merge main

requirements-min.txt

@@ -1,2 +1,3 @@
 pynwb
-ndx-ophys-devices git+https://github.com/catalystneuro/ndx-ophys-devices.git@create_specs
+git+https://github.com/catalystneuro/ndx-ophys-devices.git@main#egg=ndx-ophys-devices
+

spec/ndx-microscopy.extensions.yaml

@@ -480,3 +480,31 @@ groups:
       doc: Link to VolumetricImagingSpace object containing metadata about the region of physical space this imaging data
         was recorded from.
       target_type: VolumetricImagingSpace
+
+
+  - neurodata_type_def: MicroscopyResponseSeries
+    neurodata_type_inc: TimeSeries
+    doc: ROI responses extracted from optical imaging.
+    datasets:
+    - name: data
+      dtype: numeric
+      dims:
+      - - number_of_frames
+        - number_of_rois
+      shape:
+      - - null
+        - null
+      doc: Signals from ROIs.
+    - name: table_region
+      neurodata_type_inc: DynamicTableRegion
+      doc: DynamicTableRegion referencing plane segmentation containing more information about the ROIs
+        stored in this series.
+
+  - neurodata_type_def: MicroscopyResponseSeriesContainer
+    neurodata_type_inc: NWBDataInterface
+    default_name: MicroscopyResponseSeriesContainer
+    doc: A container of many MicroscopyResponseSeries.
+    groups:
+    - neurodata_type_inc: MicroscopyResponseSeries
+      doc: MicroscopyResponseSeries object(s) containing fluorescence data for a ROI.
+      quantity: '+'

src/pynwb/ndx_microscopy/__init__.py

@@ -1,7 +1,7 @@
 import os
 
 from pynwb import get_class, load_namespaces
-
+from pynwb.spec import NWBNamespaceBuilder
 try:
     from importlib.resources import files
 except ImportError:
@@ -36,6 +36,10 @@
 MultiChannelMicroscopyVolume = get_class("MultiChannelMicroscopyVolume", extension_name)
 VariableDepthMultiChannelMicroscopyVolume = get_class("VariableDepthMultiChannelMicroscopyVolume", extension_name)
 
+MicroscopyResponseSeries = get_class("MicroscopyResponseSeries", extension_name)
+MicroscopyResponseSeriesContainer = get_class("MicroscopyResponseSeriesContainer", extension_name)
+
+
 __all__ = [
     "OpticalFilter",
     "ExcitationSource",
@@ -53,4 +57,6 @@
     "VolumetricMicroscopySeries",
     "MultiChannelMicroscopyVolume",
     "VariableDepthMultiChannelMicroscopyVolume",
+    "MicroscopyResponseSeries",
+    "MicroscopyResponseSeriesContainer",
 ]

src/pynwb/ndx_microscopy/testing/__init__.py

@@ -3,6 +3,8 @@
     mock_ExcitationLightPath,
     mock_Microscope,
     mock_MicroscopyPlaneSegmentation,
+    mock_MicroscopyResponseSeries,
+    mock_MicroscopyResponseSeriesContainer,
     mock_MicroscopySegmentations,
     mock_MultiChannelMicroscopyVolume,
     mock_PlanarImagingSpace,
@@ -25,5 +27,7 @@
     "mock_VariableDepthMicroscopySeries",
     "mock_VolumetricMicroscopySeries",
     "mock_MultiChannelMicroscopyVolume",
+    "mock_MicroscopyResponseSeries",
+    "mock_MicroscopyResponseSeriesContainer",
     "mock_VariableDepthMultiChannelMicroscopyVolume",
 ]

src/pynwb/ndx_microscopy/testing/_mock.py

@@ -18,7 +18,7 @@
 def mock_Microscope(
     *,
     name: Optional[str] = None,
-    description: str = "This is a mock instance of a Microscope type to be used for rapid testing.",
+    description: str = "A mock instance of a Microscope type to be used for rapid testing.",
     manufacturer: str = "A fake manufacturer of the mock microscope.",
     model: str = "A fake model of the mock microscope.",
 ) -> ndx_microscopy.Microscope:
@@ -34,7 +34,7 @@ def mock_Microscope(
 def mock_ExcitationLightPath(
     *,
     name: Optional[str] = None,
-    description: str = "This is a mock instance of a ExcitationLightPath type to be used for rapid testing.",
+    description: str = "A mock instance of a ExcitationLightPath type to be used for rapid testing.",
     excitation_wavelength_in_nm: float = 500.0,
     excitation_source: ExcitationSource = None,
     excitation_filter: OpticalFilter = None,
@@ -52,7 +52,7 @@ def mock_ExcitationLightPath(
 def mock_EmissionLightPath(
     *,
     name: Optional[str] = None,
-    description: str = "This is a mock instance of a EmissionLightPath type to be used for rapid testing.",
+    description: str = "A mock instance of a EmissionLightPath type to be used for rapid testing.",
     indicator: Indicator = None,
     photodetector: Photodetector = None,
     emission_filter: OpticalFilter = None,
@@ -72,7 +72,7 @@ def mock_EmissionLightPath(
 def mock_PlanarImagingSpace(
     *,
     name: Optional[str] = None,
-    description: str = "This is a mock instance of a PlanarImagingSpace type to be used for rapid testing.",
+    description: str = "A mock instance of a PlanarImagingSpace type to be used for rapid testing.",
     origin_coordinates: Tuple[float, float, float] = (-1.2, -0.6, -2),
     grid_spacing_in_um: Tuple[float, float, float] = (20, 20),
     location: str = "The location targeted by the mock imaging space.",
@@ -92,7 +92,7 @@ def mock_PlanarImagingSpace(
 def mock_VolumetricImagingSpace(
     *,
     name: Optional[str] = None,
-    description: str = "This is a mock instance of a VolumetricImagingSpace type to be used for rapid testing.",
+    description: str = "A mock instance of a VolumetricImagingSpace type to be used for rapid testing.",
     origin_coordinates: Tuple[float, float, float] = (-1.2, -0.6, -2),
     grid_spacing_in_um: Tuple[float, float, float] = (20, 20, 50),
     location: str = "The location targeted by the mock imaging space.",
@@ -131,7 +131,7 @@ def mock_MicroscopyPlaneSegmentation(
     *,
     imaging_space: ndx_microscopy.ImagingSpace,
     name: Optional[str] = None,
-    description: str = "This is a mock instance of a MicroscopyPlaneSegmentation type to be used for rapid testing.",
+    description: str = "A mock instance of a MicroscopyPlaneSegmentation type to be used for rapid testing.",
     number_of_rois: int = 5,
     image_shape: Tuple[int, int] = (10, 10),
 ) -> ndx_microscopy.MicroscopyPlaneSegmentation:
@@ -157,7 +157,7 @@ def mock_PlanarMicroscopySeries(
     imaging_space: ndx_microscopy.PlanarImagingSpace,
     emission_light_path: ndx_microscopy.EmissionLightPath,
     name: Optional[str] = None,
-    description: str = "This is a mock instance of a PlanarMicroscopySeries type to be used for rapid testing.",
+    description: str = "A mock instance of a PlanarMicroscopySeries type to be used for rapid testing.",
     data: Optional[np.ndarray] = None,
     unit: str = "a.u.",
     conversion: float = 1.0,
@@ -212,7 +212,7 @@ def mock_VariableDepthMicroscopySeries(
     imaging_space: ndx_microscopy.PlanarImagingSpace,
     emission_light_path: ndx_microscopy.EmissionLightPath,
     name: Optional[str] = None,
-    description: str = "This is a mock instance of a PlanarMicroscopySeries type to be used for rapid testing.",
+    description: str = "A mock instance of a PlanarMicroscopySeries type to be used for rapid testing.",
     data: Optional[np.ndarray] = None,
     depth_per_frame_in_um: Optional[np.ndarray] = None,
     unit: str = "a.u.",
@@ -275,7 +275,7 @@ def mock_VolumetricMicroscopySeries(
     imaging_space: ndx_microscopy.VolumetricImagingSpace,
     emission_light_path: ndx_microscopy.EmissionLightPath,
     name: Optional[str] = None,
-    description: str = "This is a mock instance of a VolumetricMicroscopySeries type to be used for rapid testing.",
+    description: str = "A mock instance of a VolumetricMicroscopySeries type to be used for rapid testing.",
     data: Optional[np.ndarray] = None,
     unit: str = "a.u.",
     conversion: float = 1.0,
@@ -330,7 +330,7 @@ def mock_MultiChannelMicroscopyVolume(
     excitation_light_paths: pynwb.base.VectorData,
     emission_light_paths: pynwb.base.VectorData,
     name: Optional[str] = None,
-    description: str = "This is a mock instance of a MultiChannelMicroscopyVolume type to be used for rapid testing.",
+    description: str = "A mock instance of a MultiChannelMicroscopyVolume type to be used for rapid testing.",
     data: Optional[np.ndarray] = None,
     unit: str = "n.a.",
     conversion: float = 1.0,
@@ -354,14 +354,81 @@ def mock_MultiChannelMicroscopyVolume(
     return volumetric_microscopy_series
 
 
+def mock_MicroscopyResponseSeries(
+    *,
+    table_region: pynwb.core.DynamicTableRegion,
+    name: Optional[str] = None,
+    description: str = "A mock instance of a MicroscopyResponseSeries type to be used for rapid testing.",
+    data: Optional[np.ndarray] = None,
+    unit: str = "a.u.",
+    conversion: float = 1.0,
+    offset: float = 0.0,
+    starting_time: Optional[float] = None,
+    rate: Optional[float] = None,
+    timestamps: Optional[np.ndarray] = None,
+) -> ndx_microscopy.MicroscopyResponseSeries:
+    series_name = name or name_generator("MicroscopyResponseSeries")
+
+    number_of_frames = 100
+    number_of_rois = len(table_region.data)
+    series_data = data if data is not None else np.ones(shape=(number_of_frames, number_of_rois))
+
+    if timestamps is None:
+        series_starting_time = starting_time or 0.0
+        series_rate = rate or 10.0
+        series_timestamps = None
+    else:
+        if starting_time is not None or rate is not None:
+            warnings.warn(
+                message=(
+                    "Timestamps were provided in addition to either rate or starting_time! "
+                    "Please specify only timestamps, or both starting_time and rate. Timestamps will take precedence."
+                ),
+                stacklevel=2,
+            )
+
+        series_starting_time = None
+        series_rate = None
+        series_timestamps = timestamps
+
+    microscopy_response_series = ndx_microscopy.MicroscopyResponseSeries(
+        name=series_name,
+        description=description,
+        table_region=table_region,
+        data=series_data,
+        unit=unit,
+        conversion=conversion,
+        offset=offset,
+        starting_time=series_starting_time,
+        rate=series_rate,
+        timestamps=series_timestamps,
+    )
+
+    return microscopy_response_series
+
+
+def mock_MicroscopyResponseSeriesContainer(
+    *,
+    microscopy_response_series: List[ndx_microscopy.MicroscopyResponseSeries],
+    name: Optional[str] = None,
+) -> ndx_microscopy.MicroscopyResponseSeriesContainer:
+    container_name = name or name_generator("MicroscopyResponseSeriesContainer")
+
+    microscopy_response_series_container = ndx_microscopy.MicroscopyResponseSeriesContainer(
+        name=container_name, microscopy_response_series=microscopy_response_series
+    )
+
+    return microscopy_response_series_container
+
+
 def mock_VariableDepthMultiChannelMicroscopyVolume(
     *,
     microscope: ndx_microscopy.Microscope,
     imaging_space: ndx_microscopy.VolumetricImagingSpace,
     excitation_light_paths: pynwb.base.VectorData,
     emission_light_paths: pynwb.base.VectorData,
     name: Optional[str] = None,
-    description: str = "This is a mock instance of a MultiChannelMicroscopyVolume type to be used for rapid testing.",
+    description: str = "A mock instance of a MultiChannelMicroscopyVolume type to be used for rapid testing.",
     data: Optional[np.ndarray] = None,
     depth_per_frame_in_um: Optional[np.ndarray] = None,
     unit: str = "n.a.",

src/pynwb/tests/test_constructors.py

@@ -1,5 +1,6 @@
 """Test in-memory Python API constructors for the ndx-microscopy extension."""
 
+import pynwb.testing.mock.ophys
 import pytest
 
 import pynwb
@@ -9,6 +10,8 @@
     mock_Microscope,
     mock_MicroscopyPlaneSegmentation,
     mock_MicroscopySegmentations,
+    mock_MicroscopyResponseSeries,
+    mock_MicroscopyResponseSeriesContainer,
     mock_MultiChannelMicroscopyVolume,
     mock_PlanarImagingSpace,
     mock_PlanarMicroscopySeries,
@@ -103,6 +106,40 @@ def test_constructor_volumetric_microscopy_series():
     )
 
 
+def test_constructor_microscopy_response_series():
+    number_of_rois = 10
+
+    plane_segmentation = pynwb.testing.mock.ophys.mock_PlaneSegmentation()
+
+    table_region = pynwb.core.DynamicTableRegion(
+        name="table_region",
+        description="",
+        data=[x for x in range(number_of_rois)],
+        table=plane_segmentation,
+    )
+
+    mock_MicroscopyResponseSeries(table_region=table_region)
+
+
+def test_constructor_microscopy_response_series_container():
+    number_of_rois = 10
+
+    plane_segmentation = pynwb.testing.mock.ophys.mock_PlaneSegmentation()
+
+    table_region = pynwb.core.DynamicTableRegion(
+        name="table_region",
+        description="",
+        data=[x for x in range(number_of_rois)],
+        table=plane_segmentation,
+    )
+
+    microscopy_response_series = mock_MicroscopyResponseSeries(table_region=table_region)
+
+    mock_MicroscopyResponseSeriesContainer(
+        microscopy_response_series=[microscopy_response_series]
+    )
+
+
 def test_constructor_multi_channel_microscopy_volume():
     microscope = mock_Microscope()
     imaging_space = mock_VolumetricImagingSpace()