Index

Symbols

--binarize cindra-run command line option --binarize-workers 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 --discover-workers cindra-run command line option --extract cindra-run command line option --extract-workers cindra-run command line option --force cindra-omp command line option --input-path cindra-run command line option --job-id cindra-run command line option --name cindra-configure command line option --no-progress cindra-run 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 --process-workers 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 --register cindra-run command line option --register-device cindra-run command line option --register-workers cindra-run command line option --source cindra-omp command line option --target cindra-omp 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

--yes cindra-omp command line option -b cindra-run command line option -bw 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 -dw cindra-run command line option -e cindra-run command line option -ew cindra-run command line option -f cindra-omp command line option -i cindra-run command line option -id cindra-run command line option -n cindra-configure command line option -np cindra-run command line option -od cindra-configure command line option -p cindra-configure command line option cindra-run command line option -pw cindra-run command line option -r cindra-gui-registration command line option cindra-gui-roi command line option cindra-gui-tracking command line option cindra-run command line option -rd cindra-run command line option -rp cindra-run command line option -rw cindra-run command line option -s cindra-omp command line option cindra-run command line option -t cindra-gui-mcp command line option cindra-mcp command line option cindra-omp command line option -tp cindra-run command line option -tr cindra-run command line option -y cindra-omp command line option

_

_available_features (cindra.classification.Classifier attribute) _classifier_path (cindra.classification.Classifier attribute) _frame_number (cindra.io.BinaryFileCombined attribute) _grid_cell_probabilities (cindra.classification.Classifier attribute)

_model (cindra.classification.Classifier attribute) _probability_grid (cindra.classification.Classifier attribute) _read_only (cindra.io.BinaryFile attribute) _training_features (cindra.classification.Classifier attribute) _training_labels (cindra.classification.Classifier attribute)

A

acquisition (cindra.dataclasses.RuntimeContext attribute) ACQUISITION_PARAMETERS_FILENAME (in module cindra.layout) acquisition_resolved (cindra.orchestration.RecordingGeometry attribute) AcquisitionParameters (class in cindra.dataclasses) align_by_first_channel (cindra.dataclasses.Registration attribute) ALL_DEVICES_REQUEST (in module cindra.orchestration.gpu) ALL_JOBS (cindra.orchestration.PrerequisiteScope attribute)

allow_overlap (cindra.dataclasses.SignalExtraction attribute) aspect_ratio (cindra.dataclasses.DetectionData attribute) (cindra.dataclasses.ROIStatistics attribute) assigned_device (cindra.orchestration.PendingJob attribute) AVAILABLE (cindra.orchestration.GpuStatus attribute) available (cindra.orchestration.GpuSummary property) AVAILABLE (cindra.orchestration.OpenMPStatus attribute)

B

backward_transform_time (cindra.dataclasses.MultiRecordingTimingData attribute) bad_frame_threshold (cindra.dataclasses.Registration attribute) bad_frames (cindra.dataclasses.RegistrationData attribute) BAD_FRAMES (cindra.layout.RegistrationArrays 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) bin_size (cindra.dataclasses.ROITracking attribute) binarization_time (cindra.dataclasses.TimingData attribute) BINARIZATION_WORKERS (in module cindra.orchestration.allocation) BINARIZE (cindra.orchestration.SingleRecordingJobNames attribute) binarize_recording() (in module cindra.pipelines) 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

cancel_execution_session() (in module cindra.orchestration) cell_classification (cindra.dataclasses.ExtractionData attribute) CELL_CLASSIFICATION (cindra.layout.RecordingArrays attribute) cell_classification_channel_2 (cindra.dataclasses.ExtractionData attribute) cell_colocalization (cindra.dataclasses.ExtractionData attribute) CELL_COLOCALIZATION (cindra.layout.RecordingArrays attribute) cell_fluorescence (cindra.dataclasses.ExtractionData attribute) CELL_FLUORESCENCE (cindra.layout.RecordingArrays attribute) cell_fluorescence_channel_2 (cindra.dataclasses.ExtractionData attribute) cell_probability_percentile (cindra.dataclasses.SignalExtraction attribute) centroid (cindra.dataclasses.ROIMask attribute) CHANNEL_1_BINARY_FILENAME (in module cindra.layout) CHANNEL_2_BINARY_FILENAME (in module cindra.layout) 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-omp command line option --force --source --target --yes -f -s -t -y cindra-run command line option --binarize --binarize-workers --combine --data-path --discover --discover-workers --extract --extract-workers --input-path --job-id --no-progress --output-path --process --process-workers --recording-path --register --register-device --register-workers --target-plane --target-recording -b -bw -c -d -dp -dw -e -ew -i -id -np -p -pw -r -rd -rp -rw -s -tp -tr

cindra.classification module cindra.dataclasses module cindra.detection module cindra.extraction module cindra.gui module cindra.io module cindra.layout module cindra.orchestration 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) cleanup_state_file() (in module cindra.gui) clear() (cindra.dataclasses.MultiRecordingRegistrationData method) (cindra.dataclasses.RegistrationData method) clear_dataset_selection() (in module cindra.io) clear_recording_selections() (in module cindra.io) clear_registration_marker() (in module cindra.io) close() (cindra.io.BinaryFile method) (cindra.io.BinaryFileCombined method) cluster_id (cindra.dataclasses.ROIMask attribute) colocalization_threshold (cindra.dataclasses.SignalExtraction attribute) COMBINATION_WORKERS (in module cindra.orchestration.allocation) COMBINE (cindra.orchestration.SingleRecordingJobNames attribute) combine_planes() (in module cindra.io) combined_data (cindra.dataclasses.MultiRecordingRuntimeData attribute) combined_frame_count (cindra.orchestration.RecordingGeometry attribute) combined_height (cindra.dataclasses.CombinedData attribute) COMBINED_METADATA_FILENAME (in module cindra.layout) combined_pixels (cindra.orchestration.RecordingGeometry attribute) combined_width (cindra.dataclasses.CombinedData attribute) CombinedData (class in cindra.dataclasses) compactness (cindra.dataclasses.ROIStatistics attribute) compute_bidirectional_phase_offset (cindra.dataclasses.Registration attribute) compute_capability (cindra.orchestration.GpuDevice attribute) compute_registration_blocks() (in module cindra.detection) compute_roi_statistics() (in module cindra.detection) compute_spatial_taper_mask() (in module cindra.detection) concurrency_limit (cindra.orchestration.ResourceClass attribute) concurrency_reservation (cindra.orchestration.ResourceClass attribute) configuration (cindra.dataclasses.MultiRecordingRuntimeContext attribute) (cindra.dataclasses.RuntimeContext attribute) configuration_path (cindra.orchestration.PendingJob 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) cores (cindra.orchestration.JobSizing attribute) corrected_structural_mean_image (cindra.dataclasses.ExtractionData attribute) CORRECTED_STRUCTURAL_MEAN_IMAGE (cindra.layout.RecordingArrays attribute) correlation_map (cindra.dataclasses.DetectionData attribute) CORRELATION_MAP (cindra.layout.DetectionImages attribute) correlation_map_channel_2 (cindra.dataclasses.DetectionData attribute) create_registration_marker() (in module cindra.io) create_training_dataset() (cindra.classification.Classifier static 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) (cindra.dataclasses.RecordingIO attribute) (cindra.io.DatasetRecordings attribute) (cindra.orchestration.MultiRecordingJobs attribute) dataset_output_paths (cindra.dataclasses.MultiRecordingIOData attribute) dataset_paths (cindra.io.DatasetRecordings attribute) DatasetRecordings (class in cindra.io) 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_X (cindra.layout.MultiRecordingArrays attribute) deform_field_y (cindra.dataclasses.MultiRecordingRegistrationData attribute) DEFORM_FIELD_Y (cindra.layout.MultiRecordingArrays attribute) DEFORMED_MASKS_FILENAME (in module cindra.layout) deformed_roi_masks (cindra.dataclasses.MultiRecordingRegistrationData attribute) deformed_roi_masks_channel_2 (cindra.dataclasses.MultiRecordingRegistrationData attribute) denoise (cindra.dataclasses.ROIDetection attribute) describe() (cindra.orchestration.GpuSummary method) (cindra.orchestration.OpenMPSummary method)

detail (cindra.orchestration.GpuSummary 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_DATA_DIRECTORY_NAME (in module cindra.layout) detection_time (cindra.dataclasses.TimingData attribute) detection_time_channel_2 (cindra.dataclasses.TimingData attribute) DetectionData (class in cindra.dataclasses) DetectionImages (class in cindra.layout) device_memory_mb (cindra.orchestration.JobSizing attribute) device_memory_megabytes (cindra.orchestration.PendingJob attribute) devices (cindra.orchestration.GpuSummary attribute) diffeomorphic_registration (cindra.dataclasses.MultiRecordingConfiguration attribute) DiffeomorphicRegistration (class in cindra.dataclasses) DISCOVER (cindra.orchestration.MultiRecordingJobNames attribute) discover_multi_recording_cells() (in module cindra.pipelines) discovered (cindra.io.DatasetRecordings attribute) DISCOVERY_MAXIMUM_WORKERS (in module cindra.orchestration.allocation) DISCOVERY_WORKERS (in module cindra.orchestration.allocation) dispatch_key (cindra.orchestration.PendingJob property) display_progress_bars (cindra.dataclasses.RuntimeSettings attribute) dtype (cindra.io.BinaryFile attribute)

E

edge_taper_pixels (cindra.dataclasses.OnePhotonRegistration attribute) element_bytes (cindra.io.SourceFrameGeometry 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 (cindra.layout.DetectionImages attribute) enhanced_mean_image_channel_2 (cindra.dataclasses.DetectionData attribute) estimate_multi_recording_job_memory_mb() (in module cindra.orchestration) estimate_single_recording_job_memory_mb() (in module cindra.orchestration) execute_multi_recording_job() (in module cindra.orchestration) execute_single_recording_job() (in module cindra.orchestration) extend_roi() (in module cindra.detection) EXTRACT (cindra.orchestration.MultiRecordingJobNames attribute)

extract_multi_recording_fluorescence() (in module cindra.pipelines) 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) extracted_recordings (cindra.io.DatasetRecordings attribute) extraction (cindra.dataclasses.CombinedData attribute) (cindra.dataclasses.MultiRecordingRuntimeData attribute) (cindra.dataclasses.SingleRecordingRuntimeData attribute) EXTRACTION_MAXIMUM_WORKERS (in module cindra.orchestration.allocation) extraction_time (cindra.dataclasses.MultiRecordingTimingData attribute) (cindra.dataclasses.TimingData attribute) extraction_time_channel_2 (cindra.dataclasses.TimingData attribute) EXTRACTION_WORKERS (in module cindra.orchestration.allocation) ExtractionData (class in cindra.dataclasses)

F

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) final_grid_sampling (cindra.dataclasses.DiffeomorphicRegistration attribute) find_cindra_directory() (in module cindra.io) find_data_directory() (in module cindra.io) first_channel_functional (cindra.dataclasses.Main attribute) footprint (cindra.dataclasses.ROIStatistics attribute)

frame_count (cindra.dataclasses.CombinedData attribute) (cindra.dataclasses.IOData attribute) (cindra.io.SourceFrameGeometry attribute) (cindra.orchestration.PlaneGeometry attribute) frame_height (cindra.dataclasses.IOData attribute) (cindra.io.SourceFrameGeometry 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) (cindra.io.SourceFrameGeometry attribute)

G

generate_job_ids() (in module cindra.orchestration) generate_state_path() (in module cindra.gui) get_execution_state() (in module cindra.orchestration) gpu_batch_size (cindra.dataclasses.Registration attribute)

GPU_REMEDY (in module cindra.orchestration.gpu) GpuDevice (class in cindra.orchestration) GpuStatus (class in cindra.orchestration) GpuSummary (class in cindra.orchestration) grid_sampling_factor (cindra.dataclasses.DiffeomorphicRegistration attribute)

H

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

I

ignored_file_names (cindra.dataclasses.FileIO attribute) ignored_flyback_planes (cindra.dataclasses.Main attribute) image_type (cindra.dataclasses.DiffeomorphicRegistration attribute) index (cindra.orchestration.GpuDevice attribute) (cindra.orchestration.PlaneGeometry attribute) inner_neuropil_border_radius (cindra.dataclasses.SignalExtraction attribute) io (cindra.dataclasses.MultiRecordingRuntimeData attribute) (cindra.dataclasses.SingleRecordingRuntimeData attribute) IOData (class in cindra.dataclasses)

is_dataset_discovered() (in module cindra.io) is_mroi (cindra.dataclasses.AcquisitionParameters property) is_plane_converted() (in module cindra.io) is_plane_processed() (in module cindra.io) is_plane_registered() (in module cindra.io) is_recording_extractable() (in module cindra.io) is_recording_processed() (in module cindra.io) is_registered() (cindra.dataclasses.MultiRecordingRegistrationData method) (cindra.dataclasses.RegistrationData method)

J

job_id (cindra.orchestration.PendingJob attribute)

job_name (cindra.orchestration.PipelinePhase attribute) JobSizing (class in cindra.orchestration)

L

LIBRARIES_MISSING (cindra.orchestration.GpuStatus attribute) link_path (cindra.orchestration.OpenMPSummary attribute) LINKED (cindra.orchestration.OpenMPStatus attribute) 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_multi_recording_configuration() (in module cindra.orchestration) load_results() (cindra.dataclasses.ExtractionData method) load_single_recording_configuration() (in module cindra.orchestration) loadable (cindra.orchestration.OpenMPSummary attribute)

M

main (cindra.dataclasses.SingleRecordingConfiguration attribute) Main (class in cindra.dataclasses) mask (cindra.dataclasses.ROIStatistics attribute) mask_prevalence (cindra.dataclasses.ROITracking attribute) MATCHING_SPECIFIER (cindra.orchestration.PrerequisiteScope attribute) MAXIMIN (cindra.dataclasses.BaselineMethod attribute) maximum_binned_frames (cindra.dataclasses.ROIDetection attribute) maximum_block_offset (cindra.dataclasses.NonrigidRegistration attribute) MAXIMUM_CHANNEL_COUNT (in module cindra.io.context) maximum_distance (cindra.dataclasses.ROITracking 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) (cindra.layout.DetectionImages attribute) maximum_projection_channel_2 (cindra.dataclasses.DetectionData attribute) maximum_size (cindra.dataclasses.ROISelection attribute) maximum_size_channel_2 (cindra.dataclasses.ROISelection attribute) maximum_workers_per_job (cindra.orchestration.ResourceClass attribute) MEAN (cindra.dataclasses.ReferenceImageType attribute) mean_image (cindra.dataclasses.DetectionData attribute) MEAN_IMAGE (cindra.layout.DetectionImages attribute) mean_image_channel_2 (cindra.dataclasses.DetectionData attribute) MEMORY_ESTIMATE_TOLERANCE (in module cindra.orchestration.footprints) 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) memory_mb (cindra.orchestration.JobSizing attribute) memory_megabytes (cindra.orchestration.PendingJob attribute)

minimum_neuropil_pixels (cindra.dataclasses.SignalExtraction attribute) minimum_size (cindra.dataclasses.ROITracking attribute) module cindra.classification cindra.dataclasses cindra.detection cindra.extraction cindra.gui cindra.io cindra.layout cindra.orchestration cindra.pipelines cindra.registration mroi_lines (cindra.dataclasses.IOData attribute) mroi_region_borders (cindra.dataclasses.MultiRecordingIOData attribute) mroi_region_margin (cindra.dataclasses.ROISelection attribute) mroi_region_margin_channel_2 (cindra.dataclasses.ROISelection attribute) mroi_x_offset (cindra.dataclasses.IOData attribute) mroi_y_offset (cindra.dataclasses.IOData attribute) MULTI_RECORDING (cindra.dataclasses.PipelineType attribute) MULTI_RECORDING_ARRAYS_DIRECTORY_NAME (in module cindra.layout) MULTI_RECORDING_CONFIGURATION_FILENAME (in module cindra.layout) MULTI_RECORDING_DIRECTORY_NAME (in module cindra.layout) MULTI_RECORDING_PHASES (in module cindra.orchestration.jobs) MULTI_RECORDING_RUNTIME_DATA_FILENAME (in module cindra.layout) MULTI_RECORDING_TRACKER_FILENAME (in module cindra.layout) MultiRecordingArrays (class in cindra.layout) MultiRecordingConfiguration (class in cindra.dataclasses) MultiRecordingIOData (class in cindra.dataclasses) MultiRecordingJobNames (class in cindra.orchestration) MultiRecordingJobs (class in cindra.orchestration) 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

name (cindra.orchestration.GpuDevice attribute) (cindra.orchestration.ResourceClass attribute) neuropil_coefficient (cindra.dataclasses.SpikeDeconvolution attribute) neuropil_fluorescence (cindra.dataclasses.ExtractionData attribute) NEUROPIL_FLUORESCENCE (cindra.layout.RecordingArrays attribute) neuropil_fluorescence_channel_2 (cindra.dataclasses.ExtractionData attribute) neuropil_mask (cindra.dataclasses.ROIStatistics attribute) NO_DEVICES (cindra.orchestration.GpuStatus attribute) nonrigid_correlations (cindra.dataclasses.RegistrationData attribute) NONRIGID_CORRELATIONS (cindra.layout.RegistrationArrays attribute)

nonrigid_registration (cindra.dataclasses.SingleRecordingConfiguration attribute) nonrigid_x_offsets (cindra.dataclasses.RegistrationData attribute) NONRIGID_X_OFFSETS (cindra.layout.RegistrationArrays attribute) nonrigid_y_offsets (cindra.dataclasses.RegistrationData attribute) NONRIGID_Y_OFFSETS (cindra.layout.RegistrationArrays 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) OpenMPStatus (class in cindra.orchestration) OpenMPSummary (class in cindra.orchestration) order_phases_by_execution() (in module cindra.orchestration) OUTPUT_DIRECTORY_NAME (in module cindra.layout)

output_path (cindra.dataclasses.FileIO attribute) (cindra.dataclasses.IOData attribute) (cindra.dataclasses.MultiRecordingRuntimeData attribute) (cindra.dataclasses.SingleRecordingRuntimeData attribute) output_root (cindra.io.RecordingPlanes attribute) (cindra.orchestration.SingleRecordingJobs attribute) overlap_mask (cindra.dataclasses.ROIMask attribute)

P

PARAMETERS_FILENAME (in module cindra.layout) parse_plane_specifier() (in module cindra.layout) (in module cindra.orchestration) PendingJob (class in cindra.orchestration) per_specifier (cindra.orchestration.PipelinePhase attribute) pipeline_type (cindra.dataclasses.MultiRecordingConfiguration attribute) (cindra.dataclasses.SingleRecordingConfiguration attribute) PipelineArray (in module cindra.layout) PipelinePhase (class in cindra.orchestration) PipelineType (class in cindra.dataclasses) pixel_count (cindra.dataclasses.ROIStatistics attribute) pixel_prevalence (cindra.dataclasses.ROITracking attribute) pixel_weights (cindra.dataclasses.ROIMask attribute) plane_count (cindra.dataclasses.CombinedData attribute) (cindra.io.RecordingPlanes attribute) (cindra.orchestration.SingleRecordingJobs attribute) plane_frame_counts (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_paths (cindra.io.RecordingPlanes attribute) PLANE_SPECIFIER_PREFIX (in module cindra.layout) plane_specifiers (cindra.io.RecordingPlanes 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) PlaneGeometry (class in cindra.orchestration)

planes (cindra.orchestration.RecordingGeometry attribute) possible (cindra.orchestration.MultiRecordingJobs attribute) (cindra.orchestration.SingleRecordingJobs 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) prerequisite (cindra.orchestration.PipelinePhase attribute) prerequisite_scope (cindra.orchestration.PipelinePhase attribute) PrerequisiteScope (class in cindra.orchestration) PREVIEWED (cindra.orchestration.OpenMPStatus attribute) prime_dataset() (in module cindra.orchestration) prime_recording() (in module cindra.orchestration) principal_component_extreme_images (cindra.dataclasses.RegistrationData attribute) PRINCIPAL_COMPONENT_EXTREME_IMAGES (cindra.layout.RegistrationArrays attribute) principal_component_projections (cindra.dataclasses.RegistrationData attribute) PRINCIPAL_COMPONENT_PROJECTIONS (cindra.layout.RegistrationArrays attribute) principal_component_shift_metrics (cindra.dataclasses.RegistrationData attribute) PRINCIPAL_COMPONENT_SHIFT_METRICS (cindra.layout.RegistrationArrays attribute) probability_threshold (cindra.dataclasses.ROISelection attribute) probability_threshold_channel_2 (cindra.dataclasses.ROISelection attribute) PROCESS (cindra.orchestration.SingleRecordingJobNames attribute) process_plane() (in module cindra.pipelines) processed (cindra.io.RecordingPlanes attribute) PROCESSING_MAXIMUM_WORKERS (in module cindra.orchestration.allocation) processing_workers (cindra.dataclasses.TimingData attribute) PROCESSING_WORKERS (in module cindra.orchestration.allocation) 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) raw_frame_pixels (cindra.orchestration.RecordingGeometry attribute) read_tracked_recording_geometry() (in module cindra.orchestration) read_viewer_state() (in module cindra.gui) recording_count (cindra.dataclasses.ROIMask attribute) recording_directories (cindra.dataclasses.RecordingIO attribute) recording_id (cindra.dataclasses.MultiRecordingIOData attribute) recording_ids (cindra.io.DatasetRecordings attribute) (cindra.orchestration.MultiRecordingJobs attribute) recording_io (cindra.dataclasses.MultiRecordingConfiguration attribute) recording_roots (cindra.io.DatasetRecordings attribute) RecordingArrays (class in cindra.layout) RecordingGeometry (class in cindra.orchestration) RecordingIO (class in cindra.dataclasses) RecordingPlanes (class in cindra.io) reference_frame_count (cindra.dataclasses.Registration attribute) reference_image (cindra.dataclasses.RegistrationData attribute) REFERENCE_IMAGE (cindra.layout.RegistrationArrays attribute) ReferenceImageType (class in cindra.dataclasses) region_count (cindra.orchestration.RecordingGeometry attribute) REGISTER (cindra.orchestration.SingleRecordingJobNames attribute) register_plane() (in module cindra.registration) register_recording_plane() (in module cindra.pipelines) 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) registered_planes (cindra.io.RecordingPlanes attribute) registration (cindra.dataclasses.MultiRecordingRuntimeData attribute) (cindra.dataclasses.SingleRecordingConfiguration attribute) (cindra.dataclasses.SingleRecordingRuntimeData attribute) Registration (class in cindra.dataclasses) REGISTRATION_DATA_DIRECTORY_NAME (in module cindra.layout) REGISTRATION_GPU_WORKERS (in module cindra.orchestration.allocation) REGISTRATION_MAXIMUM_WORKERS (in module cindra.orchestration.allocation) 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) registration_workers (cindra.dataclasses.TimingData attribute) REGISTRATION_WORKERS (in module cindra.orchestration.allocation) RegistrationArrays (class in cindra.layout) RegistrationData (class in cindra.dataclasses) 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) remedy (cindra.orchestration.GpuSummary property) repeat_binarization (cindra.dataclasses.FileIO attribute) repeat_registration (cindra.dataclasses.DiffeomorphicRegistration attribute) (cindra.dataclasses.Registration attribute) repeat_selection (cindra.dataclasses.RecordingIO attribute) resolve_acquisition_parameters() (in module cindra.io) resolve_active_binary_marker() (in module cindra.io) resolve_array_name() (in module cindra.layout) resolve_array_path() (in module cindra.layout) resolve_binarization_marker_name() (in module cindra.layout) resolve_channel_2_name() (in module cindra.layout) resolve_dataset_path() (in module cindra.layout) resolve_dataset_recordings() (in module cindra.io) resolve_downstream_phases() (in module cindra.orchestration) resolve_gpu_devices() (in module cindra.orchestration) resolve_maximum_roi_count() (in module cindra.orchestration)

resolve_multi_recording_contexts() (in module cindra.io) resolve_multi_recording_job_universe() (in module cindra.orchestration) resolve_multi_recording_jobs() (in module cindra.orchestration) resolve_multi_recording_prerequisites() (in module cindra.orchestration) resolve_openmp_runtime() (in module cindra.orchestration) resolve_output_path() (in module cindra.layout) resolve_pipeline_jobs() (in module cindra.orchestration) resolve_plane_path() (in module cindra.layout) resolve_plane_specifier() (in module cindra.layout) (in module cindra.orchestration) resolve_recording_geometry() (in module cindra.orchestration) resolve_recording_planes() (in module cindra.io) resolve_recording_roots() (in module cindra.io) resolve_registration_marker_name() (in module cindra.layout) resolve_registration_resource_class() (in module cindra.orchestration) resolve_session_load() (in module cindra.orchestration) resolve_single_recording_contexts() (in module cindra.io) resolve_single_recording_job_universe() (in module cindra.orchestration) resolve_single_recording_jobs() (in module cindra.orchestration) resolve_single_recording_prerequisites() (in module cindra.orchestration) resolve_source_frame_geometry() (in module cindra.io) resolve_stage_workers() (in module cindra.orchestration) resolve_tiff_conversion_plan() (in module cindra.io) resolved (cindra.io.RecordingPlanes attribute) (cindra.orchestration.MultiRecordingJobs attribute) (cindra.orchestration.RecordingGeometry attribute) (cindra.orchestration.SingleRecordingJobs attribute) resolved_workers (cindra.orchestration.PendingJob attribute) resource_class (cindra.orchestration.PendingJob attribute) RESOURCE_CLASS_BY_JOB_NAME (in module cindra.orchestration.allocation) ResourceClass (class in cindra.orchestration) rigid_correlations (cindra.dataclasses.RegistrationData attribute) RIGID_CORRELATIONS (cindra.layout.RegistrationArrays attribute) rigid_x_offsets (cindra.dataclasses.RegistrationData attribute) RIGID_X_OFFSETS (cindra.layout.RegistrationArrays attribute) rigid_y_offsets (cindra.dataclasses.RegistrationData attribute) RIGID_Y_OFFSETS (cindra.layout.RegistrationArrays 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_MASKS (cindra.layout.RecordingArrays attribute) roi_number (cindra.dataclasses.AcquisitionParameters attribute) roi_selection (cindra.dataclasses.MultiRecordingConfiguration attribute) roi_statistics (cindra.dataclasses.ExtractionData attribute) ROI_STATISTICS (cindra.layout.RecordingArrays 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) ROISelection (class in cindra.dataclasses) ROIStatistics (class in cindra.dataclasses) ROITracking (class in cindra.dataclasses) run_multi_recording_pipeline() (in module cindra.orchestration) run_registration_viewer() (in module cindra.gui) run_roi_viewer() (in module cindra.gui) run_single_recording_pipeline() (in module cindra.orchestration) run_tracking_viewer() (in module cindra.gui) runtime (cindra.dataclasses.MultiRecordingConfiguration attribute) (cindra.dataclasses.MultiRecordingRuntimeContext attribute) (cindra.dataclasses.RuntimeContext attribute) (cindra.dataclasses.SingleRecordingConfiguration attribute) RUNTIME_MISSING (cindra.orchestration.GpuStatus attribute) runtime_path (cindra.orchestration.OpenMPSummary attribute) RuntimeContext (class in cindra.dataclasses) RuntimeSettings (class in cindra.dataclasses)

S

sampling_rate (cindra.dataclasses.CombinedData attribute) (cindra.dataclasses.IOData attribute) (cindra.orchestration.PlaneGeometry 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_combined_data() (in module cindra.pipelines) 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_sampling (cindra.dataclasses.DiffeomorphicRegistration attribute) searched_paths (cindra.orchestration.OpenMPSummary attribute) 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) set_execution_state() (in module cindra.orchestration) 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) single_recording (cindra.orchestration.PendingJob attribute)

SINGLE_RECORDING_CONFIGURATION_FILENAME (in module cindra.layout) SINGLE_RECORDING_PHASES (in module cindra.orchestration.jobs) SINGLE_RECORDING_RUNTIME_DATA_FILENAME (in module cindra.layout) SINGLE_RECORDING_TRACKER_FILENAME (in module cindra.layout) SingleRecordingConfiguration (class in cindra.dataclasses) SingleRecordingJobNames (class in cindra.orchestration) SingleRecordingJobs (class in cindra.orchestration) SingleRecordingRuntimeData (class in cindra.dataclasses) size (cindra.io.BinaryFile property) size_multi_recording_job() (in module cindra.orchestration) size_single_recording_job() (in module cindra.orchestration) skewness (cindra.dataclasses.ROIStatistics attribute) solidity (cindra.dataclasses.ROIStatistics attribute) soma_mask (cindra.dataclasses.ROIStatistics attribute) source_element_bytes (cindra.orchestration.RecordingGeometry attribute) source_resolved (cindra.orchestration.RecordingGeometry attribute) SourceFrameGeometry (class in cindra.io) spatial_highpass_window (cindra.dataclasses.OnePhotonRegistration attribute) (cindra.dataclasses.ROIDetection attribute) spatial_smoothing_sigma (cindra.dataclasses.Registration attribute) SPAWNED_CHILD_MEMORY_MB (in module cindra.orchestration.footprints) speed_factor (cindra.dataclasses.DiffeomorphicRegistration attribute) spike_deconvolution (cindra.dataclasses.MultiRecordingConfiguration attribute) (cindra.dataclasses.SingleRecordingConfiguration attribute) SpikeDeconvolution (class in cindra.dataclasses) spikes (cindra.dataclasses.ExtractionData attribute) SPIKES (cindra.layout.RecordingArrays attribute) spikes_channel_2 (cindra.dataclasses.ExtractionData attribute) start_execution_session() (in module cindra.orchestration) status (cindra.orchestration.GpuSummary attribute) (cindra.orchestration.OpenMPSummary attribute) step_sizes (cindra.dataclasses.ROITracking attribute) subsample_movie() (cindra.io.BinaryFile method) subtracted_fluorescence (cindra.dataclasses.ExtractionData attribute) SUBTRACTED_FLUORESCENCE (cindra.layout.RecordingArrays 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 (cindra.dataclasses.ROITracking attribute) threshold_scaling (cindra.dataclasses.ROIDetection attribute) TIFF_DECODE_CEILING (in module cindra.io.tiff) TIFF_EXTENSIONS (in module cindra.io.tiff) 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_memory_mb (cindra.orchestration.GpuDevice attribute) total_processing_time (cindra.dataclasses.TimingData attribute)

total_registration_time (cindra.dataclasses.TimingData attribute) track_rois_across_recordings() (in module cindra.detection) tracker_path (cindra.orchestration.PendingJob attribute) tracking (cindra.dataclasses.MultiRecordingRuntimeData attribute) TRACKING_TEMPLATE_MASKS_FILENAME (in module cindra.layout) tracking_time (cindra.dataclasses.MultiRecordingTimingData attribute) transformed_enhanced_mean_image (cindra.dataclasses.MultiRecordingRegistrationData attribute) TRANSFORMED_ENHANCED_MEAN_IMAGE (cindra.layout.MultiRecordingArrays attribute) transformed_enhanced_mean_image_channel_2 (cindra.dataclasses.MultiRecordingRegistrationData attribute) transformed_maximum_projection (cindra.dataclasses.MultiRecordingRegistrationData attribute) TRANSFORMED_MAXIMUM_PROJECTION (cindra.layout.MultiRecordingArrays attribute) transformed_maximum_projection_channel_2 (cindra.dataclasses.MultiRecordingRegistrationData attribute) transformed_mean_image (cindra.dataclasses.MultiRecordingRegistrationData attribute) TRANSFORMED_MEAN_IMAGE (cindra.layout.MultiRecordingArrays attribute) transformed_mean_image_channel_2 (cindra.dataclasses.MultiRecordingRegistrationData attribute) two_channels (cindra.dataclasses.Main attribute) (cindra.orchestration.RecordingGeometry attribute) two_step_registration (cindra.dataclasses.Registration attribute) two_step_registration_time (cindra.dataclasses.TimingData attribute)

U

universe (cindra.orchestration.MultiRecordingJobs attribute) (cindra.orchestration.SingleRecordingJobs attribute)

UNRESOLVED (cindra.orchestration.OpenMPStatus attribute) unresolved_reason (cindra.orchestration.OpenMPSummary attribute) UNSUPPORTED_PLATFORM (cindra.orchestration.GpuStatus attribute)

V

valid_x_range (cindra.dataclasses.RegistrationData attribute) valid_y_range (cindra.dataclasses.RegistrationData attribute)

validate_job_prerequisites() (in module cindra.orchestration) virtual_plane_count (cindra.dataclasses.AcquisitionParameters property)

W

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

WORKER_MEMORY_MB (in module cindra.orchestration.footprints) workers_per_job (cindra.orchestration.ResourceClass attribute) write_tiff() (cindra.io.BinaryFile method)

X

x_pixels (cindra.dataclasses.ROIMask attribute)

Y

y_pixels (cindra.dataclasses.ROIMask attribute)