Merge branch 'dev' into electrodes_table

Author: rly

core/nwb.behavior.yaml

@@ -38,24 +38,6 @@ groups:
         is 'meters'. Actual stored values are not necessarily stored in these units.
         To access the data in these units, multiply 'data' by 'conversion' and add 'offset'.
       required: false
-    - name: bounds
-      dtype: numeric
-      doc: The boundary range (min, max) for each dimension of `data`. The units are the same as the units for the data.
-      shape:
-      - - 1
-        - 2
-      - - 2
-        - 2
-      - - 3
-        - 2 
-      dims:
-      - - x
-        - min,max
-      - - x,y
-        - min,max
-      - - x,y,z
-        - min,max
-      required: false
   - name: reference_frame
     dtype: text
     doc: Description defining what exactly 'straight-ahead' means.

core/nwb.device.yaml

@@ -5,10 +5,22 @@ groups:
   attributes:
   - name: description
     dtype: text
-    doc: Description of the device (e.g., model, firmware version, processing software version, etc.)
-      as free-form text.
+    doc: Description of the device as free-form text. If there is any software/firmware associated
+      with the device, the names and versions of those can be added to NWBFile.was_generated_by. 
     required: false
   - name: manufacturer
     dtype: text
-    doc: The name of the manufacturer of the device.
+    doc: The name of the manufacturer of the device, e.g., Imec, Plexon, Thorlabs.
+    required: false
+  - name: model_number
+    dtype: text
+    doc: The model number (or part/product number) of the device, e.g., PRB_1_4_0480_1, PLX-VP-32-15SE(75)-(260-80)(460-10)-300-(1)CON/32m-V, BERGAMO.
+    required: false
+  - name: model_name
+    dtype: text
+    doc: The model name of the device, e.g., Neuropixels 1.0, V-Probe, Bergamo III.
+    required: false
+  - name: serial_number
+    dtype: text
+    doc: The serial number of the device.
     required: false

core/nwb.misc.yaml

@@ -158,6 +158,7 @@ groups:
       shape:
       - null
       doc: The mean Gaussian filters, in Hz.
+      quantity: '?'
     - name: band_stdev
       neurodata_type_inc: VectorData
       dtype: float32
@@ -166,6 +167,7 @@ groups:
       shape:
       - null
       doc: The standard deviation of Gaussian filters, in Hz.
+      quantity: '?'
   links:
   - name: source_timeseries
     target_type: TimeSeries
@@ -242,13 +244,7 @@ groups:
     - - null
       - null
       - null
-    doc: Spike waveform mean for each spike unit. The 'waveform_mean_index'
-      column indexes which waveforms in this column belong to a given unit, where each waveform
-      was recorded from a different electrode. The 'electrodes' column should be used to indicate which
-      electrodes are associated with each unit, and the order of the mean waveforms for a given unit 
-      in the 'waveform_mean' dataset should be the same as the order of the electrodes referenced in
-      the 'electrodes' column of this table. The number of samples for each waveform mean must be the
-      same.
+    doc: Spike waveform mean for each spike unit.
     quantity: '?'
     attributes:
     - name: sampling_rate
@@ -260,11 +256,6 @@ groups:
       value: volts
       doc: Unit of measurement. This value is fixed to 'volts'.
       required: false
-  - name: waveform_mean_index
-    neurodata_type_inc: VectorIndex
-    doc: Optional index into the 'waveform_mean' dataset to allow each unit to have a different number of mean
-      waveforms, one per electrode. See 'waveform_mean' for more details.
-    quantity: '?'
   - name: waveform_sd
     neurodata_type_inc: VectorData
     dtype: float32
@@ -280,13 +271,7 @@ groups:
     - - null
       - null
       - null
-    doc: Spike waveform standard deviation for each spike unit. The 'waveform_sd_index'
-      column indexes which waveforms in this column belong to a given unit, where each waveform
-      was recorded from a different electrode. The 'electrodes' column should be used to indicate which
-      electrodes are associated with each unit, and the order of the waveform standard deviations for a
-      given unit in the 'waveform_sd' dataset should be the same as the order of the electrodes referenced
-      in the 'electrodes' column of this table. The number of samples for each waveform standard deviation
-      must be the same.
+    doc: Spike waveform standard deviation for each spike unit.
     quantity: '?'
     attributes:
     - name: sampling_rate
@@ -298,11 +283,6 @@ groups:
       value: volts
       doc: Unit of measurement. This value is fixed to 'volts'.
       required: false
-  - name: waveform_sd_index
-    neurodata_type_inc: VectorIndex
-    doc: Optional index into the 'waveform_sd' dataset to allow each unit to have a different number of
-      waveform standard deviations, one per electrode. See 'waveform_sd' for more details.
-    quantity: '?'
   - name: waveforms
     neurodata_type_inc: VectorData
     dtype: numeric

docs/format/source/format_release_notes.rst

@@ -8,15 +8,11 @@ Release Notes
 
 Minor changes
 ^^^^^^^^^^^^^
-- Added support to set boundary metadata for ``SpatialSeries``. (#524)
-- Added columns ``waveform_mean_index`` and ``waveform_sd_index`` to ``Units`` to make the ``waveform_mean`` and
-  ``waveform_sd`` columns ragged. This allows for a different number of waveform means/SDs per unit which is useful
-  when each unit is associated with a different number of electrodes and there is a waveform mean/SD for each
-  electrode and unit. (#576)
 - Added optional ``was_generated_by`` attribute to ``NWBFile`` to store provenance information (#578)
 - Deprecated ``EventWaveform`` neurodata type. (#584)
-
 - Deprecated ``ImageMaskSeries`` neurodata type. (#583)
+- Made ``band_mean`` and ``band_std`` in ``DecompositionSeries`` optional. (#593)
+- Added ``Device.model_number``, ``Device.model_name``, ``Device.serial_number`` (#594)
 
 2.7.0 (February 7, 2024)
 ------------------------