2.7.0

2.7.0 (February 7, 2024)

Minor changes

• Fixed typos in docstrings. (#560)
• Deprecated ImagingRetinotopy neurodata type. (#565)
• Modified OptogeneticSeries to allow 2D data, primarily in extensions of OptogeneticSeries. (#564)
• Added optional stimulus_template column to IntracellularStimuliTable as part of the IntracellularRecordingsTable. (#545)
• Added support for NWBDataInterface and DynamicTable in NWBFile.stimulus. (#559)

2.6.0

2.6.0 (January 17, 2023)

Minor Changes

• Added OnePhotonSeries. (#523)
• Subject.age has a new optional attribute, reference, which can take a value of "birth" (default) or "gestational". (#525)
• Added "in seconds" to the doc of Units.spike_times. (#530)

2.5.0

2.5.0 (June 14, 2022)

Major changes

• Shape of SpatialSeries.data is more restrictive to prevent > 3 columns. (#510)

Minor changes

• The elements x, y, z, imp and filtering are now optional instead of required. (#506)
• Added an offset attribute to all TimeSeries objects to allow enhanced translation to scientific units. (#494)
• Allowed NWBFile/stimulus/templates to contain Images objects. (#459)
• Added new optional "order_of_images" dataset to Images that contains an ordered list of object references to
  Image objects stored in the same Images object. This dataset must be used if the images are referred to
  by index, e.g., from an IndexSeries object. Created new neurodata type ImageReferences which should be used
  for this dataset. (#459, #518, #519, #520)
• Overhauled IndexSeries type (#459):
  • Fixed dtype of data dataset of IndexSeries (int32 -> uint32).
  • Updated unit attribute of data to have fixed value "N/A".
  • Updated docstrings for the conversion, resolution, and offset attributes of data to indicate that
    these fields are not used.
  • Added link to an Images object, which contains an ordered collection of images.
  • Discouraged use of the indexed_timeseries link to an ImageSeries.
• Updated TimeIntervals to use the new TimeSeriesReferenceVectorData type. This does not alter the overall structure
  of TimeIntervals in a major way aside from changing the value of the neurodata_type attribute in the file
  from VectorData to TimeSeriesReferenceVectorData. This change replaces the existing TimeIntervals.timeseries
  column with a TimeSeriesReferenceVectorData type column of the same name and overall schema. This change facilitates creating
  common functionality around TimeSeriesReferenceVectorData. This change affects all existing TimeIntervals tables
  as part of the intervals/ group, i.e., intervals/epochs, intervals/trials, and intervals/invalid_times. (#486)
• Clarified the doc string for the reference column of the electrodes table. (#498)
• Added cell_id field to IntracellularElectrode. (#512)

2.4.0

Major changes

• Added new TimeSeriesReferenceVectorData type for referencing
  ranges of TimeSeries from a VectorData column (#470)

• Integrated the intracellular electrophysiology experiment metadata
  table structure developed as part of the ndx-icephys-meta
  extension project with NWB (#470). This includes the following new
  types:

  • IntracellularRecordingsTable is an AlignedDynamicTable for
    managing individual intracellular recordings and to group
    together a stimulus and response from a single electrode
    recording. The table contains the following category tables:

    • IntracellularElectrodesTable; a DynamicTable for
      storing metadata about the IntracellularElectrode used
    • IntracellularStimuliTable; a DynamicTable for
      storing metadata about the recorded stimulus
      TimeSeries using the new
      TimeSeriesReferenceVectorData type to reference
      TimeSeries
    • IntracellularResponsesTable; a DynamicTable for
      storing metadata about the recorded response
      TimeSeries using the new
      TimeSeriesReferenceVectorData type to reference
      TimeSeries

  • SimultaneousRecordingsTable is a DynamicTable for grouping
    different intracellular recordings from the
    IntracellularRecordingsTable together that were recorded
    simultaneously from different electrodes and for storing
    metdata about simultaneous recordings

  • SequentialRecordingsTable is a DynamicTable for grouping
    different sequential recordings from the
    SimultaneousRecordingsTable together and storing metadata
    about sequential recordings

  • RepetitionsTable a DynamicTable for grouping different
    sequential intracellular recordings from the
    SequentialRecordingsTable together and storing metadata
    about repetitions

  • ExperimentalConditionsTable is a DynamicTable for grouping
    different intracellular recording repetitions from the
    RepetitionsTable together and storing metadata about
    experimental conditions

• Added the new intracellular electrophysiology metadata tables to
  /general/intracellular_ephys as part of NWBFile (#470)

Deprecations

• SweepTable has been deprecated in favor of the new intracellular
  electrophysiology metadata tables. Use of SweepTable is still
  possible but no longer recommended. (#470)
• /general/intracellular_ephys/filtering has been deprecated in
  favor of IntracellularElectrode.filtering (#470)

Bug Fixes

• Fixed incorrect dtype for electrodes table column "filtering" (float
  -> text) (#478)
• Removed quantity: * from the type definitions of
  OptogeneticStimulusSite and ImagingPlane. This change improves
  clarity of the schema to follow best practices. It has no functional
  effect on the schema. (#472)
• Updated ImageSeries to have its data

2.3.0

• Add optional waveforms column to the Units table.
• Add optional strain field to Subject.
• Add to DecompositionSeries an optional DynamicTableRegion called
  source_channels.
• Add to ImageSeries an optional link to Device.
• Add optional continuity field to TimeSeries.
• Add optional filtering attribute to ElectricalSeries.
• Clarify documentation for electrode impedance and filtering.
• Add description of extra fields.
• Set the stimulus_description for IZeroCurrentClamp to have the
  fixed value N/A.
• Update hdmf-common-schema from 1.1.3 to version 1.5.0.
  • The HDMF-experimental namespace was added, which includes the
    ExternalResources and EnumData data types. Schema in the
    HDMF-experimental namespace are experimental and subject to breaking
    changes at any time.
  • Added experimental data type ExternalResources for storing
    ontology information / external resource references.
  • Added experimental data type EnumData to store data from a set
    of fixed values.
  • Changed dtype for datasets within CSRMatrix from 'int' to
    'uint' and added missing data_type_inc: Container to the
    CSRMatrix type.
  • Added data type SimpleMultiContainer, a Container for storing
    other Container and Data objects together.
  • Added data type AlignedDynamicTable, a DynamicTable type with
    support for categories (or sub-headings) each described by a
    separate DynamicTable.
  • Fixed missing dtype for VectorIndex.
  • VectorIndex now extends VectorData instead of Index.
  • Removed unused and non-functional Index data type.
  • See
    https://hdmf-common-schema.readthedocs.io/en/latest/format_release_notes.html
    for full release notes.

2.2.5 NWB format specification release

This bugfix release changes the following:

• Fix incorrect dims and shape for ImagingPlane.origin_coords and ImagingPlane.grid_spacing, and fix incorrect dims for TwoPhotonSeries.field_of_view.

This release also adds CI for schema validation.

2.2.4 NWB format specification release

This bugfix release changes the following:

• Fix typo in nwb.ophys.yaml that prevents proper parsing of the schema.

2.2.3 NWB format specification release

This bugfix release fixes:

• Move nested type definitions to root of YAML files. This does not functionally change the schema but simplifies parsing of the schema and extensions by APIs.
• Make ImagingPlane.imaging_rate optional to handle cases where an imaging plane is associated with multiple time series with different rates.
• Add release process documentation.

See the release notes at https://nwb-schema.readthedocs.io/en/stable/format_release_notes.html#april-13-2020

2.2.2 NWB format specification release

This bugfix release fixes:

• shape and dims of OpticalSeries.data for color images
• allows more than one OpticalChannel object in ImagingPlane
• fixes missing 'shape' and 'dims' key for types VectorData, VectorIndex, and DynamicTableRegion
• reverts changes to retinotopy.yaml in 2.1.0 which break backward compatibility and were not supported by the APIs

See the release notes at https://nwb-schema.readthedocs.io/en/latest/format_release_notes.html#march-2-2020

2.2.1 NWB format specification release

This bugfix release fixes an incorrect nwb_version specified in nwb.file.yaml and incorrect version in hdmf-common namespace.yaml.