SpikeLab

Contents

  • Getting Started
    • Installation
      • Basic Install
      • Optional Extras
      • Development Install
    • Quick Start
      • Creating a SpikeData Object
      • Loading from a File
      • Plotting
      • Basic Analysis
      • Further Reading
  • Guides
    • Loading Data
      • From pickle files
      • From HDF5 files
        • The spike_times_unit parameter
      • From NWB files
      • From KiloSort/Phy output
      • From SpikeInterface
      • From SpikeLab sorted .npz
      • From the IBL database
      • From Neo SpikeTrains
      • From raw data
        • From threshold detection
        • From a spike count raster
    • Spike Sorting and Curation
      • Spike Sorting
        • Prerequisites
        • Basic usage
        • Configuration and presets
        • Multi-stream recordings
        • Reusing intermediate results
        • Stimulation Artifact Removal
      • Unit Curation
        • Individual criteria
        • Merge-based deduplication
        • Batch curation
        • Curation history
      • Sorting Concatenated Recordings
      • Handling Sort Failures
    • Spike Analysis
      • Population Rate
      • Burst Detection
      • Burst Widths
      • Burst Sensitivity Analysis
      • Per-Unit Metrics
        • Firing rates
        • Inter-spike intervals
        • Spike-triggered population rate
      • Burst Participation per Unit
      • Fraction of Spikes in Bursts
      • Selecting and Combining Data
        • Unit selection
        • Time selection
        • Appending recordings
        • Combining units
      • Pairwise Metrics
      • Further Reading
    • Instantaneous Firing Rates
      • Instantaneous Firing Rates
        • ISI interpolation
        • Sliding window
        • Working with RateData
      • Dimensionality Reduction
      • Pairwise Firing-Rate Correlations
      • Further Reading
    • Event-Aligned Analysis
      • Aligning to Events
      • RateSliceStack
      • SpikeSliceStack
        • Applying a function across slices
        • Subsetting slice stacks
      • Slice-to-Slice Unit Correlations
      • Slice-to-Slice Time Correlations
      • Unit-to-Unit PCA
      • Rank-Order Analysis
      • Temporal Trends and Stability
        • Shuffled Null Distributions
    • Pairwise Analysis
      • Spike Time Tiling Coefficient (STTC)
      • Firing-Rate Correlations
      • FR Correlation vs STTC Scatter
      • Network Analysis
      • Spatial Network Visualization
    • Shuffled Data
      • Single Shuffle
      • Shuffle Stacks
      • Unit Subset Stacks
      • Comparing to the Null Distribution
    • GPLVM Analysis
      • Fitting a GPLVM
      • Post-fit Analysis
        • State entropy
        • Continuity probability
        • Average state probability
        • Consecutive state durations
      • Visualisation
    • Exporting Data
      • To HDF5
        • Ragged vs raster style
        • The spike_times_unit parameter
        • Exporting raw data
      • To NWB
      • To KiloSort
      • To pickle
    • Workspace Persistence
      • Creating a Workspace
      • Saving and Loading
      • Listing and Retrieving
      • Lazy Loading
      • Merging Workspaces
    • MCP Server
      • Starting the server
      • Tool categories
        • Data loading tools
        • Analysis tools
        • Export tools
      • Workspace addressing
    • Parallel Computing
      • Thread-Pool Parallelism
      • Numba Acceleration
    • Batch Jobs
      • Prerequisites
      • Setting Up a Session
      • Analysis Jobs
        • Submitting
        • Writing an analysis script
        • Retrieving results
      • Sorting Jobs
        • Submitting
        • Retrieving results
      • Policy Guardrails
      • Docker Images
        • Base images
        • Temporary images
      • Monitoring Jobs
  • API Reference
    • Core Data Structures
      • SpikeData
        • SpikeData
      • RateData
        • RateData
      • Pairwise Comparisons
        • PairwiseCompMatrix
        • PairwiseCompMatrixStack
      • RateSliceStack
        • RateSliceStack
      • SpikeSliceStack
        • SpikeSliceStack
    • Utilities
      • Utilities
        • get_sttc()
        • swap()
        • randomize()
        • trough_between()
        • ensure_h5py()
        • times_from_ms()
        • to_ms()
        • extract_waveforms()
        • check_neuron_attributes()
        • get_channels_for_unit()
        • compute_avg_waveform()
        • get_valid_spike_times()
        • waveforms_by_channel()
        • extract_unit_waveforms()
        • consecutive_durations()
        • gplvm_state_entropy()
        • gplvm_continuity_prob()
        • gplvm_average_state_probability()
        • shuffle_z_score()
        • shuffle_percentile()
        • slice_trend()
        • slice_stability()
      • Statistical Utilities
        • linear_regression()
        • pairwise_tests()
        • paired_test()
        • omnibus_test()
      • Plotting Utilities
        • plot_distribution()
        • plot_pvalue_matrix()
        • plot_scatter()
        • plot_scatter_with_marginals()
        • plot_manifold()
        • plot_lines()
        • plot_percentile_bands()
        • plot_burst_sensitivity()
        • plot_aligned_slice_single_unit()
        • plot_heatmap()
        • plot_recording()
        • plot_spatial_network()
    • Data I/O
      • Data Loaders
        • load_spikedata_from_hdf5()
        • load_spikedata_from_hdf5_raw_thresholded()
        • load_spikedata_from_nwb()
        • load_spikedata_from_kilosort()
        • load_spikedata_from_spikeinterface()
        • load_spikedata_from_spikeinterface_recording()
        • load_spikedata_from_pickle()
        • load_spikedata_from_ibl()
        • query_ibl_probes()
        • load_spikedata_from_spikelab_sorted_npz()
      • Data Exporters
        • export_spikedata_to_hdf5()
        • export_spikedata_to_nwb()
        • export_spikedata_to_kilosort()
        • export_to_pickle()
      • S3 Utilities
        • is_s3_url()
        • parse_s3_url()
        • download_from_s3()
        • upload_to_s3()
        • ensure_local_file()
    • Persistence
      • Workspace
        • AnalysisWorkspace
        • LazyAnalysisWorkspace
        • WorkspaceManager
        • get_workspace_manager()
    • Spike Sorting and Curation
      • Spike Sorting
        • Entry Points
        • Configuration
        • Backend Registry
        • Classified Exceptions
        • Post-Failure Classifiers
      • Curation
        • curate_by_min_spikes()
        • curate_by_firing_rate()
        • curate_by_isi_violations()
        • curate_by_snr()
        • curate_by_std_norm()
        • compute_waveform_metrics()
        • curate()
        • build_curation_history()
        • curate_by_merge_duplicates()
    • Batch Jobs
      • Batch Jobs
        • Models
        • Policy Engine
        • Profile Loading
        • Run Session
        • Kubernetes Backend
        • S3 Storage
        • Artifact Packager
        • Credentials
        • Validation
    • Server
      • MCP Server
        • main()
SpikeLab
  • Overview: module code

All modules for which code is available

  • spikelab.batch_jobs.artifact_packager
  • spikelab.batch_jobs.backend_k8s
  • spikelab.batch_jobs.credentials
  • spikelab.batch_jobs.models
  • spikelab.batch_jobs.policy
  • spikelab.batch_jobs.profiles
  • spikelab.batch_jobs.session
  • spikelab.batch_jobs.storage_s3
  • spikelab.batch_jobs.validation
  • spikelab.data_loaders.data_exporters
  • spikelab.data_loaders.data_loaders
  • spikelab.data_loaders.s3_utils
  • spikelab.mcp_server.server
  • spikelab.spike_sorting._classifier
  • spikelab.spike_sorting._exceptions
  • spikelab.spike_sorting.backends
    • spikelab.spike_sorting.backends.base
  • spikelab.spike_sorting.config
  • spikelab.spike_sorting.pipeline
  • spikelab.spikedata.curation
  • spikelab.spikedata.pairwise
  • spikelab.spikedata.plot_utils
  • spikelab.spikedata.ratedata
  • spikelab.spikedata.rateslicestack
  • spikelab.spikedata.spikedata
  • spikelab.spikedata.spikeslicestack
  • spikelab.spikedata.stat_utils
  • spikelab.spikedata.utils
  • spikelab.workspace.workspace

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