.persistence) persistence_handler() (neuralib.persistence.cli_persistence.PersistenceOptions method) persistence_info (neuralib.persistence.persistence.PersistenceHandler property) PersistenceHandler (class in neuralib.persistence.persistence) PersistenceOptions (class in neuralib.persistence.cli_persistence) pf (neuralib.locomotion.spatial.PlaceFieldResult attribute) pf_peak (neuralib.locomotion.spatial.PlaceFieldResult property) pf_width (neuralib.locomotion.spatial.PlaceFieldResult property) PickleHandler (class in neuralib.persistence.persistence) pipe() (neuralib.util.dataframe.DataFrameWrapper method) pl (neuralib.registration.coordinates.FieldOfView property) place_bayes() (in module neuralib.decoding.position) place_field() (in module neuralib.locomotion.spatial) PlaceFieldResult (class in neuralib.locomotion.spatial) placeholder_1 (neuralib.spikes.cascade.CascadeModelConfig attribute) placeholder_2 (neuralib.spikes.cascade.CascadeModelConfig attribute) PLANE (neuralib.dashboard.view_brain.AtlasBrainView attribute) plane (neuralib.dashboard.view_brain.AtlasBrainView property) (neuralib.scanbox.view.ScanBoxViewOptions attribute) plane() (neuralib.atlas.view.AbstractSliceView method) plane_at() (neuralib.atlas.view.AbstractSliceView method) plane_index (neuralib.registration.coordinates.CellularCoordinates attribute) plane_offset (neuralib.atlas.view.SlicePlane property) PLANE_TYPE (in module neuralib.atlas.typing) plane_type (neuralib.atlas.brainrender.probe.ProbeRenderCLI attribute) (neuralib.atlas.ccf.matrix.CCFTransMatrix attribute) (neuralib.atlas.view.AbstractSliceView attribute) play_video() (neuralib.widefield.transform.RegistrationApp method) plot() (neuralib.atlas.view.SlicePlane method) (neuralib.dashboard.base.ViewComponent method) (neuralib.dashboard.view_brain.AbstractBrainView method) (neuralib.plot.venn.VennDiagram method) plot_annotation_regions() (neuralib.atlas.view.SlicePlane method) plot_boundaries() (neuralib.atlas.view.SlicePlane method) plot_cellular_spatial() (in module neuralib.rastermap.plot)

plot_cmap_time_series() (in module neuralib.facemap.plot) plot_facemap_keypoints() (in module neuralib.facemap.plot) plot_figure() (in module neuralib.plot.figure) plot_max_projection() (neuralib.atlas.view.AbstractSliceView method) plot_peri_onset_1d() (in module neuralib.plot.psth) plot_rastermap() (in module neuralib.rastermap.plot) (neuralib.rastermap.plot.RasterMapPlot method) plot_retinotopic_maps() (in module neuralib.widefield.fft) plot_segments() (neuralib.rastermap.plot.RasterMapPlot method) plot_soma_center() (in module neuralib.suite2p.plot) plot_sunburst_acronym() (in module neuralib.atlas.plot) plot_swc() (in module neuralib.morpho.swc) plot_wfield_spatial() (in module neuralib.rastermap.plot) pm (neuralib.registration.coordinates.FieldOfView property) pmt0_gain (neuralib.scanbox.core.SBXInfo.ConfigInfo attribute) pmt1_gain (neuralib.scanbox.core.SBXInfo.ConfigInfo attribute) point (neuralib.morpho.swc.SwcNode property) points (neuralib.cellpose.core.CellposeSegmentation property) (neuralib.morpho.swc.SwcFile property) (neuralib.stardist.core.StarDistSegmentation property) pos (neuralib.scanbox.core.SBXInfo.KnobbyInfo attribute) position (neuralib.locomotion.spatial.SpatialInfoResult attribute) post_parsing() (neuralib.atlas.brainrender.core.BrainRenderCLI method) (neuralib.atlas.brainrender.probe.ProbeRenderCLI method) post_processing() (neuralib.atlas.ccf.dataframe.RoiClassifierDataFrame method) postTriggerSamples (neuralib.scanbox.core.SBXInfo attribute) power_depth_link (neuralib.scanbox.core.SBXInfo attribute) prctile_baseline (neuralib.suite2p.core.Suite2pGUIOptions attribute) (neuralib.suite2p.core.Suite2PResult property) pre_smooth (neuralib.suite2p.core.Suite2pGUIOptions attribute) preclassify (neuralib.suite2p.core.Suite2pGUIOptions attribute) PreprocessMeta (class in neuralib.widefield.preproc) PreprocessOptions (class in neuralib.widefield.preproc) primary_key_list (neuralib.tools.gspread.GoogleWorkSheet property) print_gpu_table() (in module neuralib.util.gpu) print_h5py() (in module neuralib.util.verbose) print_load() (in module neuralib.util.verbose) print_name (neuralib.atlas.brainrender.core.BrainRenderCLI attribute) print_save() (in module neuralib.util.verbose) print_tree (neuralib.atlas.brainrender.core.BrainRenderCLI attribute) print_tree() (in module neuralib.atlas.plot) printdf() (in module neuralib.util.verbose) prob (neuralib.stardist.core.StarDistSegmentation property) prob_thresh (neuralib.stardist.run_2d.StarDist2DOptions attribute) ProbeRenderCLI (class in neuralib.atlas.brainrender.probe) ProbeShank (class in neuralib.atlas.brainrender.probe) process_continuous() (neuralib.rastermap.plot.RasterMapPlot method) process_image() (neuralib.stardist.base.AbstractSegmentationOptions method) ProcessedInfo (class in neuralib.widefield.preproc) processing (neuralib.widefield.preproc.PreprocessMeta attribute) profile (neuralib.atlas.ccf.dataframe.RoiSubregionDataFrame property) profile_test (class in neuralib.util.profile) project_index (neuralib.atlas.view.AbstractSliceView property) publish_annotation() (in module neuralib.util.verbose) pupil (neuralib.facemap.core.SVDVariables attribute) pupil_sigma (neuralib.facemap.core.RoiDict attribute) PupilDict (class in neuralib.facemap.core)

R

r (neuralib.morpho.swc.SwcNode attribute) radii (neuralib.morpho.swc.SwcFile property) radius (neuralib.atlas.brainrender.roi.RoiRenderCLI attribute) (neuralib.suite2p.core.Suite2pRoiStat attribute) RasterMapPlot (class in neuralib.rastermap.plot) RasterMapResult (class in neuralib.rastermap.core) RasterOptions (class in neuralib.rastermap.core) read_avi() (in module neuralib.imglib.io) read_cellpose() (in module neuralib.cellpose.core) read_dlc() (in module neuralib.deeplabcut.core) read_facemap() (in module neuralib.facemap.core) read_note() (neuralib.imglib.labeller.SequenceLabeller method) READ_ONLY (neuralib.io.pyh5.H5pyData attribute) read_pdf() (in module neuralib.imglib.io) read_rastermap() (in module neuralib.rastermap.core) read_scanbox() (in module neuralib.scanbox.core) read_stardist() (in module neuralib.stardist.core) read_suite2p() (in module neuralib.suite2p.core) recordsPerBuffer (neuralib.scanbox.core.SBXInfo attribute) red_cell_prob (neuralib.suite2p.core.Suite2PResult property) redcell (neuralib.suite2p.core.Suite2PResult attribute) redcell_threshold (neuralib.suite2p.core.Suite2PResult attribute) reference (neuralib.atlas.view.AbstractSliceView attribute) (neuralib.dashboard.view_brain.BrainView attribute) (neuralib.widefield.ccf.RegionLabel attribute) REFERENCE_FROM (neuralib.atlas.view.AbstractSliceView attribute) reference_path (neuralib.widefield.align.NapariAlignmentOptions attribute) reference_point (neuralib.atlas.view.AbstractSliceView property) reference_value (neuralib.atlas.view.SlicePlane property) refImg (neuralib.suite2p.core.Suite2pGUIOptions attribute) reg_file (neuralib.suite2p.core.Suite2pGUIOptions attribute) reg_tif (neuralib.suite2p.core.Suite2pGUIOptions attribute) reg_tif_chan2 (neuralib.suite2p.core.Suite2pGUIOptions attribute) regDX (neuralib.suite2p.core.Suite2pGUIOptions attribute) region (neuralib.atlas.ccf.dataframe.RoiSubregionDataFrame property) region_col (neuralib.atlas.brainrender.roi.RoiRenderCLI attribute) region_colors (neuralib.atlas.brainrender.core.BrainRenderCLI attribute) region_dict (neuralib.widefield.ccf.DorsalCCF property) region_list (neuralib.widefield.ccf.DorsalCCF property) region_name (neuralib.registration.coordinates.FieldOfView attribute) RegionLabel (class in neuralib.widefield.ccf) regions (neuralib.atlas.brainrender.core.BrainRenderCLI attribute) regions_alpha (neuralib.atlas.brainrender.core.BrainRenderCLI attribute) RegistrationApp (class in neuralib.widefield.transform) RegistrationOptions (class in neuralib.widefield.transform) regPC (neuralib.suite2p.core.Suite2pGUIOptions attribute) regularize (neuralib.deeplabcut.core.DeepLabCutModelConfig attribute) relative_origin() (neuralib.registration.coordinates.CellularCoordinates method) remove_outside_brain (neuralib.atlas.brainrender.probe.ProbeRenderCLI attribute) rename() (neuralib.util.dataframe.DataFrameWrapper method) render() (neuralib.atlas.brainrender.core.BrainRenderCLI method) (neuralib.atlas.brainrender.probe.ProbeRenderCLI method) (neuralib.atlas.brainrender.roi.RoiRenderCLI method) render_brain_slice (neuralib.dashboard.view_brain.AbstractBrainView attribute) render_output() (neuralib.atlas.brainrender.core.BrainRenderCLI method)

resfreq (neuralib.scanbox.core.SBXInfo attribute) resize_both_images() (neuralib.widefield.transform.RegistrationApp method) resolution (neuralib.atlas.ccf.matrix.CCFTransMatrix attribute) (neuralib.atlas.view.AbstractSliceView attribute) (neuralib.dashboard.view_brain.AtlasBrainView attribute) (neuralib.widefield.ccf.RegionLabel attribute) rich_data_frame_table() (in module neuralib.util.table) right_center (neuralib.widefield.ccf.RegionLabel attribute) right_vector (neuralib.widefield.svd.SequenceSingularVector attribute) right_x (neuralib.widefield.ccf.RegionLabel attribute) right_y (neuralib.widefield.ccf.RegionLabel attribute) rigid_x_offsets (neuralib.suite2p.core.Suite2PResult property) rigid_xy_offset (neuralib.suite2p.core.Suite2PResult property) rigid_y_offsets (neuralib.suite2p.core.Suite2PResult property) rind (neuralib.facemap.core.RoiDict attribute) rmax (neuralib.suite2p.core.Suite2pGUIOptions attribute) rmin (neuralib.suite2p.core.Suite2pGUIOptions attribute) roi_alpha (neuralib.atlas.brainrender.roi.RoiRenderCLI attribute) roi_colors (neuralib.atlas.brainrender.roi.RoiRenderCLI attribute) roi_region (neuralib.atlas.brainrender.roi.RoiRenderCLI attribute) RoiClassifierDataFrame (class in neuralib.atlas.ccf.dataframe) roidetect (neuralib.suite2p.core.Suite2pGUIOptions attribute) RoiDict (class in neuralib.facemap.core) RoiNormalizedDataFrame (class in neuralib.atlas.ccf.dataframe) RoiRenderCLI (class in neuralib.atlas.brainrender.roi) rois (neuralib.facemap.core.SVDVariables attribute) ROIS_NORM_TYPE (in module neuralib.atlas.ccf.dataframe) RoiSubregionDataFrame (class in neuralib.atlas.ccf.dataframe) root_alpha (neuralib.atlas.brainrender.core.BrainRenderCLI attribute) rotate (neuralib.widefield.preproc.InputArguments attribute) (neuralib.widefield.preproc.PreprocessOptions attribute) rotate_sequence() (in module neuralib.widefield.preproc) rotation_ap (neuralib.registration.coordinates.FieldOfView attribute) rotation_applied (neuralib.widefield.preproc.ProcessedInfo attribute) rotation_degrees (neuralib.widefield.preproc.ProcessedInfo attribute) rotation_ml (neuralib.registration.coordinates.FieldOfView attribute) rtype (neuralib.facemap.core.RoiDict attribute) run() (neuralib.atlas.brainrender.core.BrainRenderCLI method) (neuralib.atlas.brainrender.probe.ProbeRenderCLI method) (neuralib.atlas.brainrender.roi.RoiRenderCLI method) (neuralib.scanbox.view.ScanBoxViewOptions method) (neuralib.stardist.run_2d.StarDist2DOptions method) (neuralib.widefield.align.NapariAlignmentOptions method) (neuralib.widefield.fft_view.WideFieldFFTViewOption method) (neuralib.widefield.preproc.PreprocessOptions method) (neuralib.widefield.transform.RegistrationOptions method) run_duration (neuralib.deeplabcut.core.DeepLabCutMeta attribute) run_later() (neuralib.dashboard.base.View method) run_periodic() (neuralib.dashboard.base.View method) run_rastermap() (in module neuralib.rastermap.run) run_spike_prediction() (neuralib.spikes.cascade.CascadeSpikePrediction method) run_timeout() (neuralib.dashboard.base.View method) running (neuralib.facemap.core.SVDVariables attribute) running_mask1d() (in module neuralib.locomotion.epoch) runtime_frate_check (neuralib.suite2p.core.Suite2PResult attribute)

S

s2p (neuralib.suite2p.signals.DFFSignal attribute) safe_call() (neuralib.widefield.transform.RegistrationApp method) sampling_rate (neuralib.spikes.cascade.CascadeModelConfig attribute) saturation (neuralib.facemap.core.RoiDict attribute) save() (in module neuralib.persistence.persistence) (neuralib.rastermap.core.RasterMapResult method) save_cache() (neuralib.persistence.cli_persistence.PersistenceOptions method) save_dorsal_image() (neuralib.widefield.transform.RegistrationApp method) save_f0 (neuralib.widefield.preproc.InputArguments attribute) (neuralib.widefield.preproc.PreprocessOptions attribute) save_folder (neuralib.suite2p.core.Suite2pGUIOptions attribute) save_ij_roi (neuralib.stardist.base.AbstractSegmentationOptions attribute) save_json() (in module neuralib.io.json) save_mat (neuralib.facemap.core.SVDVariables attribute) (neuralib.suite2p.core.Suite2pGUIOptions attribute) save_metadata() (neuralib.widefield.preproc.PreprocessOptions method) save_note() (neuralib.imglib.labeller.SequenceLabeller method) save_NWB (neuralib.suite2p.core.Suite2pGUIOptions attribute) save_path (neuralib.facemap.core.SVDVariables attribute) (neuralib.rastermap.core.RasterMapResult attribute) (neuralib.suite2p.core.Suite2pGUIOptions attribute) save_path0 (neuralib.suite2p.core.Suite2pGUIOptions attribute) save_persistence() (neuralib.persistence.persistence.PersistenceHandler method) save_rastermap() (in module neuralib.rastermap.core) save_root (neuralib.persistence.persistence.GzipHandler property) (neuralib.persistence.persistence.PersistenceHandler property) (neuralib.persistence.persistence.PickleHandler property) save_transform() (neuralib.widefield.transform.RegistrationApp method) savefig() (neuralib.plot.venn.VennDiagram static method) sbin (neuralib.facemap.core.SVDVariables attribute) sbx_map (neuralib.scanbox.view.ScanBoxView attribute) sbx_ndeadcols (neuralib.suite2p.core.Suite2pGUIOptions attribute) sbx_ndeadrows (neuralib.suite2p.core.Suite2pGUIOptions attribute) sbx_to_json() (in module neuralib.scanbox.core) SBXInfo (class in neuralib.scanbox.core) SBXInfo.AgcInfo (class in neuralib.scanbox.core) SBXInfo.CalibrationInfo (class in neuralib.scanbox.core) SBXInfo.ConfigInfo (class in neuralib.scanbox.core) SBXInfo.KnobbyInfo (class in neuralib.scanbox.core) SBXInfo.KnobbyPosInfo (class in neuralib.scanbox.core) SBXInfo.ObjectiveInfo (class in neuralib.scanbox.core) scanbox_version (neuralib.scanbox.core.SBXInfo attribute) ScanBoxView (class in neuralib.scanbox.view) ScanBoxViewOptions (class in neuralib.scanbox.view) scanmode (neuralib.scanbox.core.SBXInfo attribute) scatter_binx_plot() (in module neuralib.plot.plot) scatter_histplot() (in module neuralib.plot.plot) scene (neuralib.atlas.brainrender.core.BrainRenderCLI attribute) schedule (neuralib.scanbox.core.SBXInfo.KnobbyInfo attribute) schema (neuralib.util.dataframe.DataFrameWrapper property) scoremap_dir (neuralib.deeplabcut.core.DeepLabCutModelConfig attribute) Scorer (neuralib.deeplabcut.core.DeepLabCutMeta attribute) screenshot_to_tiff() (in module neuralib.scanbox.core) seg_output() (neuralib.stardist.base.AbstractSegmentationOptions method) (neuralib.stardist.run_2d.StarDist2DOptions method) segment_at_least_duration() (in module neuralib.util.segments) segment_bins() (in module neuralib.util.segments) segment_bool_mask() (in module neuralib.util.segments) segment_contains() (in module neuralib.util.segments) segment_diff() (in module neuralib.util.segments) segment_duration() (in module neuralib.util.segments) segment_epochs() (in module neuralib.util.segments) segment_expand_duration() (in module neuralib.util.segments) segment_flatten() (in module neuralib.util.segments) segment_gap() (in module neuralib.util.segments) segment_group_map() (in module neuralib.util.segments) segment_index() (in module neuralib.util.segments) segment_intersection() (in module neuralib.util.segments) segment_invert() (in module neuralib.util.segments) segment_join() (in module neuralib.util.segments) segment_join_index() (in module neuralib.util.segments) segment_map() (in module neuralib.util.segments) segment_mask() (in module neuralib.util.segments) segment_overlap() (in module neuralib.util.segments) segment_overlap_index() (in module neuralib.util.segments) segment_range() (in module neuralib.util.segments) segment_sample() (in module neuralib.util.segments) segment_union() (in module neuralib.util.segments) segment_universe() (in module neuralib.util.segments) SegmentLike (in module neuralib.util.segments) select (neuralib.dashboard.examples.view_animal.AnimalView attribute) select() (neuralib.util.dataframe.DataFrameWrapper method) select_animal (neuralib.dashboard.examples.view_all.AllView attribute) select_channel() (neuralib.imglib.array.ImageArrayWrapper method) select_date (neuralib.dashboard.examples.view_all.AllView attribute) select_hemisphere() (neuralib.widefield.ccf.DorsalCCF method) select_region() (neuralib.widefield.ccf.DorsalCCF method) send_slack_message() (in module neuralib.tools.slack_bot) sequence_path (neuralib.widefield.align.NapariAlignmentOptions attribute) SequenceFFT (class in neuralib.widefield.fft) SequenceLabeller (class in neuralib.imglib.labeller) SequenceSingularVector (class in neuralib.widefield.svd) Series (in module neuralib.typing.alias) server (neuralib.dashboard.base.BokehServer attribute) set() (neuralib.plot.tools.AnchoredScaleBar method) set_div (neuralib.dashboard.util.MsgLog property) set_visible() (neuralib.dashboard.base.ViewComponent method) setup() (neuralib.dashboard.base.View method) (neuralib.dashboard.examples.view_all.AllView method) (neuralib.dashboard.examples.view_animal.AnimalView method) (neuralib.dashboard.examples.view_figure.AnimalFigureView method)

setup_clogger() (in module neuralib.util.logging) setup_logger() (in module neuralib.util.logging) shader_style (neuralib.atlas.brainrender.core.BrainRenderCLI attribute) shank_interval (neuralib.atlas.brainrender.probe.ProbeRenderCLI attribute) shift_time() (in module neuralib.util.segments) show (neuralib.scanbox.view.ScanBoxViewOptions attribute) show() (neuralib.plot.venn.VennDiagram static method) (neuralib.scanbox.view.ScanBoxView method) show_polars_header_types() (in module neuralib.util.table) shuffle (neuralib.deeplabcut.core.DeepLabCutModelConfig attribute) shuffle_time() (in module neuralib.util.segments) shuffle_time_normal() (in module neuralib.util.segments) shuffle_time_uniform() (in module neuralib.util.segments) sig_baseline (neuralib.suite2p.core.Suite2pGUIOptions attribute) signal_baseline (neuralib.suite2p.core.Suite2PResult property) SIGNAL_TYPE (in module neuralib.suite2p.core) singular_value (neuralib.widefield.svd.SequenceSingularVector property) skew (neuralib.suite2p.core.Suite2pRoiStat attribute) slice (neuralib.rastermap.core.UserCluster attribute) slice() (neuralib.util.dataframe.DataFrameWrapper method) SLICE_DIMENSION_10um (in module neuralib.atlas.ccf.matrix) slice_id (neuralib.atlas.ccf.matrix.CCFTransMatrix attribute) slice_index (neuralib.atlas.ccf.matrix.CCFTransMatrix property) (neuralib.atlas.view.SlicePlane attribute) slice_transform_helper() (in module neuralib.atlas.ccf.matrix) slice_view (neuralib.atlas.view.SlicePlane attribute) SlicePlane (class in neuralib.atlas.view) smooth_sigma (neuralib.suite2p.core.Suite2pGUIOptions attribute) smooth_sigma_time (neuralib.suite2p.core.Suite2pGUIOptions attribute) smoothing (neuralib.spikes.cascade.CascadeModelConfig attribute) snapshot_prefix (neuralib.deeplabcut.core.DeepLabCutModelConfig attribute) snr_thresh (neuralib.suite2p.core.Suite2pGUIOptions attribute) solidity (neuralib.suite2p.core.Suite2pRoiStat attribute) soma_crop (neuralib.suite2p.core.Suite2pGUIOptions attribute) (neuralib.suite2p.core.Suite2pRoiStat attribute) sort() (neuralib.util.dataframe.DataFrameWrapper method) source (neuralib.atlas.brainrender.core.BrainRenderCLI attribute) (neuralib.atlas.util.SourceCoordinates attribute) source_counts (neuralib.atlas.ccf.dataframe.RoiClassifierDataFrame property) source_order (neuralib.atlas.brainrender.roi.RoiRenderCLI attribute) SourceCoordinates (class in neuralib.atlas.util) sources (neuralib.atlas.ccf.dataframe.RoiClassifierDataFrame property) (neuralib.atlas.ccf.dataframe.RoiSubregionDataFrame property) sparse_mode (neuralib.suite2p.core.Suite2pGUIOptions attribute) spatial_hp (neuralib.suite2p.core.Suite2pGUIOptions attribute) spatial_hp_detect (neuralib.suite2p.core.Suite2pGUIOptions attribute) spatial_hp_reg (neuralib.suite2p.core.Suite2pGUIOptions attribute) spatial_info (neuralib.locomotion.spatial.SpatialInfoResult attribute) spatial_info() (in module neuralib.locomotion.spatial) spatial_scale (neuralib.suite2p.core.Suite2pGUIOptions attribute) spatial_taper (neuralib.suite2p.core.Suite2pGUIOptions attribute) SpatialInfoResult (class in neuralib.locomotion.spatial) spatscale_pix (neuralib.suite2p.core.Suite2pGUIOptions attribute) speed_2d() (in module neuralib.locomotion.position) spikedetect (neuralib.suite2p.core.Suite2pGUIOptions attribute) spks (neuralib.suite2p.core.Suite2PResult attribute) StarDist2DOptions (class in neuralib.stardist.run_2d) STARDIST_MODEL (in module neuralib.stardist.core) stardist_point_roi_helper() (in module neuralib.stardist.core) StarDistSegmentation (class in neuralib.stardist.core) start (neuralib.deeplabcut.core.DeepLabCutMeta attribute) (neuralib.locomotion.spatial.PlaceFieldResult attribute) start() (neuralib.dashboard.base.BokehServer method) start_live_transform_plot() (neuralib.widefield.transform.RegistrationApp method) start_time (neuralib.rastermap.core.RasterOptions attribute) stat (neuralib.suite2p.core.Suite2PResult attribute) std (neuralib.suite2p.core.Suite2pRoiStat attribute) stop (neuralib.deeplabcut.core.DeepLabCutMeta attribute) stop_live_transform_plot() (neuralib.widefield.transform.RegistrationApp method) stride (neuralib.deeplabcut.core.DeepLabCutModelConfig attribute) (neuralib.widefield.preproc.BaselineInfo attribute) subfolders (neuralib.suite2p.core.Suite2pGUIOptions attribute) subpixel (neuralib.suite2p.core.Suite2pGUIOptions attribute) subregion (neuralib.atlas.ccf.dataframe.RoiSubregionDataFrame property) subset_a (neuralib.plot.venn.VennHandler attribute) subset_b (neuralib.plot.venn.VennHandler attribute) subset_overlap (neuralib.plot.venn.VennHandler attribute) subsets_percentage (neuralib.plot.venn.VennDiagram property) suffix_pattern (neuralib.widefield.preproc.InputArguments attribute) (neuralib.widefield.preproc.PreprocessOptions attribute) suite2p_version (neuralib.suite2p.core.Suite2pGUIOptions attribute) Suite2pGUIOptions (class in neuralib.suite2p.core) Suite2PResult (class in neuralib.suite2p.core) Suite2pRoiStat (class in neuralib.suite2p.core) super_neurons (neuralib.rastermap.core.RasterMapResult attribute) (neuralib.rastermap.plot.RasterMapPlot property) svd (neuralib.widefield.svd.SequenceSingularVector attribute) SVDVariables (class in neuralib.facemap.core) SwcFile (class in neuralib.morpho.swc) SwcNode (class in neuralib.morpho.swc) sx (neuralib.facemap.core.SVDVariables attribute) sxbin (neuralib.facemap.core.SVDVariables attribute) sy (neuralib.facemap.core.SVDVariables attribute) sybin (neuralib.facemap.core.SVDVariables attribute) sync_s2p_rigevent() (in module neuralib.suite2p.signals) sz (neuralib.scanbox.core.SBXInfo attribute)

T

t (neuralib.locomotion.position.CircularPosition attribute) table() (in module neuralib.io.pyh5) tail() (neuralib.util.dataframe.DataFrameWrapper method) tau (neuralib.suite2p.core.Suite2pGUIOptions attribute) text_color (neuralib.imglib.labeller.SequenceLabeller property) th_badframes (neuralib.suite2p.core.Suite2pGUIOptions attribute) threshold (neuralib.locomotion.spatial.PlaceFieldResult attribute) (neuralib.scanbox.core.SBXInfo.AgcInfo attribute) threshold_scaling (neuralib.suite2p.core.Suite2pGUIOptions attribute) tif_files (neuralib.widefield.preproc.DataInfo attribute) tif_to_gif() (in module neuralib.imglib.io) TiffBrainView (class in neuralib.dashboard.view_brain) TiffScanner (class in neuralib.scan.lsm) time (neuralib.rastermap.plot.Covariant attribute) time_bin (neuralib.rastermap.core.RasterOptions attribute) time_lag_window (neuralib.rastermap.core.RasterOptions attribute) TimeoutUpdateValue (class in neuralib.dashboard.tool) timestamp (neuralib.widefield.preproc.PreprocessMeta attribute) timing (neuralib.suite2p.core.Suite2pGUIOptions attribute) title (neuralib.atlas.brainrender.core.BrainRenderCLI attribute) (neuralib.dashboard.base.View property) (neuralib.dashboard.examples.view_all.AllView property) (neuralib.dashboard.examples.view_animal.AnimalView property) (neuralib.dashboard.examples.view_figure.AnimalFigureView property) (neuralib.plot.venn.VennDiagram property) (neuralib.tools.gspread.GoogleSpreadSheet property) (neuralib.tools.gspread.GoogleWorkSheet property) to_bias_index() (neuralib.atlas.ccf.dataframe.RoiNormalizedDataFrame method) to_boundary() (neuralib.widefield.ccf.DorsalCCF method)

to_dict() (neuralib.atlas.ccf.dataframe.RoiSubregionDataFrame method) to_gray() (neuralib.imglib.array.ImageArrayWrapper method) to_normalized() (neuralib.atlas.ccf.dataframe.RoiClassifierDataFrame method) to_npz() (neuralib.stardist.core.StarDistSegmentation method) to_numpy() (neuralib.atlas.ccf.dataframe.RoiSubregionDataFrame method) (neuralib.widefield.ccf.DorsalCCF method) to_pandas() (neuralib.tools.gspread.GoogleWorkSheet method) to_polars() (neuralib.tools.gspread.GoogleWorkSheet method) to_polygon() (neuralib.registration.coordinates.FieldOfView method) to_roi() (neuralib.cellpose.core.CellposeSegmentation method) (neuralib.stardist.core.StarDistSegmentation method) to_subregion() (neuralib.atlas.ccf.dataframe.RoiClassifierDataFrame method) to_tiff (neuralib.scanbox.view.ScanBoxViewOptions attribute) to_tiff() (neuralib.scanbox.view.ScanBoxView method) to_um() (neuralib.registration.coordinates.FieldOfView method) to_winner() (neuralib.atlas.ccf.dataframe.RoiNormalizedDataFrame method) to_zscore() (neuralib.facemap.core.KeyPointDataFrame method) total_frames (neuralib.facemap.core.KeyPointsMeta attribute) (neuralib.widefield.preproc.DataInfo attribute) total_set (neuralib.plot.venn.VennHandler attribute) tPC (neuralib.suite2p.core.Suite2pGUIOptions attribute) tqdm_joblib() (in module neuralib.util.tqdm) trace_line() (in module neuralib.util.profile) training_datasets (neuralib.spikes.cascade.CascadeModelConfig attribute) training_finished (neuralib.spikes.cascade.CascadeModelConfig attribute) training_set_fraction (neuralib.deeplabcut.core.DeepLabCutMeta attribute) tree_init (neuralib.atlas.brainrender.core.BrainRenderCLI attribute) trial_array (neuralib.locomotion.position.CircularPosition property) trial_time_index (neuralib.locomotion.position.CircularPosition attribute) two_step_registration (neuralib.suite2p.core.Suite2pGUIOptions attribute)

U

uglob() (in module neuralib.util.utils) undo_last_pair() (neuralib.widefield.transform.RegistrationApp method) unique_identifier (neuralib.morpho.swc.SwcFile property) unit (neuralib.atlas.view.SlicePlane attribute) (neuralib.registration.coordinates.CellularCoordinates attribute) (neuralib.registration.coordinates.FieldOfView attribute) unstable() (in module neuralib.util.unstable) update() (neuralib.dashboard.base.View method) (neuralib.dashboard.base.ViewComponent method) (neuralib.dashboard.examples.view_all.AllView method) (neuralib.dashboard.tool.TimeoutUpdateValue method) (neuralib.dashboard.view_brain.AbstractBrainView method) (neuralib.tools.gspread.GoogleWorkSheet method)

update_cell() (neuralib.tools.gspread.GoogleWorkSheet method) update_dorsal_from_region() (neuralib.widefield.transform.RegistrationApp method) update_live_overlay() (neuralib.widefield.transform.RegistrationApp method) update_ransac_threshold() (neuralib.widefield.transform.RegistrationApp method) upload_dataframe_to_spreadsheet() (in module neuralib.tools.gspread) use_builtin_classifier (neuralib.suite2p.core.Suite2pGUIOptions attribute) use_gpu (neuralib.widefield.preproc.InputArguments attribute) (neuralib.widefield.preproc.PreprocessOptions attribute) user_clusters (neuralib.rastermap.core.RasterMapResult attribute) UserCluster (class in neuralib.rastermap.core) usernotes (neuralib.scanbox.core.SBXInfo attribute) uv (neuralib.scanbox.core.SBXInfo.CalibrationInfo attribute)

V

v (neuralib.locomotion.position.CircularPosition attribute) validate() (neuralib.persistence.persistence.PersistenceHandler method) validate_cache() (neuralib.persistence.cli_persistence.PersistenceOptions method) validate_ccf_array() (in module neuralib.widefield.ccf) validate_concat_etl_persistence() (in module neuralib.persistence.validator) value (neuralib.rastermap.plot.Covariant attribute) (neuralib.registration.coordinates.CellularCoordinates attribute) value_column (neuralib.atlas.ccf.dataframe.RoiNormalizedDataFrame property) values() (neuralib.tools.gspread.GoogleWorkSheet method) Vcorr (neuralib.suite2p.core.Suite2pGUIOptions attribute) VennDiagram (class in neuralib.plot.venn) VennHandler (class in neuralib.plot.venn) verbose (neuralib.rastermap.core.RasterOptions attribute) (neuralib.scanbox.view.ScanBoxViewOptions attribute) (neuralib.spikes.cascade.CascadeModelConfig attribute) verbose_sorting (neuralib.rastermap.core.RasterOptions attribute)

version (neuralib.scanbox.view.ScanBoxView property) video_maker() (neuralib.atlas.brainrender.core.BrainRenderCLI method) video_output (neuralib.atlas.brainrender.core.BrainRenderCLI attribute) View (class in neuralib.dashboard.base) view() (neuralib.scan.core.AbstractScanner method) (neuralib.scan.czi.CziScanner method) (neuralib.scan.lsm.TiffScanner method) view_2d() (neuralib.imglib.array.ImageArrayWrapper method) VIEW_TYPE (in module neuralib.atlas.view) view_type (neuralib.atlas.view.AbstractSliceView attribute) ViewComponent (class in neuralib.dashboard.base) violin_boxplot() (in module neuralib.plot.plot) Vmap (neuralib.suite2p.core.Suite2pGUIOptions attribute) Vmax (neuralib.suite2p.core.Suite2pGUIOptions attribute) volscan (neuralib.scanbox.core.SBXInfo attribute) Vsplit (neuralib.suite2p.core.Suite2pGUIOptions attribute)

W

wavelength (neuralib.scanbox.core.SBXInfo.ConfigInfo attribute) weigh_negatives (neuralib.deeplabcut.core.DeepLabCutModelConfig attribute) weigh_only_present_joints (neuralib.deeplabcut.core.DeepLabCutModelConfig attribute) weigh_part_predictions (neuralib.deeplabcut.core.DeepLabCutModelConfig attribute) weight_decay (neuralib.deeplabcut.core.DeepLabCutModelConfig attribute) WideFieldFFTViewOption (class in neuralib.widefield.fft_view) width (neuralib.atlas.view.AbstractSliceView property) (neuralib.cellpose.core.CellposeSegmentation property) (neuralib.dashboard.view_brain.AbstractBrainView property) (neuralib.dashboard.view_brain.AtlasBrainView property) (neuralib.imglib.array.ImageArrayWrapper property) (neuralib.scanbox.view.ScanBoxView property) (neuralib.stardist.core.StarDistSegmentation property) (neuralib.widefield.fft.SequenceFFT property) width_mm (neuralib.atlas.view.AbstractSliceView property) width_n (neuralib.dashboard.view_brain.AtlasBrainView property) win_baseline (neuralib.suite2p.core.Suite2pGUIOptions attribute) window_baseline (neuralib.suite2p.core.Suite2PResult property) window_size (neuralib.widefield.preproc.InputArguments attribute) (neuralib.widefield.preproc.PreprocessOptions attribute) window_title (neuralib.imglib.labeller.SequenceLabeller attribute) windowsize (neuralib.spikes.cascade.CascadeModelConfig attribute) with_angle_offset() (neuralib.atlas.view.SlicePlane method) with_animal_column() (neuralib.atlas.ccf.dataframe.RoiNormalizedDataFrame method) (neuralib.atlas.ccf.dataframe.RoiSubregionDataFrame method)

with_cell_density_column() (neuralib.atlas.ccf.dataframe.RoiNormalizedDataFrame method) with_columns() (neuralib.util.dataframe.DataFrameWrapper method) with_density_column() (neuralib.atlas.ccf.dataframe.RoiNormalizedDataFrame method) with_family_columns() (neuralib.atlas.ccf.dataframe.RoiClassifierDataFrame method) with_hemisphere_column() (neuralib.atlas.ccf.dataframe.RoiClassifierDataFrame method) with_intersection() (neuralib.plot.venn.VennDiagram method) with_keypoint (neuralib.facemap.core.FaceMapResult property) with_masking() (neuralib.registration.coordinates.CellularCoordinates method) with_norm (neuralib.stardist.base.AbstractSegmentationOptions property) with_offset() (neuralib.atlas.view.SlicePlane method) with_outlier_filter() (neuralib.facemap.core.KeyPointDataFrame method) with_overlap_copy() (neuralib.atlas.ccf.dataframe.RoiClassifierDataFrame method) with_peak_filter() (neuralib.locomotion.spatial.PlaceFieldResult method) with_reliability_filter() (neuralib.locomotion.spatial.PlaceFieldResult method) with_row_index() (neuralib.util.dataframe.DataFrameWrapper method) with_run_mask1d() (neuralib.locomotion.position.CircularPosition method) with_time_range() (neuralib.locomotion.position.CircularPosition method) with_total() (neuralib.plot.venn.VennHandler method) with_tree_columns() (neuralib.atlas.ccf.dataframe.RoiClassifierDataFrame method) with_value() (neuralib.registration.coordinates.CellularCoordinates method) with_width_filter() (neuralib.locomotion.spatial.PlaceFieldResult method) worksheet_list (neuralib.tools.gspread.GoogleSpreadSheet property) write_avi() (in module neuralib.imglib.io) write_note() (neuralib.imglib.labeller.SequenceLabeller method)

X

x (neuralib.morpho.swc.SwcNode attribute) (neuralib.scanbox.core.SBXInfo.CalibrationInfo attribute) (neuralib.scanbox.core.SBXInfo.KnobbyPosInfo attribute) xbar() (neuralib.plot.tools.AxesExtendHelper method) xblock (neuralib.suite2p.core.Suite2pGUIOptions attribute) xhist() (neuralib.plot.tools.AxesExtendHelper method)

xoff (neuralib.suite2p.core.Suite2pGUIOptions attribute) xoff1 (neuralib.suite2p.core.Suite2pGUIOptions attribute) xpix (neuralib.suite2p.core.Suite2pRoiStat attribute) xrange (neuralib.facemap.core.RoiDict attribute) (neuralib.suite2p.core.Suite2pGUIOptions attribute) xrange_bin (neuralib.facemap.core.RoiDict attribute)

Y

y (neuralib.morpho.swc.SwcNode attribute) (neuralib.scanbox.core.SBXInfo.CalibrationInfo attribute) (neuralib.scanbox.core.SBXInfo.KnobbyPosInfo attribute) ybar() (neuralib.plot.tools.AxesExtendHelper method) yblock (neuralib.suite2p.core.Suite2pGUIOptions attribute) yhist() (neuralib.plot.tools.AxesExtendHelper method)

yoff (neuralib.suite2p.core.Suite2pGUIOptions attribute) yoff1 (neuralib.suite2p.core.Suite2pGUIOptions attribute) ypix (neuralib.suite2p.core.Suite2pRoiStat attribute) yrange (neuralib.facemap.core.RoiDict attribute) (neuralib.suite2p.core.Suite2pGUIOptions attribute) yrange_bin (neuralib.facemap.core.RoiDict attribute)

Z

z (neuralib.morpho.swc.SwcNode attribute) (neuralib.scanbox.core.SBXInfo.KnobbyPosInfo attribute)

z_projection() (neuralib.scan.core.AbstractScanner static method) zoom_to_fit_views() (neuralib.widefield.transform.RegistrationApp method)