Add imaging modality definitions for various microscopy techniques

Author: alessandratrapani

spec/ndx-microscopy.extensions.yaml

@@ -54,6 +54,102 @@ groups:
         doc: Link to DichroicMirror object which contains metadata about the dichroic mirror in the emission light path.
         quantity: "?"
 
+  - neurodata_type_def: ImagingModality
+    neurodata_type_inc: NWBContainer
+    doc: Base class for describing microscopy imaging modalities.
+    attributes:
+      - name: description
+        dtype: text
+        doc: General description of the imaging modality.
+
+  - neurodata_type_def: LineScanning
+    neurodata_type_inc: ImagingModality
+    doc: Line scanning method used in microscopy, particularly common in two-photon imaging.
+    attributes:
+      - name: scan_direction
+        dtype: text
+        doc: Direction of line scanning (horizontal, vertical, or diagonal). # specify fast direction vs slow direction
+        required: false
+      - name: line_rate
+        dtype: float64
+        doc: Rate of line scanning in lines per second.
+        required: false
+      - name: dwell_time
+        dtype: float64
+        doc: Average time spent at each scanned point.
+        required: false
+
+  - neurodata_type_def: RasterScanning
+    neurodata_type_inc: ImagingModality
+    doc: Raster scanning method with grid-like point-by-point or line-by-line acquisition.
+    attributes:
+      - name: scan_pattern
+        dtype: text
+        doc: Specific raster scanning pattern (e.g., bidirectional, unidirectional).
+        required: false
+      - name: dwell_time
+        dtype: float64
+        doc: Average time spent at each scanned point.
+        required: false
+
+  - neurodata_type_def: ResonantScanning
+    neurodata_type_inc: ImagingModality
+    doc: Resonant scanning method using a rapidly oscillating mirror for high-speed imaging.
+    attributes:
+      - name: resonant_frequency
+        dtype: float64
+        doc: Frequency of the resonant scanner in Hz.
+        required: false
+      - name: resonant_amplitude
+        dtype: float64
+        doc: Amplitude of the resonant scanner's oscillation.
+        required: false
+
+  - neurodata_type_def: TemporalFocusing
+    neurodata_type_inc: ImagingModality
+    doc: Temporal focusing scanning method for depth-resolved imaging.
+    attributes:
+      - name: lateral_point_spread_function_in_um
+        dtype: text
+        doc: Estimated lateral spatial profile or point spread function, expressed as mean [um] ± s.d [um].
+      - name: axial_point_spread_function_in_um
+        dtype: text
+        doc: Estimated axial spatial profile or point spread function, expressed as mean [um] ± s.d [um].
+      - name: pulse_duration
+        dtype: float64
+        doc: Duration of excitation pulses in seconds.
+        required: false
+
+  - neurodata_type_def: LightSheet
+    neurodata_type_inc: ImagingModality
+    doc: Light sheet method.
+    attributes:
+      - name: sheet_thickness_in_um
+        dtype: float64
+        doc: Thickness of the light sheet in micrometers.
+        required: false
+      - name: illumination_angle
+        dtype: float64
+        doc: Angle of light sheet illumination in degrees.
+        required: false
+
+  - neurodata_type_def: RandomAccessScanning
+    neurodata_type_inc: ImagingModality
+    doc: Random access scanning method for targeted, high-speed imaging of specific regions.
+    attributes:
+      - name: max_scan_points
+        dtype: uint32
+        doc: Maximum number of points that can be scanned in a single frame.
+        required: false
+      - name: dwell_time
+        dtype: float64
+        doc: Average time spent at each scanned point.
+        required: false
+      - name: scanning_pattern
+        dtype: text
+        doc: Description of the point selection strategy.
+        required: false
+
   - neurodata_type_def: ImagingSpace
     neurodata_type_inc: NWBContainer
     doc: Abstract class to contain metadata about the region of physical space that imaging data was recorded from. Extended by PlanarImagingSpace and VolumetricImagingSpace.
@@ -99,6 +195,10 @@ groups:
           'RAS' corresponds to coordinates in the order of (ML (x), AP (y), DV (z))."
         dtype: text
         required: false
+    groups:
+      - neurodata_type_inc: ImagingModality
+        doc: ImagingModality object containing metadata about the method used to acquire this imaging data.
+        quantity: 1
 
   - neurodata_type_def: PlanarImagingSpace
     neurodata_type_inc: ImagingSpace