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.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.imaging.registration.coordinates.CellularCoordinates method), [1] (neuralib.imaging.registration.coordinates.FieldOfView method), [1] (neuralib.imaging.scanbox.core.SBXInfo method), [1] (neuralib.imaging.scanbox.core.SBXInfo.AgcInfo method) (neuralib.imaging.scanbox.core.SBXInfo.CalibrationInfo method) (neuralib.imaging.scanbox.core.SBXInfo.ConfigInfo method) (neuralib.imaging.scanbox.core.SBXInfo.KnobbyInfo method) (neuralib.imaging.scanbox.core.SBXInfo.KnobbyPosInfo method) (neuralib.imaging.scanbox.core.SBXInfo.ObjectiveInfo method) (neuralib.imaging.scanbox.view.ScanBoxView method), [1] (neuralib.imaging.scanbox.view.ScanBoxViewOptions method) (neuralib.imaging.spikes.cascade.CascadeModelConfig method) (neuralib.imaging.spikes.cascade.CascadeSpikePrediction method), [1] (neuralib.imaging.suite2p.core.Suite2pGUIOptions method) (neuralib.imaging.suite2p.core.Suite2PResult method), [1] (neuralib.imaging.suite2p.core.Suite2pRoiStat method) (neuralib.imaging.suite2p.signals.DFFSignal method) (neuralib.imaging.widefield.align.NapariAlignmentOptions method) (neuralib.imaging.widefield.fft.SequenceFFT method), [1] (neuralib.imaging.widefield.fft_view.WideFieldFFTViewOption method) (neuralib.imaging.widefield.svd.SequenceSingularVector 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.model.rastermap.core.RasterMapResult method), [1] (neuralib.model.rastermap.core.RasterOptions method) (neuralib.model.rastermap.core.UserCluster method) (neuralib.model.rastermap.plot.Covariant method) (neuralib.model.rastermap.plot.RasterMapPlot method), [1] (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.scan.core.AbstractScanner method), [1] (neuralib.scan.czi.CziScanner method), [1] (neuralib.scan.lsm.TiffScanner method), [1] (neuralib.segmentation.base.AbstractSegmentationOptions method) (neuralib.segmentation.cellpose.core.CellposeSegmentation method), [1] (neuralib.segmentation.stardist.core.StarDistSegmentation method), [1] (neuralib.segmentation.stardist.run_2d.StarDist2DOptions method) (neuralib.tools.gspread.GoogleSpreadSheet method), [1] (neuralib.tools.gspread.GoogleWorkSheet method), [1] (neuralib.tracking.deeplabcut.core.DeepLabCutDataFrame method), [1] (neuralib.tracking.deeplabcut.core.DeepLabCutMeta method) (neuralib.tracking.deeplabcut.core.DeepLabCutModelConfig method) (neuralib.tracking.deeplabcut.core.JointDataFrame method), [1] (neuralib.tracking.facemap.core.FaceMapResult method), [1] (neuralib.tracking.facemap.core.KeyPointDataFrame method), [1] (neuralib.tracking.facemap.core.KeyPointsMeta method) (neuralib.tracking.facemap.core.PupilDict method) (neuralib.tracking.facemap.core.RoiDict method) (neuralib.tracking.facemap.core.SVDVariables method) (neuralib.util.dataframe.DataFrameWrapper method) (neuralib.util.profile.profile_test method), [1] (neuralib.util.table.Column method), [1] (neuralib.util.table.Table method), [1]

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

A

a (neuralib.imaging.scanbox.core.SBXInfo.KnobbyPosInfo attribute) abort_bit (neuralib.imaging.scanbox.core.SBXInfo attribute) AbstractBrainView (class in neuralib.dashboard.view_brain) AbstractScanner (class in neuralib.scan.core) AbstractSegmentationOptions (class in neuralib.segmentation.base) AbstractSliceView (class in neuralib.atlas.view) add_column() (neuralib.util.table.Table method) add_html_format() (in module neuralib.dashboard.util) add_intersection() (neuralib.plot.venn.VennDiagram method) add_row() (neuralib.util.table.Table method) add_section() (neuralib.util.table.Table method) add_total() (neuralib.plot.venn.VennDiagram method) affine_transform() (in module neuralib.imglib.transform) agc (neuralib.imaging.scanbox.core.SBXInfo.ConfigInfo attribute) agc_prctile (neuralib.imaging.scanbox.core.SBXInfo.AgcInfo attribute) al (neuralib.imaging.registration.coordinates.FieldOfView property) align_by_chan (neuralib.imaging.suite2p.core.Suite2pGUIOptions attribute) all_joints (neuralib.tracking.deeplabcut.core.DeepLabCutModelConfig attribute) all_joints_names (neuralib.tracking.deeplabcut.core.DeepLabCutModelConfig attribute) ALLEN_CCF_10um_BREGMA (in module neuralib.atlas.util) ALLEN_FAMILY_TYPE (in module neuralib.atlas.map) allen_to_brainrender_coord() (in module neuralib.atlas.util) allow_overlap (neuralib.imaging.suite2p.core.Suite2pGUIOptions attribute) AllView (class in neuralib.dashboard.examples.view_all) am (neuralib.imaging.registration.coordinates.FieldOfView property) anatomical_only (neuralib.imaging.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.imaging.registration.coordinates.CellularCoordinates attribute) ap_distance (neuralib.imaging.registration.coordinates.FieldOfView property) apply_transformation() (in module neuralib.imglib.transform) Area (in module neuralib.atlas.typing) area (neuralib.tracking.facemap.core.PupilDict attribute) area_line (neuralib.imaging.scanbox.core.SBXInfo attribute) area_smooth (neuralib.tracking.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.imaging.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.imaging.scanbox.core.SBXInfo method) (neuralib.model.rastermap.core.RasterMapResult method) aspect (neuralib.imaging.suite2p.core.Suite2pGUIOptions attribute) aspect_ratio (neuralib.imaging.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.imaging.spikes.cascade.CascadeSpikePrediction property) avgframe (neuralib.tracking.facemap.core.SVDVariables attribute) avgframe_reshape (neuralib.tracking.facemap.core.SVDVariables attribute) avgmotion (neuralib.tracking.facemap.core.SVDVariables attribute) avgmotion_reshape (neuralib.tracking.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.tracking.facemap.core.PupilDict attribute) AxesArray (in module neuralib.typing.alias) AxesExtendHelper (class in neuralib.plot.tools) axlen (neuralib.tracking.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.imaging.suite2p.core.Suite2pGUIOptions attribute) ballmotion (neuralib.imaging.scanbox.core.SBXInfo attribute) baseline (neuralib.imaging.suite2p.core.Suite2pGUIOptions attribute) baseline_fluctuation (neuralib.imaging.suite2p.signals.DFFSignal property) batch_mode (neuralib.segmentation.base.AbstractSegmentationOptions property) batch_size (neuralib.imaging.spikes.cascade.CascadeModelConfig attribute) (neuralib.imaging.suite2p.core.Suite2pGUIOptions attribute) (neuralib.tracking.deeplabcut.core.DeepLabCutMeta attribute) (neuralib.tracking.deeplabcut.core.DeepLabCutModelConfig attribute) (neuralib.tracking.facemap.core.KeyPointsMeta attribute) bbox (neuralib.tracking.facemap.core.KeyPointsMeta attribute) before_frac (neuralib.imaging.spikes.cascade.CascadeModelConfig attribute) bidi_corrected (neuralib.imaging.suite2p.core.Suite2pGUIOptions attribute) bidiphase (neuralib.imaging.suite2p.core.Suite2pGUIOptions attribute) binarize() (neuralib.imglib.array.ImageArrayWrapper method)

binsize (neuralib.model.rastermap.core.UserCluster attribute) blink (neuralib.tracking.facemap.core.SVDVariables attribute) block_size (neuralib.imaging.suite2p.core.Suite2pGUIOptions attribute) bodyparts (neuralib.tracking.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.imaging.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.imaging.scanbox.core.SBXInfo attribute)

C

calc_signal_baseline() (in module neuralib.imaging.suite2p.signals) CALCIUM_TYPE (in module neuralib.imaging.suite2p.core) calibration (neuralib.imaging.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.imaging.spikes.cascade) cascade_predict() (in module neuralib.imaging.spikes.cascade) CascadeModelConfig (class in neuralib.imaging.spikes.cascade) CascadeSpikePrediction (class in neuralib.imaging.spikes.cascade) causal_kernel (neuralib.imaging.spikes.cascade.CascadeModelConfig attribute) CCFTransMatrix (class in neuralib.atlas.ccf.matrix) cell_prob (neuralib.imaging.suite2p.core.Suite2PResult property) cell_prob_thres (neuralib.imaging.suite2p.core.Suite2PResult attribute) cellpose_point_roi_helper() (in module neuralib.segmentation.cellpose.core) CellposeSegmentation (class in neuralib.segmentation.cellpose.core) cells (neuralib.util.table.Column property) CellularCoordinates (class in neuralib.imaging.registration.coordinates) chan2_thres (neuralib.imaging.suite2p.core.Suite2pGUIOptions attribute) chan_choose (neuralib.segmentation.cellpose.core.CellposeSegmentation property) chance_level (neuralib.plot.venn.VennHandler property) change_html_format() (in module neuralib.dashboard.util) Channel (in module neuralib.atlas.typing) channel (neuralib.imaging.scanbox.view.ScanBoxViewOptions attribute) channel_counts (neuralib.atlas.ccf.dataframe.RoiClassifierDataFrame property) channels (neuralib.atlas.ccf.dataframe.RoiClassifierDataFrame property) (neuralib.imaging.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) 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.imaging.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_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.imaging.widefield.align.NapariAlignmentOptions attribute) (neuralib.model.rastermap.core.UserCluster attribute) (neuralib.tracking.facemap.core.RoiDict attribute)

ColorBarView (class in neuralib.dashboard.util) Column (class in neuralib.util.table) columns (neuralib.util.dataframe.DataFrameWrapper property) (neuralib.util.table.Table attribute) com (neuralib.tracking.facemap.core.PupilDict attribute) com_smooth (neuralib.tracking.facemap.core.PupilDict attribute) combined (neuralib.imaging.suite2p.core.Suite2pGUIOptions attribute) compact (neuralib.imaging.suite2p.core.Suite2pRoiStat attribute) component (neuralib.imaging.widefield.fft.SequenceFFT property) compute_cache() (neuralib.persistence.cli_persistence.PersistenceOptions method) compute_singular_vector() (in module neuralib.imaging.widefield.svd) concat_etl() (neuralib.persistence.validator.ETLConcatable method) config (neuralib.imaging.scanbox.core.SBXInfo attribute) config_file (neuralib.imaging.spikes.cascade.CascadeSpikePrediction property) connected (neuralib.imaging.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) coor_on() (neuralib.atlas.view.AbstractSliceView method) coord_abs (neuralib.imaging.scanbox.core.SBXInfo.ConfigInfo attribute) coord_rel (neuralib.imaging.scanbox.core.SBXInfo.ConfigInfo attribute) coordinate_space (neuralib.atlas.brainrender.core.BrainRenderCLI attribute) coordinates (neuralib.atlas.util.SourceCoordinates attribute) copy() (neuralib.util.table.Column method) cords (neuralib.segmentation.stardist.core.StarDistSegmentation property) corners (neuralib.imaging.registration.coordinates.FieldOfView attribute) corrXY (neuralib.imaging.suite2p.core.Suite2pGUIOptions attribute) corrXY1 (neuralib.imaging.suite2p.core.Suite2pGUIOptions attribute) Covariant (class in neuralib.model.rastermap.plot) create_date_validate() (in module neuralib.persistence.validator) create_fn() (in module neuralib.util.func) crop_pad (neuralib.tracking.deeplabcut.core.DeepLabCutModelConfig attribute) cropping (neuralib.tracking.deeplabcut.core.DeepLabCutMeta attribute) cropping_parameters (neuralib.tracking.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_path (neuralib.imaging.suite2p.core.Suite2pGUIOptions attribute) DATA_TYPE (in module neuralib.model.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.tracking.deeplabcut.core.DeepLabCutDataFrame method) (neuralib.tracking.deeplabcut.core.JointDataFrame method) (neuralib.tracking.facemap.core.KeyPointDataFrame method) (neuralib.util.dataframe.DataFrameWrapper method) DataFrameWrapper (class in neuralib.util.dataframe) DataIndex (in module neuralib.tools.gspread) dataset (neuralib.tracking.deeplabcut.core.DeepLabCutModelConfig attribute) dataset_type (neuralib.tracking.deeplabcut.core.DeepLabCutModelConfig attribute) date_proc (neuralib.imaging.suite2p.core.Suite2pGUIOptions attribute) DeepLabCutDataFrame (class in neuralib.tracking.deeplabcut.core) DeepLabCutMeta (class in neuralib.tracking.deeplabcut.core) DeepLabCutModelConfig (class in neuralib.tracking.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.tracking.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.imaging.suite2p.core.Suite2pGUIOptions attribute) delta (neuralib.imaging.scanbox.core.SBXInfo.CalibrationInfo attribute) delta_xy (neuralib.atlas.ccf.matrix.CCFTransMatrix property) denoise (neuralib.imaging.suite2p.core.Suite2pGUIOptions attribute) denoise() (neuralib.imglib.array.ImageArrayWrapper method) dense_expansion (neuralib.imaging.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.imaging.scanbox.view.ScanBoxViewOptions attribute) (neuralib.imaging.widefield.align.NapariAlignmentOptions attribute) (neuralib.imaging.widefield.fft_view.WideFieldFFTViewOption attribute) (neuralib.segmentation.base.AbstractSegmentationOptions attribute) (neuralib.segmentation.stardist.run_2d.StarDist2DOptions attribute)

deterministic (neuralib.tracking.deeplabcut.core.DeepLabCutModelConfig attribute) dff (neuralib.imaging.suite2p.signals.DFFSignal attribute) dff_baseline (neuralib.imaging.suite2p.signals.DFFSignal property) dff_signal() (in module neuralib.imaging.suite2p.signals) DFFSignal (class in neuralib.imaging.suite2p.signals) dh (neuralib.atlas.view.SlicePlane attribute) diag_heatmap() (in module neuralib.plot.plot) diag_histplot() (in module neuralib.plot.plot) diameter (neuralib.imaging.suite2p.core.Suite2pGUIOptions attribute) (neuralib.segmentation.cellpose.core.CellposeSegmentation property) DimCode (in module neuralib.scan.core) 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.imaging.scanbox.view.ScanBoxViewOptions attribute) (neuralib.imaging.suite2p.core.Suite2PResult attribute) (neuralib.segmentation.base.AbstractSegmentationOptions attribute) directory_suffix (neuralib.segmentation.base.AbstractSegmentationOptions attribute) DiscreteColorMapper (class in neuralib.plot.colormap) do_bidiphase (neuralib.imaging.suite2p.core.Suite2pGUIOptions attribute) do_registration (neuralib.imaging.suite2p.core.Suite2pGUIOptions attribute) document (neuralib.dashboard.base.View attribute) dorsal_map_path (neuralib.imaging.widefield.align.NapariAlignmentOptions attribute) 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.model.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.tracking.facemap.core.RoiDict attribute) embedding (neuralib.model.rastermap.core.RasterMapResult attribute) empty_cache() (neuralib.persistence.cli_persistence.PersistenceOptions method) enable (neuralib.imaging.scanbox.core.SBXInfo.AgcInfo attribute) end_time (neuralib.model.rastermap.core.RasterOptions attribute) enhance_contrast() (neuralib.imglib.array.ImageArrayWrapper method) enqueue_message() (neuralib.imglib.labeller.SequenceLabeller method) ensemble_size (neuralib.imaging.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.segmentation.base.AbstractSegmentationOptions method) (neuralib.segmentation.stardist.run_2d.StarDist2DOptions method) EX_GROUP_SOURCE (neuralib.segmentation.base.AbstractSegmentationOptions attribute) expand (neuralib.util.table.Table property) export() (neuralib.atlas.brainrender.core.BrainRenderCLI class method)

F

f (neuralib.imaging.suite2p.signals.DFFSignal attribute) f0 (neuralib.imaging.suite2p.signals.DFFSignal attribute) f_neu (neuralib.imaging.suite2p.core.Suite2PResult attribute) f_raw (neuralib.imaging.suite2p.core.Suite2PResult attribute) FaceMapResult (class in neuralib.tracking.facemap.core) fast_disk (neuralib.imaging.suite2p.core.Suite2pGUIOptions attribute) fcorr (neuralib.imaging.suite2p.signals.DFFSignal attribute) fg_fraction (neuralib.tracking.deeplabcut.core.DeepLabCutModelConfig attribute) field() (in module neuralib.persistence.persistence) FieldOfView (class in neuralib.imaging.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.imaging.widefield.fft_view.WideFieldFFTViewOption attribute) (neuralib.io.pyh5.H5pyData property) (neuralib.segmentation.base.AbstractSegmentationOptions attribute) file_mode (neuralib.segmentation.base.AbstractSegmentationOptions property) file_type (neuralib.scan.lsm.TiffScanner property) filelist (neuralib.imaging.suite2p.core.Suite2pGUIOptions attribute) filename (neuralib.model.rastermap.core.RasterMapResult attribute) (neuralib.segmentation.cellpose.core.CellposeSegmentation property) (neuralib.segmentation.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.tracking.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.imaging.spikes.cascade.CascadeModelConfig attribute) filter_overlap() (neuralib.atlas.ccf.dataframe.RoiSubregionDataFrame method) filter_sizes (neuralib.imaging.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) flexible (neuralib.util.table.Column property) fliplr() (neuralib.imglib.array.ImageArrayWrapper method) flipud() (neuralib.imglib.array.ImageArrayWrapper method) flows (neuralib.segmentation.cellpose.core.CellposeSegmentation property) fneu (neuralib.imaging.suite2p.signals.DFFSignal attribute) footer (neuralib.util.table.Column attribute) footer_style (neuralib.util.table.Column attribute) footprint (neuralib.imaging.suite2p.core.Suite2pRoiStat attribute) force_refImg (neuralib.imaging.suite2p.core.Suite2pGUIOptions attribute) force_sktiff (neuralib.imaging.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.segmentation.base.AbstractSegmentationOptions method) fov_distance (neuralib.imaging.scanbox.core.SBXInfo property) fprint() (in module neuralib.util.verbose) fps (neuralib.tracking.deeplabcut.core.DeepLabCutDataFrame property) (neuralib.tracking.deeplabcut.core.DeepLabCutMeta attribute) frame_dimensions (neuralib.tracking.deeplabcut.core.DeepLabCutMeta attribute) frame_times (neuralib.imaging.scanbox.core.SBXInfo.ConfigInfo attribute) frames (neuralib.imaging.scanbox.core.SBXInfo.ConfigInfo attribute) (neuralib.imaging.scanbox.view.ScanBoxViewOptions attribute) frames_include (neuralib.imaging.suite2p.core.Suite2pGUIOptions attribute) from_dict() (in module neuralib.persistence.persistence) from_directory() (neuralib.tracking.facemap.core.FaceMapResult class method) fs (neuralib.imaging.suite2p.core.Suite2pGUIOptions attribute) (neuralib.imaging.suite2p.core.Suite2PResult property) fullSVD (neuralib.tracking.facemap.core.SVDVariables attribute) functional_chan (neuralib.imaging.suite2p.core.Suite2pGUIOptions attribute)

G

gain_resonant_mult (neuralib.imaging.scanbox.core.SBXInfo.CalibrationInfo attribute) gaussian_blur() (neuralib.imglib.array.ImageArrayWrapper method) gen_offset_matrix() (neuralib.dashboard.view_brain.AtlasBrainView method) get() (neuralib.tracking.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.imaging.spikes.cascade.CascadeSpikePrediction method) get_blink() (neuralib.tracking.facemap.core.FaceMapResult method) get_cell() (neuralib.tools.gspread.GoogleWorkSheet method) get_cellular_coordinate() (in module neuralib.imaging.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.imaging.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.imaging.registration.coordinates) get_freq_map() (neuralib.imaging.widefield.fft.SequenceFFT method) get_func_default() (in module neuralib.util.func) get_intensity() (neuralib.imaging.widefield.fft.SequenceFFT method) get_intersection() (neuralib.plot.venn.VennDiagram method) get_joint() (neuralib.tracking.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.imaging.suite2p.core.Suite2PResult method) get_neuron_signal() (in module neuralib.imaging.suite2p.signals) get_options_and_cache() (in module neuralib.persistence.cli_persistence) get_percentile_value() (in module neuralib.imglib.norm) get_phase() (neuralib.imaging.widefield.fft.SequenceFFT method) get_pupil() (neuralib.tracking.facemap.core.FaceMapResult method) get_pupil_area() (neuralib.tracking.facemap.core.FaceMapResult method) get_pupil_center_of_mass() (neuralib.tracking.facemap.core.FaceMapResult method) get_pupil_location_movement() (neuralib.tracking.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.imaging.suite2p.core.Suite2PResult method) get_row_style() (neuralib.util.table.Table method) get_s2p_coords() (in module neuralib.imaging.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.imaging.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.tracking.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) grey2rgb() (in module neuralib.imglib.color) grid() (neuralib.util.table.Table class method) grid_subplots() (in module neuralib.plot.plot) grid_upsample (neuralib.model.rastermap.core.RasterOptions attribute) grid_x (neuralib.atlas.view.AbstractSliceView attribute) grid_y (neuralib.atlas.view.AbstractSliceView attribute) group() (in module neuralib.io.pyh5) group_by() (neuralib.util.dataframe.DataFrameWrapper method) GROUP_CACHE (neuralib.persistence.cli_persistence.PersistenceOptions attribute) GROUP_IO (neuralib.segmentation.base.AbstractSegmentationOptions 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_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.imaging.suite2p.core.Suite2pGUIOptions attribute) h5py_key (neuralib.imaging.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.imaging.suite2p.core.Suite2PResult property) has_gap() (in module neuralib.util.segments) has_worksheet() (neuralib.tools.gspread.GoogleSpreadSheet method) head() (neuralib.util.dataframe.DataFrameWrapper method) header (neuralib.util.table.Column attribute) header_style (neuralib.util.table.Column attribute) headers (neuralib.tools.gspread.GoogleWorkSheet property) height (neuralib.atlas.view.AbstractSliceView property) (neuralib.dashboard.view_brain.AbstractBrainView property) (neuralib.dashboard.view_brain.AtlasBrainView property) (neuralib.imaging.scanbox.view.ScanBoxView property) (neuralib.imaging.widefield.fft.SequenceFFT property) (neuralib.imglib.array.ImageArrayWrapper property) (neuralib.segmentation.cellpose.core.CellposeSegmentation property) (neuralib.segmentation.stardist.core.StarDistSegmentation 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) HEMISPHERE_TYPE (in module neuralib.atlas.typing) high_pass (neuralib.imaging.suite2p.core.Suite2pGUIOptions attribute) highlight (neuralib.util.table.Column attribute) host_name (neuralib.imaging.scanbox.core.SBXInfo.ConfigInfo attribute)

I

identifier (neuralib.morpho.swc.SwcNode attribute) identifier_name (neuralib.morpho.swc.SwcNode property) ids (neuralib.model.rastermap.core.UserCluster attribute) ihop (neuralib.imaging.suite2p.core.Suite2pGUIOptions attribute) ij_roi_output() (neuralib.segmentation.base.AbstractSegmentationOptions method) image (neuralib.atlas.view.SlicePlane property) (neuralib.scan.lsm.TiffScanner property) image_array() (in module neuralib.imglib.array) image_height (neuralib.imaging.suite2p.core.Suite2PResult property) image_mean (neuralib.imaging.suite2p.core.Suite2PResult property) image_mean_ch2 (neuralib.imaging.suite2p.core.Suite2PResult property) image_size (neuralib.tracking.facemap.core.KeyPointsMeta attribute) image_width (neuralib.imaging.suite2p.core.Suite2PResult property) ImageArrayWrapper (class in neuralib.imglib.array) implant_depth (neuralib.atlas.brainrender.probe.ProbeRenderCLI attribute) indicator_tau (neuralib.imaging.suite2p.core.Suite2PResult property) inference_speed (neuralib.tracking.facemap.core.KeyPointsMeta attribute) info (neuralib.imaging.scanbox.view.ScanBoxView attribute) init_weights (neuralib.tracking.deeplabcut.core.DeepLabCutModelConfig attribute) inner_neuropil_radius (neuralib.imaging.suite2p.core.Suite2pGUIOptions attribute) input_format (neuralib.imaging.suite2p.core.Suite2pGUIOptions attribute) 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.tracking.deeplabcut.core.DeepLabCutModelConfig attribute) intermediate_supervision_layer (neuralib.tracking.deeplabcut.core.DeepLabCutModelConfig attribute) interp() (neuralib.atlas.brainrender.probe.ProbeShank method) interp1d_nan() (in module neuralib.util.interp)

interp_activity() (neuralib.model.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.segmentation.base.AbstractSegmentationOptions attribute) inverse_lut (neuralib.atlas.brainrender.roi.RoiRenderCLI attribute) invert_axes() (neuralib.imaging.registration.coordinates.FieldOfView method) iROI (neuralib.tracking.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.segmentation.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.imaging.suite2p.core.Suite2PResult attribute) isort (neuralib.model.rastermap.core.RasterMapResult attribute) iter_source_coordinates() (in module neuralib.atlas.util) iteration (neuralib.tracking.deeplabcut.core.DeepLabCutMeta attribute) ivid (neuralib.tracking.facemap.core.RoiDict attribute)

J

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

joints (neuralib.tracking.deeplabcut.core.DeepLabCutDataFrame property) JsonEncodeHandler (class in neuralib.io.json) jump_mask2d() (in module neuralib.locomotion.epoch) justify (neuralib.util.table.Column attribute)

K

keep_movie_raw (neuralib.imaging.suite2p.core.Suite2pGUIOptions attribute) KeyPoint (in module neuralib.tracking.facemap.core) KeyPointDataFrame (class in neuralib.tracking.facemap.core)

keypoints (neuralib.tracking.facemap.core.FaceMapResult property) KeyPointsMeta (class in neuralib.tracking.facemap.core) keys_with_value() (in module neuralib.util.utils) knobby (neuralib.imaging.scanbox.core.SBXInfo.ConfigInfo attribute)

L

labels (neuralib.plot.venn.VennDiagram property) (neuralib.segmentation.stardist.core.StarDistSegmentation property) lam (neuralib.imaging.suite2p.core.Suite2pRoiStat attribute) lam_percentile (neuralib.imaging.suite2p.core.Suite2pGUIOptions attribute) laser_power (neuralib.imaging.scanbox.core.SBXInfo.ConfigInfo attribute) laser_power_perc (neuralib.imaging.scanbox.core.SBXInfo.ConfigInfo attribute) launch_napari() (neuralib.segmentation.base.AbstractSegmentationOptions method) (neuralib.segmentation.stardist.run_2d.StarDist2DOptions method) lazy() (neuralib.util.dataframe.DataFrameWrapper method) left_vector (neuralib.imaging.widefield.svd.SequenceSingularVector attribute) limit() (neuralib.util.dataframe.DataFrameWrapper method) lines (neuralib.imaging.scanbox.core.SBXInfo.ConfigInfo attribute) list_renders() (neuralib.dashboard.base.ViewComponent method) load() (in module neuralib.persistence.persistence) (neuralib.imaging.scanbox.core.SBXInfo class method) (neuralib.imaging.suite2p.core.Suite2PResult class method) (neuralib.model.rastermap.core.RasterMapResult class method) (neuralib.morpho.swc.SwcFile class method) (neuralib.segmentation.cellpose.core.CellposeSegmentation class method) (neuralib.segmentation.stardist.core.StarDistSegmentation class 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_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_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_sequence() (in module neuralib.imglib.io) load_sequences() (neuralib.imglib.labeller.SequenceLabeller class method) load_total_neuron_number() (neuralib.imaging.suite2p.core.Suite2PResult class method) load_transform_matrix() (in module neuralib.atlas.ccf.matrix) local_maxima() (neuralib.imglib.array.ImageArrayWrapper method) locality (neuralib.model.rastermap.core.RasterOptions attribute) location_refinement (neuralib.tracking.deeplabcut.core.DeepLabCutModelConfig attribute) locref_huber_loss (neuralib.tracking.deeplabcut.core.DeepLabCutModelConfig attribute) locref_loss_weight (neuralib.tracking.deeplabcut.core.DeepLabCutModelConfig attribute) locref_stdev (neuralib.tracking.deeplabcut.core.DeepLabCutModelConfig attribute) log_dir (neuralib.tracking.deeplabcut.core.DeepLabCutModelConfig attribute) logger (neuralib.atlas.brainrender.core.BrainRenderCLI attribute) LOGGING_IO_LEVEL (in module neuralib.util.logging) look_one_level_down (neuralib.imaging.suite2p.core.Suite2pGUIOptions attribute) loss_function (neuralib.imaging.spikes.cascade.CascadeModelConfig attribute) lsm_file() (in module neuralib.scan.lsm) Lx (neuralib.imaging.suite2p.core.Suite2pGUIOptions attribute) (neuralib.tracking.facemap.core.SVDVariables attribute) LXbin (neuralib.tracking.facemap.core.SVDVariables attribute) Lxbin (neuralib.tracking.facemap.core.SVDVariables attribute) Lxc (neuralib.imaging.suite2p.core.Suite2pGUIOptions attribute) Ly (neuralib.imaging.suite2p.core.Suite2pGUIOptions attribute) (neuralib.tracking.facemap.core.SVDVariables attribute) LYbin (neuralib.tracking.facemap.core.SVDVariables attribute) Lybin (neuralib.tracking.facemap.core.SVDVariables attribute) Lyc (neuralib.imaging.suite2p.core.Suite2pGUIOptions attribute)

M

magidx (neuralib.imaging.scanbox.core.SBXInfo property) magnification (neuralib.imaging.scanbox.core.SBXInfo.ConfigInfo attribute) magnification_list (neuralib.imaging.scanbox.core.SBXInfo.ConfigInfo attribute) main() (neuralib.imglib.labeller.SequenceLabeller method) map_brainrender() (neuralib.atlas.brainrender.probe.ProbeShank method) mask_probability() (neuralib.segmentation.stardist.core.StarDistSegmentation method) masking_time() (neuralib.model.rastermap.plot.Covariant method) masks (neuralib.segmentation.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.imaging.suite2p.core.Suite2pGUIOptions attribute) max_overlap (neuralib.imaging.suite2p.core.Suite2pGUIOptions attribute) max_proj (neuralib.imaging.suite2p.core.Suite2pGUIOptions attribute) max_projection_axis (neuralib.atlas.view.AbstractSliceView property) max_width (neuralib.util.table.Column attribute) maxregshift (neuralib.imaging.suite2p.core.Suite2pGUIOptions attribute) maxregshiftNR (neuralib.imaging.suite2p.core.Suite2pGUIOptions attribute) mean_pixel (neuralib.tracking.deeplabcut.core.DeepLabCutModelConfig attribute) mean_time (neuralib.model.rastermap.core.RasterOptions attribute) meanImg (neuralib.imaging.suite2p.core.Suite2pGUIOptions attribute) meanImg_chan2 (neuralib.imaging.suite2p.core.Suite2pGUIOptions attribute) meanImgE (neuralib.imaging.suite2p.core.Suite2pGUIOptions attribute) med (neuralib.imaging.suite2p.core.Suite2pRoiStat attribute) merge_until_level() (in module neuralib.atlas.map) mesoscan (neuralib.imaging.suite2p.core.Suite2pGUIOptions attribute) messages (neuralib.imaging.scanbox.core.SBXInfo attribute) meta (neuralib.imaging.scanbox.view.ScanBoxView property) (neuralib.tracking.deeplabcut.core.DeepLabCutDataFrame property) metadata (neuralib.scan.core.AbstractScanner property) min_neuropil_pixels (neuralib.imaging.suite2p.core.Suite2pGUIOptions attribute) min_width (neuralib.util.table.Column attribute) mirror (neuralib.tracking.deeplabcut.core.DeepLabCutModelConfig attribute) mkdir_version() (in module neuralib.io.output) ml (neuralib.atlas.util.SourceCoordinates property) (neuralib.imaging.registration.coordinates.CellularCoordinates attribute) ml_distance (neuralib.imaging.registration.coordinates.FieldOfView property) model (neuralib.segmentation.base.AbstractSegmentationOptions attribute) (neuralib.segmentation.stardist.core.StarDistSegmentation property) (neuralib.segmentation.stardist.run_2d.StarDist2DOptions attribute) model_config (neuralib.tracking.deeplabcut.core.DeepLabCutDataFrame property) (neuralib.tracking.deeplabcut.core.DeepLabCutMeta attribute) model_dir (neuralib.imaging.spikes.cascade.CascadeSpikePrediction property) model_link (neuralib.imaging.spikes.cascade.CascadeSpikePrediction property) model_name (neuralib.imaging.spikes.cascade.CascadeModelConfig attribute)

module neuralib.atlas neuralib.atlas.brainrender neuralib.atlas.ccf neuralib.atlas.cellatlas neuralib.dashboard neuralib.dashboard.examples neuralib.imaging neuralib.imaging.registration neuralib.imaging.scanbox neuralib.imaging.spikes neuralib.imaging.suite2p neuralib.imaging.widefield neuralib.imglib neuralib.io neuralib.locomotion neuralib.model neuralib.model.bayes_decoding neuralib.model.rastermap neuralib.morpho neuralib.persistence neuralib.plot neuralib.scan neuralib.segmentation neuralib.segmentation.cellpose neuralib.segmentation.stardist neuralib.tools neuralib.tracking neuralib.tracking.deeplabcut neuralib.tracking.facemap neuralib.typing neuralib.util motion (neuralib.tracking.facemap.core.SVDVariables attribute) motMask (neuralib.tracking.facemap.core.SVDVariables attribute) motMask_reshape (neuralib.tracking.facemap.core.SVDVariables attribute) motSv (neuralib.tracking.facemap.core.SVDVariables attribute) motSVD (neuralib.tracking.facemap.core.SVDVariables attribute) move_bin (neuralib.imaging.suite2p.core.Suite2pGUIOptions attribute) movMask (neuralib.tracking.facemap.core.SVDVariables attribute) movMask_reshape (neuralib.tracking.facemap.core.SVDVariables attribute) movSv (neuralib.tracking.facemap.core.SVDVariables attribute) movSVD (neuralib.tracking.facemap.core.SVDVariables attribute) mrs (neuralib.imaging.suite2p.core.Suite2pRoiStat attribute) mrs0 (neuralib.imaging.suite2p.core.Suite2pRoiStat attribute) MsgLog (class in neuralib.dashboard.util) multiplane_parallel (neuralib.imaging.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.imaging.scanbox.view.ScanBoxView property) n_clusters (neuralib.model.rastermap.core.RasterMapResult property) (neuralib.model.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.imaging.suite2p.core.Suite2PResult property) n_frames (neuralib.imaging.scanbox.view.ScanBoxView property) (neuralib.imaging.widefield.fft.SequenceFFT property) (neuralib.imglib.labeller.SequenceLabeller property) n_ml (neuralib.atlas.view.AbstractSliceView property) (neuralib.dashboard.view_brain.AtlasBrainView property) n_neurons (neuralib.imaging.suite2p.core.Suite2PResult property) n_PCs (neuralib.model.rastermap.core.RasterOptions attribute) n_plane (neuralib.imaging.suite2p.core.Suite2PResult property) n_planes (neuralib.atlas.view.AbstractSliceView property) (neuralib.imaging.scanbox.view.ScanBoxView property) n_red_neuron (neuralib.imaging.suite2p.core.Suite2PResult property) n_samples (neuralib.model.rastermap.core.RasterMapResult property) n_scenes (neuralib.scan.core.AbstractScanner property) (neuralib.scan.czi.CziScanner property) (neuralib.scan.lsm.TiffScanner property) n_segmentation (neuralib.segmentation.cellpose.core.CellposeSegmentation property) (neuralib.segmentation.stardist.core.StarDistSegmentation property) n_shanks (neuralib.atlas.brainrender.probe.ProbeShank property) n_sources (neuralib.atlas.ccf.dataframe.RoiClassifierDataFrame property) n_splits (neuralib.model.rastermap.core.RasterOptions attribute) n_subregion (neuralib.atlas.ccf.dataframe.RoiSubregionDataFrame property) name (neuralib.imaging.scanbox.core.SBXInfo.ObjectiveInfo attribute) (neuralib.model.rastermap.plot.Covariant attribute) nan_masks (neuralib.segmentation.cellpose.core.CellposeSegmentation property) nan_outlines (neuralib.segmentation.cellpose.core.CellposeSegmentation property) napari_view (neuralib.segmentation.base.AbstractSegmentationOptions attribute) NapariAlignmentOptions (class in neuralib.imaging.widefield.align) nbinned (neuralib.imaging.suite2p.core.Suite2pGUIOptions attribute) nblocks (neuralib.imaging.suite2p.core.Suite2pGUIOptions attribute) nchan (neuralib.imaging.scanbox.core.SBXInfo attribute) nchannels (neuralib.imaging.suite2p.core.Suite2pGUIOptions attribute) net_type (neuralib.tracking.deeplabcut.core.DeepLabCutModelConfig attribute) neucoeff (neuralib.imaging.suite2p.core.Suite2pGUIOptions attribute) (neuralib.imaging.suite2p.core.Suite2PResult property) neuralib.atlas module neuralib.atlas.brainrender module neuralib.atlas.ccf module neuralib.atlas.cellatlas module neuralib.dashboard module neuralib.dashboard.examples module neuralib.imaging module neuralib.imaging.registration module neuralib.imaging.scanbox module neuralib.imaging.spikes module neuralib.imaging.suite2p module neuralib.imaging.widefield module neuralib.imglib module

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

O

oasis_dcnv() (in module neuralib.imaging.spikes.oasis) oasis_matrix() (in module neuralib.imaging.spikes.oasis) objective (neuralib.imaging.scanbox.core.SBXInfo attribute) (neuralib.imaging.scanbox.core.SBXInfo.ConfigInfo attribute) objective_type (neuralib.imaging.scanbox.core.SBXInfo.ConfigInfo 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_message() (neuralib.dashboard.base.View method) (neuralib.dashboard.util.MsgLog method) on_select_animal() (neuralib.dashboard.examples.view_all.AllView method)

on_select_date() (neuralib.dashboard.examples.view_all.AllView method) oneP_reg (neuralib.imaging.suite2p.core.Suite2pGUIOptions attribute) only_source (neuralib.atlas.brainrender.roi.RoiRenderCLI attribute) ops (neuralib.imaging.suite2p.core.Suite2PResult attribute) (neuralib.model.rastermap.core.RasterMapResult attribute) ops_path (neuralib.imaging.suite2p.core.Suite2pGUIOptions attribute) optimizer (neuralib.imaging.spikes.cascade.CascadeModelConfig attribute) (neuralib.tracking.deeplabcut.core.DeepLabCutModelConfig attribute) opto2pow (neuralib.imaging.scanbox.core.SBXInfo attribute) otparam (neuralib.imaging.scanbox.core.SBXInfo attribute) otwave (neuralib.imaging.scanbox.core.SBXInfo attribute) otwave_um (neuralib.imaging.scanbox.core.SBXInfo attribute) otwavestyle (neuralib.imaging.scanbox.core.SBXInfo attribute) outlines (neuralib.segmentation.cellpose.core.CellposeSegmentation property) output (neuralib.atlas.brainrender.core.BrainRenderCLI attribute) overflow (neuralib.util.table.Column attribute) overlap (neuralib.imaging.suite2p.core.Suite2pRoiStat attribute)

P

p (neuralib.locomotion.position.CircularPosition attribute) pad_fft (neuralib.imaging.suite2p.core.Suite2pGUIOptions attribute) padding (neuralib.util.table.Table property) page() (neuralib.dashboard.base.BokehServer method) pairwise_huber_loss (neuralib.tracking.deeplabcut.core.DeepLabCutModelConfig attribute) pairwise_predict (neuralib.tracking.deeplabcut.core.DeepLabCutModelConfig attribute) parent (neuralib.morpho.swc.SwcNode attribute) parents (neuralib.morpho.swc.SwcFile property) partaffinityfield_predict (neuralib.tracking.deeplabcut.core.DeepLabCutModelConfig attribute) partition_by() (neuralib.util.dataframe.DataFrameWrapper method) PathLike (in module neuralib.typing.alias) perpendicular (neuralib.imaging.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) PickleHandler (class in neuralib.persistence.persistence) pipe() (neuralib.util.dataframe.DataFrameWrapper method) pl (neuralib.imaging.registration.coordinates.FieldOfView property) place_bayes() (in module neuralib.model.bayes_decoding.position) placeholder_1 (neuralib.imaging.spikes.cascade.CascadeModelConfig attribute) placeholder_2 (neuralib.imaging.spikes.cascade.CascadeModelConfig attribute) PLANE (neuralib.dashboard.view_brain.AtlasBrainView attribute) plane (neuralib.dashboard.view_brain.AtlasBrainView property) (neuralib.imaging.scanbox.view.ScanBoxViewOptions attribute) plane() (neuralib.atlas.view.AbstractSliceView method) plane_at() (neuralib.atlas.view.AbstractSliceView method) plane_index (neuralib.imaging.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) 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.model.rastermap.plot) plot_cmap_time_series() (in module neuralib.tracking.facemap.plot) plot_facemap_keypoints() (in module neuralib.tracking.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.model.rastermap.plot) (neuralib.model.rastermap.plot.RasterMapPlot method) plot_retinotopic_maps() (in module neuralib.imaging.widefield.plot) plot_segments() (neuralib.model.rastermap.plot.RasterMapPlot method) plot_soma_center() (in module neuralib.imaging.suite2p.plot) plot_structure_tree() (in module neuralib.atlas.plot) plot_sunburst_acronym() (in module neuralib.atlas.plot) plot_swc() (in module neuralib.morpho.swc) plot_wfield_spatial() (in module neuralib.model.rastermap.plot) pm (neuralib.imaging.registration.coordinates.FieldOfView property) pmt0_gain (neuralib.imaging.scanbox.core.SBXInfo.ConfigInfo attribute) pmt1_gain (neuralib.imaging.scanbox.core.SBXInfo.ConfigInfo attribute) point (neuralib.morpho.swc.SwcNode property) points (neuralib.morpho.swc.SwcFile property) (neuralib.segmentation.cellpose.core.CellposeSegmentation property) (neuralib.segmentation.stardist.core.StarDistSegmentation property) pos (neuralib.imaging.scanbox.core.SBXInfo.KnobbyInfo 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.imaging.scanbox.core.SBXInfo attribute) power_depth_link (neuralib.imaging.scanbox.core.SBXInfo attribute) prctile_baseline (neuralib.imaging.suite2p.core.Suite2pGUIOptions attribute) (neuralib.imaging.suite2p.core.Suite2PResult property) pre_smooth (neuralib.imaging.suite2p.core.Suite2pGUIOptions attribute) preclassify (neuralib.imaging.suite2p.core.Suite2pGUIOptions attribute) 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) printdf() (in module neuralib.util.verbose) prob (neuralib.segmentation.stardist.core.StarDistSegmentation property) prob_thresh (neuralib.segmentation.stardist.run_2d.StarDist2DOptions attribute) ProbeRenderCLI (class in neuralib.atlas.brainrender.probe) ProbeShank (class in neuralib.atlas.brainrender.probe) process_continuous() (neuralib.model.rastermap.plot.RasterMapPlot method) process_image() (neuralib.segmentation.base.AbstractSegmentationOptions method) 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.tracking.facemap.core.SVDVariables attribute) pupil_sigma (neuralib.tracking.facemap.core.RoiDict attribute) PupilDict (class in neuralib.tracking.facemap.core)

R

r (neuralib.morpho.swc.SwcNode attribute) radii (neuralib.morpho.swc.SwcFile property) radius (neuralib.atlas.brainrender.roi.RoiRenderCLI attribute) (neuralib.imaging.suite2p.core.Suite2pRoiStat attribute) RasterMapPlot (class in neuralib.model.rastermap.plot) RasterMapResult (class in neuralib.model.rastermap.core) RasterOptions (class in neuralib.model.rastermap.core) ratio (neuralib.util.table.Column attribute) read_avi() (in module neuralib.imglib.io) read_cellpose() (in module neuralib.segmentation.cellpose.core) read_dlc() (in module neuralib.tracking.deeplabcut.core) read_facemap() (in module neuralib.tracking.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.model.rastermap.core) read_scanbox() (in module neuralib.imaging.scanbox.core) read_stardist() (in module neuralib.segmentation.stardist.core) read_suite2p() (in module neuralib.imaging.suite2p.core) recordsPerBuffer (neuralib.imaging.scanbox.core.SBXInfo attribute) red_cell_prob (neuralib.imaging.suite2p.core.Suite2PResult property) redcell (neuralib.imaging.suite2p.core.Suite2PResult attribute) redcell_threshold (neuralib.imaging.suite2p.core.Suite2PResult attribute) reference (neuralib.atlas.view.AbstractSliceView attribute) REFERENCE_FROM (neuralib.atlas.view.AbstractSliceView attribute) reference_path (neuralib.imaging.widefield.align.NapariAlignmentOptions attribute) reference_point (neuralib.atlas.view.AbstractSliceView property) reference_value (neuralib.atlas.view.SlicePlane property) refImg (neuralib.imaging.suite2p.core.Suite2pGUIOptions attribute) reg_file (neuralib.imaging.suite2p.core.Suite2pGUIOptions attribute) reg_tif (neuralib.imaging.suite2p.core.Suite2pGUIOptions attribute) reg_tif_chan2 (neuralib.imaging.suite2p.core.Suite2pGUIOptions attribute) regDX (neuralib.imaging.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_name (neuralib.imaging.registration.coordinates.FieldOfView attribute) regions (neuralib.atlas.brainrender.core.BrainRenderCLI attribute) regions_alpha (neuralib.atlas.brainrender.core.BrainRenderCLI attribute) regPC (neuralib.imaging.suite2p.core.Suite2pGUIOptions attribute) regularize (neuralib.tracking.deeplabcut.core.DeepLabCutModelConfig attribute) relative_origin() (neuralib.imaging.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.imaging.scanbox.core.SBXInfo attribute) resolution (neuralib.atlas.ccf.matrix.CCFTransMatrix attribute) (neuralib.atlas.view.AbstractSliceView attribute) rich_data_frame_table() (in module neuralib.util.table) rich_default_table() (in module neuralib.util.table) rich_table() (in module neuralib.util.table) rich_table_content() (in module neuralib.util.table) right_vector (neuralib.imaging.widefield.svd.SequenceSingularVector attribute) rigid_x_offsets (neuralib.imaging.suite2p.core.Suite2PResult property) rigid_xy_offset (neuralib.imaging.suite2p.core.Suite2PResult property) rigid_y_offsets (neuralib.imaging.suite2p.core.Suite2PResult property) rind (neuralib.tracking.facemap.core.RoiDict attribute) rmax (neuralib.imaging.suite2p.core.Suite2pGUIOptions attribute) rmin (neuralib.imaging.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.imaging.suite2p.core.Suite2pGUIOptions attribute) RoiDict (class in neuralib.tracking.facemap.core) RoiNormalizedDataFrame (class in neuralib.atlas.ccf.dataframe) RoiRenderCLI (class in neuralib.atlas.brainrender.roi) rois (neuralib.tracking.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) rotation_ap (neuralib.imaging.registration.coordinates.FieldOfView attribute) rotation_ml (neuralib.imaging.registration.coordinates.FieldOfView attribute) row_count (neuralib.util.table.Table property) rows (neuralib.util.table.Table attribute) rtype (neuralib.tracking.facemap.core.RoiDict attribute) run() (neuralib.atlas.brainrender.core.BrainRenderCLI method) (neuralib.atlas.brainrender.probe.ProbeRenderCLI method) (neuralib.atlas.brainrender.roi.RoiRenderCLI method) (neuralib.imaging.scanbox.view.ScanBoxViewOptions method) (neuralib.imaging.widefield.align.NapariAlignmentOptions method) (neuralib.imaging.widefield.fft_view.WideFieldFFTViewOption method) (neuralib.segmentation.stardist.run_2d.StarDist2DOptions method) run_duration (neuralib.tracking.deeplabcut.core.DeepLabCutMeta attribute) run_later() (neuralib.dashboard.base.View method) run_periodic() (neuralib.dashboard.base.View method) run_rastermap() (in module neuralib.model.rastermap.run) run_spike_prediction() (neuralib.imaging.spikes.cascade.CascadeSpikePrediction method) run_timeout() (neuralib.dashboard.base.View method) running (neuralib.tracking.facemap.core.SVDVariables attribute) running_mask1d() (in module neuralib.locomotion.epoch) runtime_frate_check (neuralib.imaging.suite2p.core.Suite2PResult attribute)

S

s2p (neuralib.imaging.suite2p.signals.DFFSignal attribute) sampling_rate (neuralib.imaging.spikes.cascade.CascadeModelConfig attribute) saturation (neuralib.tracking.facemap.core.RoiDict attribute) save() (in module neuralib.persistence.persistence) (neuralib.model.rastermap.core.RasterMapResult method) save_cache() (neuralib.persistence.cli_persistence.PersistenceOptions method) save_folder (neuralib.imaging.suite2p.core.Suite2pGUIOptions attribute) save_ij_roi (neuralib.segmentation.base.AbstractSegmentationOptions attribute) save_json() (in module neuralib.io.json) save_mat (neuralib.imaging.suite2p.core.Suite2pGUIOptions attribute) (neuralib.tracking.facemap.core.SVDVariables attribute) save_note() (neuralib.imglib.labeller.SequenceLabeller method) save_NWB (neuralib.imaging.suite2p.core.Suite2pGUIOptions attribute) save_path (neuralib.imaging.suite2p.core.Suite2pGUIOptions attribute) (neuralib.model.rastermap.core.RasterMapResult attribute) (neuralib.tracking.facemap.core.SVDVariables attribute) save_path0 (neuralib.imaging.suite2p.core.Suite2pGUIOptions attribute) save_persistence() (neuralib.persistence.persistence.PersistenceHandler method) save_rastermap() (in module neuralib.model.rastermap.core) save_root (neuralib.persistence.persistence.GzipHandler property) (neuralib.persistence.persistence.PersistenceHandler property) (neuralib.persistence.persistence.PickleHandler property) savefig() (neuralib.plot.venn.VennDiagram static method) sbin (neuralib.tracking.facemap.core.SVDVariables attribute) sbx_map (neuralib.imaging.scanbox.view.ScanBoxView attribute) sbx_ndeadcols (neuralib.imaging.suite2p.core.Suite2pGUIOptions attribute) sbx_ndeadrows (neuralib.imaging.suite2p.core.Suite2pGUIOptions attribute) sbx_to_json() (in module neuralib.imaging.scanbox.core) SBXInfo (class in neuralib.imaging.scanbox.core) SBXInfo.AgcInfo (class in neuralib.imaging.scanbox.core) SBXInfo.CalibrationInfo (class in neuralib.imaging.scanbox.core) SBXInfo.ConfigInfo (class in neuralib.imaging.scanbox.core) SBXInfo.KnobbyInfo (class in neuralib.imaging.scanbox.core) SBXInfo.KnobbyPosInfo (class in neuralib.imaging.scanbox.core) SBXInfo.ObjectiveInfo (class in neuralib.imaging.scanbox.core) scanbox_version (neuralib.imaging.scanbox.core.SBXInfo attribute) ScanBoxView (class in neuralib.imaging.scanbox.view) ScanBoxViewOptions (class in neuralib.imaging.scanbox.view) scanmode (neuralib.imaging.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) SceneIdx (in module neuralib.scan.core) schedule (neuralib.imaging.scanbox.core.SBXInfo.KnobbyInfo attribute) schema (neuralib.util.dataframe.DataFrameWrapper property) scoremap_dir (neuralib.tracking.deeplabcut.core.DeepLabCutModelConfig attribute) Scorer (neuralib.tracking.deeplabcut.core.DeepLabCutMeta attribute) screenshot_to_tiff() (in module neuralib.imaging.scanbox.core) seg_output() (neuralib.segmentation.base.AbstractSegmentationOptions method) (neuralib.segmentation.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) send_slack_message() (in module neuralib.tools.slack_bot) sequence_path (neuralib.imaging.widefield.align.NapariAlignmentOptions attribute) SequenceFFT (class in neuralib.imaging.widefield.fft) SequenceLabeller (class in neuralib.imglib.labeller) SequenceSingularVector (class in neuralib.imaging.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.imaging.scanbox.view.ScanBoxViewOptions attribute) show() (neuralib.imaging.scanbox.view.ScanBoxView method) (neuralib.plot.venn.VennDiagram static method) show_polars_header_types() (in module neuralib.util.table) shuffle (neuralib.tracking.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.imaging.suite2p.core.Suite2pGUIOptions attribute) signal_baseline (neuralib.imaging.suite2p.core.Suite2PResult property) SIGNAL_TYPE (in module neuralib.imaging.suite2p.core) singular_value (neuralib.imaging.widefield.svd.SequenceSingularVector property) skew (neuralib.imaging.suite2p.core.Suite2pRoiStat attribute) slice (neuralib.model.rastermap.core.UserCluster attribute) slice() (neuralib.util.dataframe.DataFrameWrapper method) slice_id (neuralib.atlas.ccf.matrix.CCFTransMatrix attribute) slice_index (neuralib.atlas.ccf.matrix.CCFTransMatrix property) (neuralib.atlas.view.SlicePlane attribute) slice_view (neuralib.atlas.view.SlicePlane attribute) SlicePlane (class in neuralib.atlas.view) smooth_sigma (neuralib.imaging.suite2p.core.Suite2pGUIOptions attribute) smooth_sigma_time (neuralib.imaging.suite2p.core.Suite2pGUIOptions attribute) smoothing (neuralib.imaging.spikes.cascade.CascadeModelConfig attribute) snapshot_prefix (neuralib.tracking.deeplabcut.core.DeepLabCutModelConfig attribute) snr_thresh (neuralib.imaging.suite2p.core.Suite2pGUIOptions attribute) solidity (neuralib.imaging.suite2p.core.Suite2pRoiStat attribute) soma_crop (neuralib.imaging.suite2p.core.Suite2pGUIOptions attribute) (neuralib.imaging.suite2p.core.Suite2pRoiStat attribute) sort() (neuralib.util.dataframe.DataFrameWrapper method) Source (in module neuralib.atlas.typing) 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.imaging.suite2p.core.Suite2pGUIOptions attribute) spatial_hp (neuralib.imaging.suite2p.core.Suite2pGUIOptions attribute) spatial_hp_detect (neuralib.imaging.suite2p.core.Suite2pGUIOptions attribute) spatial_hp_reg (neuralib.imaging.suite2p.core.Suite2pGUIOptions attribute) spatial_scale (neuralib.imaging.suite2p.core.Suite2pGUIOptions attribute) spatial_taper (neuralib.imaging.suite2p.core.Suite2pGUIOptions attribute) spatscale_pix (neuralib.imaging.suite2p.core.Suite2pGUIOptions attribute) speed_2d() (in module neuralib.locomotion.position) spikedetect (neuralib.imaging.suite2p.core.Suite2pGUIOptions attribute) spks (neuralib.imaging.suite2p.core.Suite2PResult attribute) SpreadSheetName (in module neuralib.tools.gspread) StarDist2DOptions (class in neuralib.segmentation.stardist.run_2d) STARDIST_MODEL (in module neuralib.segmentation.stardist.core) stardist_point_roi_helper() (in module neuralib.segmentation.stardist.core) StarDistSegmentation (class in neuralib.segmentation.stardist.core) start (neuralib.tracking.deeplabcut.core.DeepLabCutMeta attribute) start() (neuralib.dashboard.base.BokehServer method) start_time (neuralib.model.rastermap.core.RasterOptions attribute) stat (neuralib.imaging.suite2p.core.Suite2PResult attribute) std (neuralib.imaging.suite2p.core.Suite2pRoiStat attribute) stop (neuralib.tracking.deeplabcut.core.DeepLabCutMeta attribute) stride (neuralib.tracking.deeplabcut.core.DeepLabCutModelConfig attribute) style (neuralib.util.table.Column attribute) subfolders (neuralib.imaging.suite2p.core.Suite2pGUIOptions attribute) subpixel (neuralib.imaging.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) suite2p_version (neuralib.imaging.suite2p.core.Suite2pGUIOptions attribute) Suite2pGUIOptions (class in neuralib.imaging.suite2p.core) Suite2PResult (class in neuralib.imaging.suite2p.core) Suite2pRoiStat (class in neuralib.imaging.suite2p.core) super_neurons (neuralib.model.rastermap.core.RasterMapResult attribute) (neuralib.model.rastermap.plot.RasterMapPlot property) svd (neuralib.imaging.widefield.svd.SequenceSingularVector attribute) SVDVariables (class in neuralib.tracking.facemap.core) SwcFile (class in neuralib.morpho.swc) SwcNode (class in neuralib.morpho.swc) sx (neuralib.tracking.facemap.core.SVDVariables attribute) sxbin (neuralib.tracking.facemap.core.SVDVariables attribute) sy (neuralib.tracking.facemap.core.SVDVariables attribute) sybin (neuralib.tracking.facemap.core.SVDVariables attribute) sync_s2p_rigevent() (in module neuralib.imaging.suite2p.signals) sz (neuralib.imaging.scanbox.core.SBXInfo attribute)

T

t (neuralib.locomotion.position.CircularPosition attribute) Table (class in neuralib.util.table) table() (in module neuralib.io.pyh5) tail() (neuralib.util.dataframe.DataFrameWrapper method) tau (neuralib.imaging.suite2p.core.Suite2pGUIOptions attribute) text_color (neuralib.imglib.labeller.SequenceLabeller property) th_badframes (neuralib.imaging.suite2p.core.Suite2pGUIOptions attribute) threshold (neuralib.imaging.scanbox.core.SBXInfo.AgcInfo attribute) threshold_scaling (neuralib.imaging.suite2p.core.Suite2pGUIOptions attribute) tif_to_gif() (in module neuralib.imglib.io) TiffBrainView (class in neuralib.dashboard.view_brain) TiffScanner (class in neuralib.scan.lsm) time (neuralib.model.rastermap.plot.Covariant attribute) time_bin (neuralib.model.rastermap.core.RasterOptions attribute) time_lag_window (neuralib.model.rastermap.core.RasterOptions attribute) TimeoutUpdateValue (class in neuralib.dashboard.tool) timing (neuralib.imaging.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_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.segmentation.stardist.core.StarDistSegmentation method) to_numpy() (neuralib.atlas.ccf.dataframe.RoiSubregionDataFrame method) to_pandas() (neuralib.tools.gspread.GoogleWorkSheet method) to_polars() (neuralib.tools.gspread.GoogleWorkSheet method) to_polygon() (neuralib.imaging.registration.coordinates.FieldOfView method) to_roi() (neuralib.segmentation.cellpose.core.CellposeSegmentation method) (neuralib.segmentation.stardist.core.StarDistSegmentation method) to_subregion() (neuralib.atlas.ccf.dataframe.RoiClassifierDataFrame method) to_tiff (neuralib.imaging.scanbox.view.ScanBoxViewOptions attribute) to_tiff() (neuralib.imaging.scanbox.view.ScanBoxView method) to_um() (neuralib.imaging.registration.coordinates.FieldOfView method) to_winner() (neuralib.atlas.ccf.dataframe.RoiNormalizedDataFrame method) to_zscore() (neuralib.tracking.facemap.core.KeyPointDataFrame method) total_frames (neuralib.tracking.facemap.core.KeyPointsMeta attribute) total_set (neuralib.plot.venn.VennHandler attribute) tPC (neuralib.imaging.suite2p.core.Suite2pGUIOptions attribute) tqdm_joblib() (in module neuralib.util.tqdm) trace_line() (in module neuralib.util.profile) training_datasets (neuralib.imaging.spikes.cascade.CascadeModelConfig attribute) training_finished (neuralib.imaging.spikes.cascade.CascadeModelConfig attribute) training_set_fraction (neuralib.tracking.deeplabcut.core.DeepLabCutMeta attribute) tree_init (neuralib.atlas.brainrender.core.BrainRenderCLI attribute) TreeLevel (in module neuralib.atlas.typing) trial_array (neuralib.locomotion.position.CircularPosition property) trial_time_index (neuralib.locomotion.position.CircularPosition attribute) two_step_registration (neuralib.imaging.suite2p.core.Suite2pGUIOptions attribute)

U

uglob() (in module neuralib.util.utils) unique_identifier (neuralib.morpho.swc.SwcFile property) unit (neuralib.atlas.view.SlicePlane attribute) (neuralib.imaging.registration.coordinates.CellularCoordinates attribute) (neuralib.imaging.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) upload_dataframe_to_spreadsheet() (in module neuralib.tools.gspread) use_builtin_classifier (neuralib.imaging.suite2p.core.Suite2pGUIOptions attribute) user_clusters (neuralib.model.rastermap.core.RasterMapResult attribute) UserCluster (class in neuralib.model.rastermap.core) usernotes (neuralib.imaging.scanbox.core.SBXInfo attribute) uv (neuralib.imaging.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_concat_etl_persistence() (in module neuralib.persistence.validator) value (neuralib.imaging.registration.coordinates.CellularCoordinates attribute) (neuralib.model.rastermap.plot.Covariant attribute) value_column (neuralib.atlas.ccf.dataframe.RoiNormalizedDataFrame property) values() (neuralib.tools.gspread.GoogleWorkSheet method) Vcorr (neuralib.imaging.suite2p.core.Suite2pGUIOptions attribute) VennDiagram (class in neuralib.plot.venn) VennHandler (class in neuralib.plot.venn) verbose (neuralib.imaging.scanbox.view.ScanBoxViewOptions attribute) (neuralib.imaging.spikes.cascade.CascadeModelConfig attribute) (neuralib.model.rastermap.core.RasterOptions attribute) verbose_sorting (neuralib.model.rastermap.core.RasterOptions attribute) version (neuralib.imaging.scanbox.view.ScanBoxView property)

vertical (neuralib.util.table.Column attribute) 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.imaging.suite2p.core.Suite2pGUIOptions attribute) Vmax (neuralib.imaging.suite2p.core.Suite2pGUIOptions attribute) volscan (neuralib.imaging.scanbox.core.SBXInfo attribute) Vsplit (neuralib.imaging.suite2p.core.Suite2pGUIOptions attribute)

W

wavelength (neuralib.imaging.scanbox.core.SBXInfo.ConfigInfo attribute) weigh_negatives (neuralib.tracking.deeplabcut.core.DeepLabCutModelConfig attribute) weigh_only_present_joints (neuralib.tracking.deeplabcut.core.DeepLabCutModelConfig attribute) weigh_part_predictions (neuralib.tracking.deeplabcut.core.DeepLabCutModelConfig attribute) weight_decay (neuralib.tracking.deeplabcut.core.DeepLabCutModelConfig attribute) WideFieldFFTViewOption (class in neuralib.imaging.widefield.fft_view) width (neuralib.atlas.view.AbstractSliceView property) (neuralib.dashboard.view_brain.AbstractBrainView property) (neuralib.dashboard.view_brain.AtlasBrainView property) (neuralib.imaging.scanbox.view.ScanBoxView property) (neuralib.imaging.widefield.fft.SequenceFFT property) (neuralib.imglib.array.ImageArrayWrapper property) (neuralib.segmentation.cellpose.core.CellposeSegmentation property) (neuralib.segmentation.stardist.core.StarDistSegmentation property) (neuralib.util.table.Column attribute) width_mm (neuralib.atlas.view.AbstractSliceView property) width_n (neuralib.dashboard.view_brain.AtlasBrainView property) win_baseline (neuralib.imaging.suite2p.core.Suite2pGUIOptions attribute) window_baseline (neuralib.imaging.suite2p.core.Suite2PResult property) window_title (neuralib.imglib.labeller.SequenceLabeller attribute) windowsize (neuralib.imaging.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.tracking.facemap.core.FaceMapResult property) with_masking() (neuralib.imaging.registration.coordinates.CellularCoordinates method) with_norm (neuralib.segmentation.base.AbstractSegmentationOptions property) with_offset() (neuralib.atlas.view.SlicePlane method) with_outlier_filter() (neuralib.tracking.facemap.core.KeyPointDataFrame method) with_overlap_copy() (neuralib.atlas.ccf.dataframe.RoiClassifierDataFrame 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.imaging.registration.coordinates.CellularCoordinates method) WorkPageName (in module neuralib.tools.gspread) worksheet_list (neuralib.tools.gspread.GoogleSpreadSheet property) write_avi() (in module neuralib.imglib.io) write_note() (neuralib.imglib.labeller.SequenceLabeller method)

X

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

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

Y

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

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

Z

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

z_projection() (neuralib.scan.core.AbstractScanner static method)