NWBInspector
  • Best Practices
    • General
      • Neurodata Types
        • Naming Conventions
        • Do Not Use Slashes or Colons in Names
        • Descriptions
        • Empty Strings
        • Empty Data
        • Avoid Duplication of Metadata
    • NWBFile Metadata
      • File Extensions
      • File Organization
        • Global Date and Time Reference
        • Acquisition & Processing
        • Processing Module Names
      • File Metadata
        • Session ID
        • Identifier
        • Experimenter
        • Experiment Description
        • Institution
        • Keywords
        • Link to DOI Publications
      • Subject
        • Subject ID
        • Subject Sex
        • Subject Species
        • Subject Strain
        • Subject Weight
        • Subject Age
        • Date of Birth
    • Time Series
      • Data Orientation
      • Units of Measurement
      • Time Series: Time References
      • Subtypes
      • Breaks in Continuity
      • Timestamps without NaNs
      • Timestamps vs. Start & Rate
      • Avoid Negative Timestamps
      • Chunk Data
      • Compress Data
      • Unknown Resolution
      • Zero Rate
      • Positive Rate
    • Tables
      • Table Values
      • Empty Tables
      • Tables With Only a Single Row
      • Tables With an Entire Column as NaN
      • Table Region Data
      • Boolean Columns
      • Timing Columns
      • Unique ids
    • Behavior
      • SpatialSeries
        • SpatialSeries Dimensionality
        • SpatialSeries Units
        • SpatialSeries General Units
        • SpatialSeries Data Values
    • Extracellular electrophysiology
      • Electrodes
        • Location
        • Ontologies
        • Anatomical Coordinates
        • Relative Coordinates
        • Avoid Duplication of Metadata
      • Units Table
        • Spike Times Column Required
        • Duration
        • Units Resolution
        • Spike Times in Seconds
        • Negative Spike Times
        • Observation Intervals
        • No NaN Spike Times
        • Ascending Spike Times
      • ElectricalSeries
        • Data Type and Conversion
    • Optical physiology
      • Plane Segmentation
        • Image Shape Consistency
      • ImagingPlane
        • Location
    • Intracellular electrophysiology
      • IntracellularElectrode
        • Location
    • Optogenetics
      • OptogeneticSeries
    • ImageSeries
      • Storage of ImageSeries
        • Use external mode for videos of animals
        • Use internal dataset for videos of neurophysiological data
        • Use relative path for external mode
        • Starting frame only with external file
    • Images
      • Storage of Images
        • Storing the order of images in an Images object
        • Use of IndexSeries
    • Simulated Data
    • Extensions
      • Define new neurodata_types at the top-level (do not nest type definitions)
      • Build on and reuse existing neurodata types
      • Strive for backward compatible changes
      • Provide documentation
      • Write the specification to the NWBFile
      • Use Attributes for small metadata related to a particular data object (Group or Dataset)
      • Link data to relevant metadata
      • Best practices for object names
      • Best practices for naming neurodata_types
      • Limit flexibility: Consider data reuse and tool developers
      • Use the ndx-template to create new extensions
      • Get the community involved
  • User Guide: Inspecting an NWBFile
    • Installation
    • Using the Command Line Interface (CLI)
      • Using the DANDI Configuration
      • Streaming
      • Formatting the Report
      • Saving the Report
      • Faster Inspection
      • Skipping Specific Checks
      • Selecting Specific Checks
      • External Modules
    • Using the Library
      • InspectorMesssage objects
      • Inspect a single NWBFile
      • Inspect a Directory or List of Paths to NWBFiles
      • Using the DANDI Configuration
      • Inspect a Dandiset
      • Examining the Default Check Registry
    • Using the Library: Advanced
      • Yielding and Iterating
      • Fetching and inspecting individual DANDI assets
      • Format Reports
  • Developer Guide
    • Coding Style and pre-commit
    • Adding Custom Checks to the Registry
    • Disable Tests That Require Network Connection
    • Making a Release
  • Contributing New Checks
    • Overview
    • Step-by-Step Guide
      • 1. Propose Your Check
      • 2. Choose the Right Location
      • 3. Write Your Check
      • 4. Choose the Right Importance Level
      • 5. Write Tests
      • 6. Add Check to the Public Interface
      • 7. Add Check to the Documentation
      • 7. Best Practices for Check Implementation
      • 8. Submit Your PR
    • Example Check
    • Common Pitfalls
    • Need Help?
  • Checks by Importance
    • CRITICAL (24)
    • BEST PRACTICE VIOLATION (44)
    • BEST PRACTICE SUGGESTION (20)

API Documentation

  • Check Functions
    • NWBFile Metadata
      • check_session_start_time_old_date()
      • check_session_start_time_future_date()
      • check_experimenter_exists()
      • check_experimenter_form()
      • check_experiment_description()
      • check_institution()
      • check_keywords()
      • check_subject_exists()
      • check_doi_publications()
      • check_publication_list_format()
      • check_subject_age()
      • check_subject_proper_age_range()
      • check_subject_age_reference()
      • check_subject_id_exists()
      • check_subject_weight()
      • _check_subject_sex_defaults()
      • _check_subject_sex_c_elegans()
      • check_subject_sex()
      • check_subject_species_exists()
      • check_subject_species_form()
      • check_processing_module_name()
      • check_session_id_no_slashes()
      • check_subject_id_no_slashes()
      • check_file_extension()
    • General
      • check_name_slashes()
      • check_name_colons()
      • check_description()
    • NWB Containers
      • check_large_dataset_compression()
      • check_small_dataset_compression()
      • check_empty_string_for_optional_attribute()
    • Time Series
      • check_regular_timestamps()
      • check_data_orientation()
      • check_timestamps_match_first_dimension()
      • check_timestamps_ascending()
      • check_timestamps_without_nans()
      • check_timestamp_of_the_first_sample_is_not_negative()
      • check_missing_unit()
      • check_resolution()
      • check_time_series_duration()
      • check_time_series_data_is_not_empty()
      • check_rate_not_below_threshold()
    • Tables
      • check_dynamic_table_region_data_validity()
      • check_empty_table()
      • check_time_intervals_start_time_not_constant()
      • check_time_interval_time_columns()
      • check_time_intervals_stop_after_start()
      • check_column_binary_capability()
      • check_single_row()
      • check_table_values_for_dict()
      • check_col_not_nan()
      • check_ids_unique()
      • check_table_time_columns_are_not_negative()
      • check_time_intervals_duration()
    • Behavior
      • check_spatial_series_dims()
      • check_compass_direction_unit()
      • check_spatial_series_radians_magnitude()
      • check_spatial_series_degrees_magnitude()
      • check_spatial_series_unit()
    • Intracellular Electrophysiology (icephys)
      • check_intracellular_electrode_cell_id_exists()
      • check_sweeptable_deprecated()
      • check_intracellular_electrode_location_allen_ccf()
    • Extracellular Electrophysiology (ecephys)
      • check_units_table_has_spikes()
      • check_negative_spike_times()
      • check_units_resolution_is_set()
      • check_units_resolution_is_valid()
      • check_spike_times_not_in_samples()
      • check_electrical_series_dims()
      • check_electrical_series_reference_electrodes_table()
      • check_spike_times_not_in_unobserved_interval()
      • check_spike_times_without_nans()
      • check_ascending_spike_times()
      • check_electrical_series_unscaled_data()
      • check_units_table_duration()
      • check_electrodes_location_allen_ccf()
    • Optical Electrophysiology (ophys)
      • check_roi_response_series_dims()
      • check_roi_response_series_link_to_plane_segmentation()
      • check_emission_lambda_in_nm()
      • check_excitation_lambda_in_nm()
      • check_plane_segmentation_image_mask_shape_against_ref_images()
      • check_imaging_plane_location_allen_ccf()
    • Optogenetics (ogen)
      • check_optogenetic_stimulus_site_has_optogenetic_series()
    • ImageSeries
      • check_image_series_external_file_valid()
      • check_image_series_external_file_relative()
      • check_image_series_data_size()
      • check_image_series_starting_frame_without_external_file()
    • Images
      • check_order_of_images_unique()
      • check_order_of_images_len()
  • Core Functions
    • inspect_all()
    • _pickle_inspect_nwb()
    • inspect_nwbfile()
    • _intercept_in_vitro_protein()
    • inspect_nwbfile_object()
    • run_checks()
    • inspect_dandiset()
    • inspect_dandi_file_path()
    • inspect_url()
  • Data Classes and Check Registration
    • Importance
    • Severity
    • InspectorMessage
      • InspectorMessage.__repr__()
    • register_check()
    • _auto_parse()
    • _parse_location()
  • Organization and Display Tools
  • Generic Utils
NWBInspector
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