Index

Symbols

--binarize cindra-run command line option --combine cindra-run command line option --data-path cindra-run command line option --dataset cindra-gui-roi command line option cindra-gui-tracking command line option --discover cindra-run command line option --extract cindra-run command line option --input-path cindra-run command line option --job-id cindra-run command line option --name cindra-configure command line option --output-path cindra-configure command line option cindra-run command line option --pipeline cindra-configure command line option --process cindra-run command line option --progress-bars cindra-run command line option --recording-path cindra-gui-registration command line option cindra-gui-roi command line option cindra-gui-tracking command line option cindra-run command line option --target-plane cindra-run command line option --target-recording cindra-run command line option --transport cindra-gui-mcp command line option cindra-mcp command line option --workers cindra-run command line option

-b cindra-run command line option -c cindra-run command line option -d cindra-gui-roi command line option cindra-gui-tracking command line option cindra-run command line option -dp cindra-run command line option -e cindra-run command line option -i cindra-run command line option -id cindra-run command line option -n cindra-configure command line option -od cindra-configure command line option -p cindra-configure command line option cindra-run command line option -pb cindra-run command line option -r cindra-gui-registration command line option cindra-gui-roi command line option cindra-gui-tracking command line option -rp cindra-run command line option -s cindra-run command line option -t cindra-gui-mcp command line option cindra-mcp command line option -tp cindra-run command line option -tr cindra-run command line option -w cindra-run command line option

_

_available_features (cindra.classification.Classifier attribute) _cache (cindra.registration.DiffeomorphicDemonsRegistration attribute) _classifier_path (cindra.classification.Classifier attribute) _deformation_limit (cindra.registration.DiffeomorphicDemonsRegistration attribute) _deformations (cindra.registration.DiffeomorphicDemonsRegistration attribute) _field_shape (cindra.registration.Deformation attribute) _fields (cindra.registration.Deformation attribute) _final_grid_sampling (cindra.registration.DiffeomorphicDemonsRegistration attribute) _final_scale (cindra.registration.DiffeomorphicDemonsRegistration attribute) _freeze_edges (cindra.registration.DiffeomorphicDemonsRegistration attribute) _grid_cell_probabilities (cindra.classification.Classifier attribute) _grid_sampling_factor (cindra.registration.DiffeomorphicDemonsRegistration attribute)

_images (cindra.registration.DiffeomorphicDemonsRegistration attribute) _injective (cindra.registration.DiffeomorphicDemonsRegistration attribute) _interpolation_order (cindra.registration.DiffeomorphicDemonsRegistration attribute) _model (cindra.classification.Classifier attribute) _noise_factor (cindra.registration.DiffeomorphicDemonsRegistration attribute) _probability_grid (cindra.classification.Classifier attribute) _pyramids (cindra.registration.DiffeomorphicDemonsRegistration attribute) _read_only (cindra.io.BinaryFile attribute) _scale_sampling (cindra.registration.DiffeomorphicDemonsRegistration attribute) _smooth_scale (cindra.registration.DiffeomorphicDemonsRegistration attribute) _speed_factor (cindra.registration.DiffeomorphicDemonsRegistration attribute) _training_features (cindra.classification.Classifier attribute) _training_labels (cindra.classification.Classifier attribute)

A

acquisition (cindra.dataclasses.RuntimeContext attribute) AcquisitionParameters (class in cindra.dataclasses) add() (cindra.registration.Deformation method) align_by_first_channel (cindra.dataclasses.Registration attribute)

allow_overlap (cindra.dataclasses.SignalExtraction attribute) apply_deformation() (cindra.registration.Deformation method) apply_oasis_deconvolution() (in module cindra.extraction) aspect_ratio (cindra.dataclasses.DetectionData attribute) (cindra.dataclasses.ROIStatistics attribute)

B

backward_transform_time (cindra.dataclasses.MultiRecordingTimingData attribute) bad_frame_threshold (cindra.dataclasses.Registration attribute) bad_frames (cindra.dataclasses.RegistrationData attribute) baseline_method (cindra.dataclasses.SpikeDeconvolution attribute) baseline_percentile (cindra.dataclasses.SpikeDeconvolution attribute) baseline_sigma (cindra.dataclasses.SpikeDeconvolution attribute) baseline_window (cindra.dataclasses.SpikeDeconvolution attribute) BaselineMethod (class in cindra.dataclasses) batch_size (cindra.dataclasses.Registration attribute) (cindra.dataclasses.SignalExtraction attribute) bidirectional_phase_corrected (cindra.dataclasses.RegistrationData attribute)

bidirectional_phase_offset (cindra.dataclasses.RegistrationData attribute) bidirectional_phase_offset_override (cindra.dataclasses.Registration attribute) bin_movie() (cindra.io.BinaryFile method) binarization_time (cindra.dataclasses.TimingData attribute) BINARIZE (cindra.pipelines.SingleRecordingJobNames attribute) BinaryFile (class in cindra.io) BinaryFileCombined (class in cindra.io) block_size (cindra.dataclasses.NonrigidRegistration attribute) byte_number (cindra.io.BinaryFile property) (cindra.io.BinaryFileCombined property) bytes_per_frame (cindra.io.BinaryFile property)

C

cell_classification (cindra.dataclasses.ExtractionData attribute) cell_classification_channel_2 (cindra.dataclasses.ExtractionData attribute) cell_colocalization (cindra.dataclasses.ExtractionData attribute) cell_fluorescence (cindra.dataclasses.ExtractionData attribute) cell_fluorescence_channel_2 (cindra.dataclasses.ExtractionData attribute) cell_probability_percentile (cindra.dataclasses.SignalExtraction attribute) centroid (cindra.dataclasses.ROIMask attribute) channel_number (cindra.dataclasses.AcquisitionParameters attribute) cindra-configure command line option --name --output-path --pipeline -n -od -p cindra-gui-mcp command line option --transport -t cindra-gui-registration command line option --recording-path -r cindra-gui-roi command line option --dataset --recording-path -d -r cindra-gui-tracking command line option --dataset --recording-path -d -r cindra-mcp command line option --transport -t cindra-run command line option --binarize --combine --data-path --discover --extract --input-path --job-id --output-path --process --progress-bars --recording-path --target-plane --target-recording --workers -b -c -d -dp -e -i -id -p -pb -rp -s -tp -tr -w

cindra.classification module cindra.dataclasses module cindra.detection module cindra.extraction module cindra.gui module cindra.io module cindra.pipelines module cindra.registration module cindra_version (cindra.dataclasses.MultiRecordingTimingData attribute) (cindra.dataclasses.TimingData attribute) circle_pixels (cindra.dataclasses.ROIMask property) classification_threshold (cindra.dataclasses.SignalExtraction attribute) classification_time (cindra.dataclasses.TimingData attribute) classification_time_channel_2 (cindra.dataclasses.TimingData attribute) Classifier (class in cindra.classification) classify() (cindra.classification.Classifier method) (in module cindra.classification) clear() (cindra.dataclasses.MultiRecordingRegistrationData method) (cindra.dataclasses.RegistrationData method) close() (cindra.io.BinaryFile method) (cindra.io.BinaryFileCombined method) cluster_id (cindra.dataclasses.ROIMask attribute) colocalization_threshold (cindra.dataclasses.SignalExtraction attribute) COMBINE (cindra.pipelines.SingleRecordingJobNames attribute) combine_planes() (in module cindra.io) combined_data (cindra.dataclasses.MultiRecordingRuntimeData attribute) combined_height (cindra.dataclasses.CombinedData attribute) combined_width (cindra.dataclasses.CombinedData attribute) CombinedData (class in cindra.dataclasses) compactness (cindra.dataclasses.ROIStatistics attribute) compose() (cindra.registration.Deformation method) compute_bidirectional_phase_offset (cindra.dataclasses.Registration attribute) compute_block_smoothing_kernel() (in module cindra.detection) compute_delta_fluorescence() (in module cindra.extraction) compute_median_pixel_position() (in module cindra.detection) compute_plane_offsets() (in module cindra.io) compute_registration_blocks() (in module cindra.detection) compute_roi_statistics() (in module cindra.detection) compute_spatial_taper_mask() (in module cindra.detection) configuration (cindra.dataclasses.MultiRecordingRuntimeContext attribute) (cindra.dataclasses.RuntimeContext attribute) CONSTANT (cindra.dataclasses.BaselineMethod attribute) CONSTANT_PERCENTILE (cindra.dataclasses.BaselineMethod attribute) convert_numpy_file_to_binary() (cindra.io.BinaryFile static method) convert_tiffs_to_binary() (in module cindra.io) copy() (cindra.registration.Deformation method) corrected_structural_mean_image (cindra.dataclasses.ExtractionData attribute) correlation_map (cindra.dataclasses.DetectionData attribute) correlation_map_channel_2 (cindra.dataclasses.DetectionData attribute) create_masks() (in module cindra.extraction) create_training_dataset() (cindra.classification.Classifier static method) crop() (cindra.registration.Deformation method) crop_to_soma (cindra.dataclasses.ROIDetection attribute) custom_classifier_path (cindra.dataclasses.Main attribute)

D

data (cindra.io.BinaryFile property) data_path (cindra.dataclasses.FileIO attribute) (cindra.dataclasses.MultiRecordingIOData attribute) dataset_name (cindra.dataclasses.MultiRecordingIOData attribute) dataset_output_paths (cindra.dataclasses.MultiRecordingIOData attribute) date_processed (cindra.dataclasses.MultiRecordingTimingData attribute) (cindra.dataclasses.TimingData attribute) deconvolution_time (cindra.dataclasses.MultiRecordingTimingData attribute) (cindra.dataclasses.TimingData attribute) deconvolution_time_channel_2 (cindra.dataclasses.TimingData attribute) deform_field_x (cindra.dataclasses.MultiRecordingRegistrationData attribute) deform_field_y (cindra.dataclasses.MultiRecordingRegistrationData attribute) Deformation (class in cindra.registration) deformed_roi_masks (cindra.dataclasses.MultiRecordingRegistrationData attribute)

deformed_roi_masks_channel_2 (cindra.dataclasses.MultiRecordingRegistrationData attribute) denoise (cindra.dataclasses.ROIDetection attribute) detect_pipeline_type() (in module cindra.dataclasses) detect_plane_rois() (in module cindra.detection) detection (cindra.dataclasses.CombinedData attribute) (cindra.dataclasses.SingleRecordingRuntimeData attribute) detection_time (cindra.dataclasses.TimingData attribute) detection_time_channel_2 (cindra.dataclasses.TimingData attribute) DetectionData (class in cindra.dataclasses) diffeomorphic_registration (cindra.dataclasses.MultiRecordingConfiguration attribute) DiffeomorphicDemonsRegistration (class in cindra.registration) DISCOVER (cindra.pipelines.MultiRecordingJobNames attribute) display_progress_bars (cindra.dataclasses.RuntimeSettings attribute) dtype (cindra.io.BinaryFile attribute)

E

edge_taper_pixels (cindra.dataclasses.OnePhotonRegistration attribute) enabled (cindra.dataclasses.NonrigidRegistration attribute) (cindra.dataclasses.OnePhotonRegistration attribute) (cindra.dataclasses.ROIDetection attribute) ENHANCED_MEAN (cindra.dataclasses.ReferenceImageType attribute) enhanced_mean_image (cindra.dataclasses.DetectionData attribute) enhanced_mean_image_channel_2 (cindra.dataclasses.DetectionData attribute) estimate_diameter_from_rois() (in module cindra.detection) extend_roi() (in module cindra.detection) EXTRACT (cindra.pipelines.MultiRecordingJobNames attribute)

extract_neuropil (cindra.dataclasses.SignalExtraction attribute) extract_spikes (cindra.dataclasses.SpikeDeconvolution attribute) extract_traces() (in module cindra.extraction) extract_unique_components() (in module cindra.io) extraction (cindra.dataclasses.CombinedData attribute) (cindra.dataclasses.MultiRecordingRuntimeData attribute) (cindra.dataclasses.SingleRecordingRuntimeData attribute) extraction_time (cindra.dataclasses.MultiRecordingTimingData attribute) (cindra.dataclasses.TimingData attribute) extraction_time_channel_2 (cindra.dataclasses.TimingData attribute) ExtractionData (class in cindra.dataclasses)

F

field_shape (cindra.registration.Deformation property) file (cindra.io.BinaryFile attribute) file_io (cindra.dataclasses.SingleRecordingConfiguration attribute) file_path (cindra.io.BinaryFile attribute) file_paths (cindra.io.BinaryFileCombined attribute) FileIO (class in cindra.dataclasses) files (cindra.io.BinaryFileCombined attribute) first_channel_functional (cindra.dataclasses.Main attribute)

footprint (cindra.dataclasses.ROIStatistics attribute) frame_count (cindra.dataclasses.IOData attribute) frame_height (cindra.dataclasses.IOData attribute) frame_number (cindra.io.BinaryFile property) (cindra.io.BinaryFileCombined property) frame_rate (cindra.dataclasses.AcquisitionParameters attribute) frame_width (cindra.dataclasses.IOData attribute) (cindra.dataclasses.ROIMask attribute)

G

get_deformation() (cindra.registration.DiffeomorphicDemonsRegistration method)

get_deformation_locations() (cindra.registration.Deformation method) get_field() (cindra.registration.Deformation method)

H

height (cindra.io.BinaryFile attribute) (cindra.io.BinaryFileCombined attribute)

I

identity() (cindra.registration.Deformation class method) ignored_file_names (cindra.dataclasses.FileIO attribute) ignored_flyback_planes (cindra.dataclasses.Main attribute) inner_neuropil_border_radius (cindra.dataclasses.SignalExtraction attribute) inverse() (cindra.registration.Deformation method) io (cindra.dataclasses.MultiRecordingRuntimeData attribute) (cindra.dataclasses.SingleRecordingRuntimeData attribute)

IOData (class in cindra.dataclasses) is_identity (cindra.registration.Deformation property) is_mroi (cindra.dataclasses.AcquisitionParameters property) is_registered() (cindra.dataclasses.MultiRecordingRegistrationData method) (cindra.dataclasses.RegistrationData method)

L

load() (cindra.dataclasses.CombinedData class method) (cindra.dataclasses.MultiRecordingConfiguration class method) (cindra.dataclasses.MultiRecordingRuntimeContext class method) (cindra.dataclasses.MultiRecordingRuntimeData class method) (cindra.dataclasses.RuntimeContext class method) (cindra.dataclasses.SingleRecordingConfiguration class method) (cindra.dataclasses.SingleRecordingRuntimeData class method) load_arrays() (cindra.dataclasses.DetectionData method) (cindra.dataclasses.ExtractionData method) (cindra.dataclasses.MultiRecordingRegistrationData method) (cindra.dataclasses.MultiRecordingRuntimeData method) (cindra.dataclasses.MultiRecordingTrackingData method) (cindra.dataclasses.RegistrationData method) (cindra.dataclasses.SingleRecordingRuntimeData method)

load_list() (cindra.dataclasses.ROIMask static method) (cindra.dataclasses.ROIStatistics static method) load_results() (cindra.dataclasses.ExtractionData method)

M

main (cindra.dataclasses.SingleRecordingConfiguration attribute) Main (class in cindra.dataclasses) mask (cindra.dataclasses.ROIStatistics attribute) MAXIMIN (cindra.dataclasses.BaselineMethod attribute) maximum_binned_frames (cindra.dataclasses.ROIDetection attribute) maximum_block_offset (cindra.dataclasses.NonrigidRegistration attribute) maximum_iterations (cindra.dataclasses.ROIDetection attribute) maximum_offset_fraction (cindra.dataclasses.Registration attribute) maximum_overlap (cindra.dataclasses.ROIDetection attribute) maximum_projection (cindra.dataclasses.DetectionData attribute) MAXIMUM_PROJECTION (cindra.dataclasses.ReferenceImageType attribute) maximum_projection_channel_2 (cindra.dataclasses.DetectionData attribute) MEAN (cindra.dataclasses.ReferenceImageType attribute) mean_centered_meshgrid() (in module cindra.detection) mean_image (cindra.dataclasses.DetectionData attribute) mean_image_channel_2 (cindra.dataclasses.DetectionData attribute) memory_map_arrays() (cindra.dataclasses.DetectionData method) (cindra.dataclasses.ExtractionData method) (cindra.dataclasses.MultiRecordingRegistrationData method) (cindra.dataclasses.MultiRecordingRuntimeData method) (cindra.dataclasses.MultiRecordingTrackingData method) (cindra.dataclasses.RegistrationData method) (cindra.dataclasses.SingleRecordingRuntimeData method)

memory_map_results() (cindra.dataclasses.ExtractionData method) minimum_neuropil_pixels (cindra.dataclasses.SignalExtraction attribute) module cindra.classification cindra.dataclasses cindra.detection cindra.extraction cindra.gui cindra.io cindra.pipelines cindra.registration mroi_lines (cindra.dataclasses.IOData attribute) mroi_region_borders (cindra.dataclasses.MultiRecordingIOData attribute) mroi_x_offset (cindra.dataclasses.IOData attribute) mroi_y_offset (cindra.dataclasses.IOData attribute) MULTI_RECORDING (cindra.dataclasses.PipelineType attribute) MultiRecordingConfiguration (class in cindra.dataclasses) MultiRecordingIOData (class in cindra.dataclasses) MultiRecordingJobNames (class in cindra.pipelines) MultiRecordingRegistrationData (class in cindra.dataclasses) MultiRecordingRuntimeContext (class in cindra.dataclasses) MultiRecordingRuntimeData (class in cindra.dataclasses) MultiRecordingTimingData (class in cindra.dataclasses) MultiRecordingTrackingData (class in cindra.dataclasses)

N

ndim (cindra.registration.Deformation property) neuropil_coefficient (cindra.dataclasses.SpikeDeconvolution attribute) neuropil_fluorescence (cindra.dataclasses.ExtractionData attribute) neuropil_fluorescence_channel_2 (cindra.dataclasses.ExtractionData attribute) neuropil_mask (cindra.dataclasses.ROIStatistics attribute) nonrigid_correlations (cindra.dataclasses.RegistrationData attribute) nonrigid_registration (cindra.dataclasses.SingleRecordingConfiguration attribute)

nonrigid_x_offsets (cindra.dataclasses.RegistrationData attribute) nonrigid_y_offsets (cindra.dataclasses.RegistrationData attribute) NonrigidRegistration (class in cindra.dataclasses) normalization_maximum (cindra.dataclasses.RegistrationData attribute) normalization_minimum (cindra.dataclasses.RegistrationData attribute) normalize_frames (cindra.dataclasses.Registration attribute) normalized_pixel_count (cindra.dataclasses.ROIStatistics attribute)

O

one_photon_registration (cindra.dataclasses.SingleRecordingConfiguration attribute) OnePhotonRegistration (class in cindra.dataclasses) output_path (cindra.dataclasses.FileIO attribute) (cindra.dataclasses.IOData attribute) (cindra.dataclasses.MultiRecordingRuntimeData attribute) (cindra.dataclasses.SingleRecordingRuntimeData attribute)

overlap_mask (cindra.dataclasses.ROIMask attribute)

P

parallel_workers (cindra.dataclasses.RuntimeSettings attribute) pipeline_type (cindra.dataclasses.MultiRecordingConfiguration attribute) (cindra.dataclasses.SingleRecordingConfiguration attribute) PipelineType (class in cindra.dataclasses) pixel_count (cindra.dataclasses.ROIStatistics attribute) pixel_weights (cindra.dataclasses.ROIMask attribute) plane_count (cindra.dataclasses.CombinedData attribute) plane_heights (cindra.dataclasses.CombinedData attribute) (cindra.io.BinaryFileCombined attribute) plane_index (cindra.dataclasses.IOData attribute) (cindra.dataclasses.ROIStatistics attribute) plane_number (cindra.dataclasses.AcquisitionParameters attribute) plane_widths (cindra.dataclasses.CombinedData attribute) (cindra.io.BinaryFileCombined attribute) plane_x_coordinates (cindra.io.BinaryFileCombined attribute) plane_x_offsets (cindra.dataclasses.CombinedData attribute)

plane_y_coordinates (cindra.io.BinaryFileCombined attribute) plane_y_offsets (cindra.dataclasses.CombinedData attribute) pre_smoothing_sigma (cindra.dataclasses.OnePhotonRegistration attribute) preclassification_threshold (cindra.dataclasses.ROIDetection attribute) prepare_for_saving() (cindra.dataclasses.DetectionData method) (cindra.dataclasses.ExtractionData method) (cindra.dataclasses.MultiRecordingRegistrationData method) (cindra.dataclasses.MultiRecordingTrackingData method) (cindra.dataclasses.RegistrationData method) principal_component_extreme_images (cindra.dataclasses.RegistrationData attribute) principal_component_projections (cindra.dataclasses.RegistrationData attribute) principal_component_shift_metrics (cindra.dataclasses.RegistrationData attribute) PROCESS (cindra.pipelines.SingleRecordingJobNames attribute) project_templates_to_recordings() (in module cindra.registration) python_version (cindra.dataclasses.MultiRecordingTimingData attribute) (cindra.dataclasses.TimingData attribute)

R

radius (cindra.dataclasses.ROIMask attribute) raveled_pixels (cindra.dataclasses.ROIMask property) recording_count (cindra.dataclasses.ROIMask attribute) recording_id (cindra.dataclasses.MultiRecordingIOData attribute) recording_io (cindra.dataclasses.MultiRecordingConfiguration attribute) reference_frame_count (cindra.dataclasses.Registration attribute) reference_image (cindra.dataclasses.RegistrationData attribute) ReferenceImageType (class in cindra.dataclasses) register() (cindra.registration.DiffeomorphicDemonsRegistration method) register_plane() (in module cindra.registration) register_recordings() (in module cindra.registration) registered_binary_path (cindra.dataclasses.IOData attribute) registered_binary_path_channel_2 (cindra.dataclasses.IOData attribute) registered_binary_paths (cindra.dataclasses.CombinedData attribute) registered_binary_paths_channel_2 (cindra.dataclasses.CombinedData attribute) registration (cindra.dataclasses.MultiRecordingRuntimeData attribute) (cindra.dataclasses.SingleRecordingConfiguration attribute) (cindra.dataclasses.SingleRecordingRuntimeData attribute) Registration (class in cindra.dataclasses) registration_metric_principal_components (cindra.dataclasses.Registration attribute) registration_metrics_time (cindra.dataclasses.TimingData attribute) registration_time (cindra.dataclasses.MultiRecordingTimingData attribute) (cindra.dataclasses.TimingData attribute) RegistrationData (class in cindra.dataclasses) regularize() (cindra.registration.Deformation method) release_arrays() (cindra.dataclasses.DetectionData method) (cindra.dataclasses.ExtractionData method) (cindra.dataclasses.MultiRecordingRegistrationData method) (cindra.dataclasses.MultiRecordingRuntimeData method) (cindra.dataclasses.MultiRecordingTrackingData method) (cindra.dataclasses.RegistrationData method) (cindra.dataclasses.SingleRecordingRuntimeData method) repeat_binarization (cindra.dataclasses.FileIO attribute)

repeat_registration (cindra.dataclasses.Registration attribute) resize_field() (cindra.registration.Deformation method) resolve_multi_recording_contexts() (in module cindra.io) resolve_recording_roots() (in module cindra.io) resolve_single_recording_contexts() (in module cindra.io) rigid_correlations (cindra.dataclasses.RegistrationData attribute) rigid_x_offsets (cindra.dataclasses.RegistrationData attribute) rigid_y_offsets (cindra.dataclasses.RegistrationData attribute) roi_detection (cindra.dataclasses.SingleRecordingConfiguration attribute) roi_diameter (cindra.dataclasses.DetectionData attribute) roi_diameter_channel_2 (cindra.dataclasses.DetectionData attribute) roi_lines (cindra.dataclasses.AcquisitionParameters attribute) roi_number (cindra.dataclasses.AcquisitionParameters attribute) roi_selection (cindra.dataclasses.MultiRecordingConfiguration attribute) roi_statistics (cindra.dataclasses.ExtractionData attribute) roi_statistics_channel_2 (cindra.dataclasses.ExtractionData attribute) roi_tracking (cindra.dataclasses.MultiRecordingConfiguration attribute) roi_x_coordinates (cindra.dataclasses.AcquisitionParameters attribute) roi_y_coordinates (cindra.dataclasses.AcquisitionParameters attribute) ROIDetection (class in cindra.dataclasses) ROIMask (class in cindra.dataclasses) ROIStatistics (class in cindra.dataclasses) run_multi_recording_pipeline() (in module cindra.pipelines) run_registration_viewer() (in module cindra.gui) run_roi_viewer() (in module cindra.gui) run_single_recording_pipeline() (in module cindra.pipelines) run_tracking_viewer() (in module cindra.gui) runtime (cindra.dataclasses.MultiRecordingConfiguration attribute) (cindra.dataclasses.MultiRecordingRuntimeContext attribute) (cindra.dataclasses.RuntimeContext attribute) (cindra.dataclasses.SingleRecordingConfiguration attribute) RuntimeContext (class in cindra.dataclasses) RuntimeSettings (class in cindra.dataclasses)

S

sampling_rate (cindra.dataclasses.CombinedData attribute) (cindra.dataclasses.IOData attribute) save() (cindra.dataclasses.CombinedData method) (cindra.dataclasses.MultiRecordingConfiguration method) (cindra.dataclasses.MultiRecordingRuntimeData method) (cindra.dataclasses.SingleRecordingConfiguration method) (cindra.dataclasses.SingleRecordingRuntimeData method) save_arrays() (cindra.dataclasses.DetectionData method) (cindra.dataclasses.ExtractionData method) (cindra.dataclasses.MultiRecordingRegistrationData method) (cindra.dataclasses.MultiRecordingTrackingData method) (cindra.dataclasses.RegistrationData method) save_list() (cindra.dataclasses.ROIMask static method) (cindra.dataclasses.ROIStatistics static method) save_runtime() (cindra.dataclasses.MultiRecordingRuntimeContext method) (cindra.dataclasses.RuntimeContext method) save_shared() (cindra.dataclasses.MultiRecordingRuntimeContext method) (cindra.dataclasses.RuntimeContext method) scale() (cindra.registration.Deformation method) second_channel_functional (cindra.dataclasses.Main attribute) select_recording_rois() (in module cindra.io) selected_roi_indices (cindra.dataclasses.MultiRecordingIOData attribute) selected_roi_indices_channel_2 (cindra.dataclasses.MultiRecordingIOData attribute) shape (cindra.io.BinaryFile property) (cindra.io.BinaryFileCombined property)

signal_extraction (cindra.dataclasses.MultiRecordingConfiguration attribute) (cindra.dataclasses.SingleRecordingConfiguration attribute) signal_to_noise_threshold (cindra.dataclasses.NonrigidRegistration attribute) SignalExtraction (class in cindra.dataclasses) SINGLE_RECORDING (cindra.dataclasses.PipelineType attribute) SingleRecordingConfiguration (class in cindra.dataclasses) SingleRecordingJobNames (class in cindra.pipelines) SingleRecordingRuntimeData (class in cindra.dataclasses) size (cindra.io.BinaryFile property) skewness (cindra.dataclasses.ROIStatistics attribute) solidity (cindra.dataclasses.ROIStatistics attribute) soma_mask (cindra.dataclasses.ROIStatistics attribute) spatial_highpass_window (cindra.dataclasses.OnePhotonRegistration attribute) (cindra.dataclasses.ROIDetection attribute) spatial_smoothing_sigma (cindra.dataclasses.Registration attribute) spike_deconvolution (cindra.dataclasses.MultiRecordingConfiguration attribute) (cindra.dataclasses.SingleRecordingConfiguration attribute) SpikeDeconvolution (class in cindra.dataclasses) spikes (cindra.dataclasses.ExtractionData attribute) spikes_channel_2 (cindra.dataclasses.ExtractionData attribute) subsample_movie() (cindra.io.BinaryFile method) subtracted_fluorescence (cindra.dataclasses.ExtractionData attribute) subtracted_fluorescence_channel_2 (cindra.dataclasses.ExtractionData attribute)

T

tau (cindra.dataclasses.CombinedData attribute) (cindra.dataclasses.Main attribute) template_diameter (cindra.dataclasses.MultiRecordingTrackingData attribute) template_diameter_channel_2 (cindra.dataclasses.MultiRecordingTrackingData attribute) template_masks (cindra.dataclasses.MultiRecordingTrackingData attribute) template_masks_channel_2 (cindra.dataclasses.MultiRecordingTrackingData attribute) temporal_highpass_window (cindra.dataclasses.ROIDetection attribute) temporal_smoothing_sigma (cindra.dataclasses.Registration attribute) threshold_scaling (cindra.dataclasses.ROIDetection attribute) timing (cindra.dataclasses.MultiRecordingRuntimeData attribute) (cindra.dataclasses.SingleRecordingRuntimeData attribute) TimingData (class in cindra.dataclasses) total_discovery_time (cindra.dataclasses.MultiRecordingTimingData attribute)

total_extraction_time (cindra.dataclasses.MultiRecordingTimingData attribute) total_plane_time (cindra.dataclasses.TimingData attribute) track_rois_across_recordings() (in module cindra.detection) tracking (cindra.dataclasses.MultiRecordingRuntimeData attribute) tracking_time (cindra.dataclasses.MultiRecordingTimingData attribute) transformed_enhanced_mean_image (cindra.dataclasses.MultiRecordingRegistrationData attribute) transformed_enhanced_mean_image_channel_2 (cindra.dataclasses.MultiRecordingRegistrationData attribute) transformed_maximum_projection (cindra.dataclasses.MultiRecordingRegistrationData attribute) transformed_maximum_projection_channel_2 (cindra.dataclasses.MultiRecordingRegistrationData attribute) transformed_mean_image (cindra.dataclasses.MultiRecordingRegistrationData attribute) transformed_mean_image_channel_2 (cindra.dataclasses.MultiRecordingRegistrationData attribute) two_channels (cindra.dataclasses.Main attribute) two_step_registration (cindra.dataclasses.Registration attribute) two_step_registration_time (cindra.dataclasses.TimingData attribute)

V

valid_x_range (cindra.dataclasses.RegistrationData attribute)

valid_y_range (cindra.dataclasses.RegistrationData attribute) virtual_plane_count (cindra.dataclasses.AcquisitionParameters property)

W

width (cindra.io.BinaryFile attribute) (cindra.io.BinaryFileCombined attribute)

write_tiff() (cindra.io.BinaryFile method)

X

x_pixels (cindra.dataclasses.ROIMask attribute)

Y

y_pixels (cindra.dataclasses.ROIMask attribute)