Best Practices

The goal of the following document is to provide users of the NWB:N with additional guidelines on common best practices to facilitate consistent use of the standard and help avoid common problems and most effectively leverage the NWB:N data standard and its ecosystem of software tools.

Authors

Oliver Ruebel, Andrew Tritt, Ryan Ly, and Ben Dichter

last edited: January 22, 2021

Preamble

To enable NWB:N to accommodate the needs of the diverse neuroscience community, NWB:N provides a great degree of flexibility. In particular, the number of instances of a particular neurodata_type and corresponding names are often not fixed, to enable, e.g., storage of data from arbitrary numbers of devices withing the same file. While this flexibility is essential to enable coverage of a broad range of use-cases, it can also lead to ambiguity. At the same time, we ultimately have the desire to have the schema as strict-as-possible to provide users and tool builders with a consistent organization of data. As such, we need to strike a fine balance between flexibility to enable support for varying experiments and use-cases and strictness in the schema to enforce standard organization of data. The following “best practices” provide advice from developers and experienced users that outline some of the pitfalls to avoid and common usage patterns to emulate.

NWBFile

An NWBFile object generally contains data from a single experimental session.

file organization

The /acquisition group is specifically for time series measurements that are acquired from an acquisition system, e.g. an ElectricalSeries with the voltages from the recording systems or the output of the position sensors (like your wheel position). The processing modules are for intermediate data. If you take the wheel position and derive the position of the animal in meters, that would go in /processing/behavior/Position/SpatialSeries. An LFP signal that is a downsampled version of the acquired data would go in /processing/ecephys/LFP/ElectricalSeries. It may not always be 100% clear whether data is acquired or derived, so in those cases you should just use your best judgement.

identifiers

NWBFile has two distinct places for ids: session_id and identifier.

  • The session_id field marks unique experimental sessions. The session_id should have a one-to-one relationship with a recording session. Sometimes you may find yourself having multiple NWB files that correspond to the same session. This can happen for instance if you separate out processing steps into multiple files or if you want to compare different processing systems. In this case, the session_id should be the same for each file. Each lab should use a standard for session_id so that sessions have unique names within the lab and the sessions ids are human-readable.
  • The identifier tag should be a globally unique value for the NWBFile. Two different NWBFiles from the same session should have different identifier values if they differ in any way. It is recommended that you use a unique id generator like uuid to ensure its uniqueness and it is not important that the identifier field is human readable.

TimeSeries

Many of the neurodata_types in NWB inherit from the TimeSeries neurodata_type. When using TimeSeries or any of its descendants, make sure the following are followed.

  • Time dimension goes first. In TimeSeries.data, the first dimension on the disk is always time. Keep in mind that the dimensions are reversed in MatNWB, so in memory in MatNWB the time dimension must be last. In PyNWB the order of the dimensions is the same in memory as on disk, so the time index should be first.
  • ElectrialSeries are reserved for neural data. ElectrialSeries holds signal from electrodes positioned in or around the brain that are monitoring neural activity, and only those electrodes should be in the electrodes table. Use TimeSeries for other data in units Volts, such as the reading on a force-sensitive resistor.
  • times are always in seconds. timestamps or starting_time should be in seconds with respect to the timestamps_reference_time.
  • TimeSeries data should be stored as one continuous stream. Data should be stored in one continuous stream, as it is acquired, not by trial as is often reshaped for analysis. Data can be trial-aligned on-the-fly using the trials table. Storing measured data as a continuous stream ensures that other users have access to the inter-trial data, and that we can align the data with whatever window they need. If you only have data in specific segments of time, then only include those timepoints in the data. Use timestamps, even if there is a constant sampling rate within each segment, and have the timestamps correctly reflect the gaps in the recording. Use the TimeSeries.description field to explain how the data was segmented.
  • If the sampling rate is constant, use rate. TimeSeries allows you to specify time using either timestamps or rate and starting_time (which defaults to 0). For TimeSeries objects that have a constant sampling rate, rate should be used instead of timestamps. This will ensure that you can use analysis and visualization tools that rely on a constant sampling rate.
  • Use chunking to optimize reading of large data for your use case. By default, when using the HDF5 backend, TimeSeries data are stored on disk in C-ordering. This means that if “data” dataset of a TimeSeries has multiple dimensions, then all data from a single timestamp are stored contiguously on disk, then data from the next timestamp are stored contiguously. This storage scheme may be optimal for certain uses, such as slicing TimeSeries by time; however, it may be sub-optimal for other uses, such as reading data from all timestamps for a particular value in the second or third dimension. Data writers can optimize the storage of large data arrays for particular uses by using chunking and compression. For more information about chunking and compression, consult the PyNWB documentation and MatNWB documentation.

DynamicTables

DynamicTable allow you to define custom columns, which offer a high degree of flexibility.

  • Store data with long columns rather than long rows. When constructing dynamic tables, keep in mind that the data is stored by column, so it will be inefficient to store data in a table with many columns.

bools

  • Use boolean values where appropriate. Although boolean values (True/False) are not used in the core schema, they are a supported data type, and we encourage the use of DynamicTable columns with boolean values. For instance, boolean values would be appropriate for a correct custom column to the trials table.

times

  • Times are always stored in seconds in NWB:N. This rule applies to times in TimeSeries, TimeIntervals and across NWB:N in general. E.g., in TimeInterval objects such as the trials and epochs table, start_time and stop_time should both be in seconds with respect to the timestamps_reference_time (which by default is set to the session_start_time).
  • Additional time columns in TimeInterval tables (e.g., trials) should have _time as name suffix. E.g., if you add more times in the trials table, for instance a subject response time, name it with _time at the end (e.g. response_time) and store the time values in seconds from the timestamps_reference_time, just like start_time and stop_time.
  • Set the timestamps_reference_time if you need to use a different reference time. Rather than relative times, it can in practice be useful to use a common global reference time across files (e.g., Posix time). To do so, NWB:N allows users to set the timestamps_reference_time which serves as reference for all timestamps in a file. By default, timestamp_reference_time is usually set to the session_start_time to use relative times.

electrodes: ‘location’

  • The ‘location’ field should reflect your best estimate of the recorded brain area. The 'location' column of the electrodes table is meant to store the brain region that the electrode as in. Different labs have different standards for electrode localization. Some use atlases and coordinate maps to precisely place an electrode, and use physiological measures to confirm its placement. Others use histology or imaging processing algorithms to identify regions after-the-fact. You fill this column with localization results from your most accurate method. For instance, if you target electrodes using physiology, and later use histology to confirm placement, we would recommend that you add a new column to the electrodes table called 'location_target', set those values to the original intended target, and alter the values of 'location' to match the histology results.
  • Use established ontologies for naming areas It is preferable to use established ontologies instead of lab conventions for indicating anatomical region. We recommend the Allen Brain Atlas terms for mice, and you may use either the full name or the abbreviation (do not make up your own terms.)
  • x,y,z is for the anatomical coordinates. For mice, use the Allen Institute Common Coordinate Framework v3, which follows the convention (+x = posterior, +y = inferior, +z = right).
  • For relative position of an electrode on a probe, use rel_x, rel_y[, rel_z]. These positions will be used by spike sorting software to determine electrodes that are close enough to share a neuron.

The location column of the electrodes table is required. If you do not know the location of an electrode, use 'unknown'.

Naming of neurodata_types

  • As a default, name class instances with the same name as the class. Many of the neurodata_types in NWB:N allow you to set their name to something other than the default name. This allows multiple objects of the same type to be stored side-by-side and allows data writers to provide human-readable information about the contents of the neurodata_type. If appropriate, simply use the name of the neurodata_type as the name of that object. For instance, if you are placing an ElectricalSeries object in /acquisition that holds voltage traces for a multichannel recording, consider simply naming that object "ElectricalSeries". This is the default_name for that object, and naming it like this will increase your chances that analysis and visualization tools will operate seamlessly with you data.There may be cases where you have multiple neurodata instances of the same type in the same Group. In this case the instances must have unique names. If they are both equally important data sources, build upon the class name (e.g. "ElectricalSeries_1" and "ElectricalSeries_2"). If one of the instances is an extra of less importance, name that one something different (e.g. "ElectricalSeries" and "ElectricalSeries_extra_electrode").
  • Names are not for storing meta-data. If you need to place other data of the same neurodata_type, you will need to choose another name. Keep in mind that meta-data should not be stored solely in the name of objects. It is OK to name an object something like “ElectricalSeries_large_array” however the name alone is not sufficient documentation. In this case, the source of the signal will be clear from the device of the rows from the linked electrodes table region, and you should also include any important distinguishing information in the description field of the object. Make an effort to make meta-data as explicit as possible. Good names help users but do not help applications parse your file.
  • ’/’ is not allowed in names. When creating a custom name, using the forward slash (/) is not allowed, as this can confuse h5py and lead to the creation of an additional group. Instead of including a forward slash in the name, please use “Over” like in DfOverF.

Naming of processing modules

  • Give preference to default processing module names. In NWB:N version [ver], optional ProcessingModules will be added to increase standardization of processing module names. These names mirror the extension module names: “ecephys”, “icephys”, “behavior”, “ophys”, “misc”. We encourage the use of these defaults, but there may be some cases when deviating from this pattern is appropriate. For instance, if there is a processing step that involves data from multiple modalities, or if the user wants to compare two processing pipelines for a single modality (e.g. different spike sorters), you should create ProcessingModules with custom names. ProcessingModules are themselves neurodata_types, and the other rules for neurodata_types also apply here.

Unit of measurement

  • Use SI units where possible. Every TimeSeries instance has a unit as an attribute of the data Dataset, which is meant to indicate the unit of measurement of that data. We advise using SI units. Time is always in units of seconds.

Times

  • All times are in seconds. All session times are in seconds with respect to the timestamps_reference_time if present, otherwise they should be with respect to the session_start_time. This includes:
    • spike_times in the Units table.
    • start_time, stop_time, and any other custom times in any TimeIntervals object, including trials and epochs.
    • the starting_time or timestamps of any TimeSeries. The rate of TimeSeries should be in Hz.
  • World times are in ISO 8601 format. This includes:
    • session_start_time
    • timestamps_reference_time
    • the date_of_birth parameter of Subject
    • The age parameter of Subject should use the ISO 8601 Duration format. For instance indicating an age of 90 days would be 'P90D'.

Extensions

  • Extend only when necessary Extensions are an essential mechanism to integrate data with NWB:N that is otherwise not supported. However, we here need to consider that there are certain cost associated with extensions, e.g., cost for creating, supporting, documenting, and maintaining new extensions and effort for users to use and learn extensions. As such, we should create new extensions only when necessary and use existing neurodata_types as much as possible. DynamicTables used in NWB:N, e.g., to store information about time intervals and electrodes, provide the ability to dynamically add columns without the need for extensions and, as such, can help avoid the need for custom extensions in many cases.
  • Use/Reuse existing neurodata_types When possible, use existing types when creating extensions either by creating new neurodata_types that inherit from existing ones, or by creating neurodata_types that contain existing ones. Building on existing types facilitates the reuse of existing functionality and interpretation of the data. If a community extension already exists that has a similar scope, it is preferable to use that extension rather than creating a new one.
  • Provide meaningful docs When creating extensions be sure to provide as part of the extension specification, meaningful documentation of all fields (groups, datasets, attributes, links etc.) to describe what they store and how they are used.
  • Write the specification to the file. When using pynwb, you can store the specification (core and extension(s)) within the NWB file by using io.write(filepath, cache_spec=True). Caching the specification is preferable, particularly if you are using a custom extension, because this ensures that anybody who receives the data also receives the necessary data to interpret it.

Simulated data

The output of a simulation should be stored in NWB, but not the settings of the simulation. You may store the result of simulations in NWB files. NWB:N allows you to store data as if it were recorded in vivo to facilitate comparison between simulated results and in vivo results. Core components of the NWB:N schema and HDF5 backend have been engineered to handle data from hundreds of thousands of units, and natively support parallel data access via MPI, so much of the NWB:N format should work for large-scale simulations out-of-the-box. The neurodata extension “simulation_output” provides a neurodata_type for storing continuous recordings from multiple cells and multiple compartments per cell. The extension only supports storing the output data of a simulation and does not support parameters for simulation configuration. This is out-of-scope for NWB:N, since it does not facilitate side-by-side comparison between simulated and in vivo results, and is quite difficult to generalize given the diversity of ways one can parametrize a simulation. That said, if you would benefit from storing such data in your NWB:N file, you might consider creating your own custom extension.

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