minor fixes

Author: alessandratrapani

README.md

@@ -41,7 +41,7 @@ A Neurodata Without Borders (NWB) extension for storing microscopy data and asso
     - `SegmentationContainer`
     - `MicroscopyResponseSeries`
     - `MicroscopyResponseSeriesContainer`
-- Abstract Neurodata types: `ImagingSpace`, `MicroscopySeries`,`Segmentation`
+- Abstract Neurodata types: `ImagingSpace`, `MicroscopySeries`, `MicroscopyStaticImage`, `Segmentation`
 
 ## Entity Relationship Diagrams
 
@@ -334,7 +334,7 @@ classDiagram
         datasets
         --------------------------------------
         pixel_size_in_um : float64[2], optional
-        dimensions_in_pixels : float64[2], optional 
+        dimensions_in_pixels : uint32[2], optional
         --------------------------------------
         methods
         --------------------------------------
@@ -347,7 +347,7 @@ classDiagram
         datasets
         --------------------------------------
         voxel_size_in_um : float64[3], optional
-        dimensions_in_voxels : float64[3], optional 
+        dimensions_in_voxels : uint32[3], optional
         --------------------------------------
         methods
         --------------------------------------

docs/source/examples.rst

@@ -872,11 +872,19 @@ Example of multi-plane imaging with an electrically tunable lens:
     response_series_list = []
     depths = [-100, -50, 0, 50, 100]  # Depths in µm
 
-    # Create illumination pattern
+    # Create illumination pattern and channel once — shared across all planes
     plane_acquisition = PlaneAcquisition(
-        name=f'plane_acquisition',
-        description=f'Plane acquisition',
-        point_spread_function_in_um="32 um ± 1.6 um"
+        name='plane_acquisition',
+        description='Plane acquisition',
+        point_spread_function_in_um="32 um ± 1.6 um",
+    )
+
+    microscopy_channel = MicroscopyChannel(
+        name='gcamp_channel',
+        description='GCaMP6f channel',
+        excitation_wavelength_in_nm=920.0,
+        emission_wavelength_in_nm=510.0,
+        indicator=indicator,
     )
 
     for depth in depths:
@@ -887,25 +895,16 @@ Example of multi-plane imaging with an electrically tunable lens:
         width = 512
         data = np.random.rand(frames, height, width)
 
-        # Create imaging space for this depth with illumination pattern
+        # Create imaging space for this depth
         plane_space = PlanarImagingSpace(
             name=f'plane_depth_{depth}',
             description=f'Imaging plane at {depth} µm depth',
             pixel_size_in_um=[1.0, 1.0],
             dimensions_in_pixels=[height, width],
             anatomical_target='Visual cortex',
-            illumination_pattern=plane_acquisition  # Include the illumination pattern
+            illumination_pattern=plane_acquisition,
         )
 
-        # Create microscopy channel for this plane
-        microscopy_channel = MicroscopyChannel(
-            name=f'gcamp_channel_{depth}',
-            description=f'GCaMP6f channel at {depth} µm depth',
-            excitation_wavelength_in_nm=920.0,
-            emission_wavelength_in_nm=510.0,
-            indicator=indicator
-        )
-        
         # Create imaging series for this plane
         plane_series = PlanarMicroscopySeries(
             name=f'imaging_depth_{depth}',

docs/source/getting_started.rst

@@ -63,8 +63,10 @@ Data Series
 ----------
 - **PlanarMicroscopySeries**: 2D time series data
 - **VolumetricMicroscopySeries**: 3D time series data
-- **MultiPlaneMicroscopyContainer**: Multiple imaging planes
-- **MultiChannelMicroscopyContainer**: Multiple channel imaging data
+- **PlanarMicroscopyStaticImage**: Single 2D static image (e.g. anatomical reference)
+- **VolumetricMicroscopyStaticImage**: Single 3D static image
+- **MultiPlaneMicroscopyContainer**: Multiple imaging planes (time series or static images)
+- **MultiChannelMicroscopyContainer**: Multiple channel imaging data, optionally nesting ``MultiPlaneMicroscopyContainer``
 
 Quick Start Example
 ================

docs/source/user_guide.rst

@@ -196,7 +196,7 @@ Other optical components (filters, sources, detectors) are provided by the ndx-o
        indicator = Indicator(
            name="indicator",
            description="Green indicator",
-           label="GCamp6f",
+           label="GCaMP6f",
            viral_vector_injection=viral_vector_injection,
        )
 
@@ -218,8 +218,8 @@ Other optical components (filters, sources, detectors) are provided by the ndx-o
        microscopy_channel = MicroscopyChannel(
            name='gcamp_channel',
            description='GCaMP6f channel',
-           excitation_wavelength_in_nm=488.0,
-           emission_wavelength_in_nm=520.0,
+           excitation_wavelength_in_nm=920.0,
+           emission_wavelength_in_nm=510.0,
            indicator=indicator  # Link to indicator from MicroscopyExperimentMetadata
        )
 
@@ -334,6 +334,8 @@ Basic workflow for 2D imaging:
 
 .. code-block:: python
 
+    from ndx_ophys_devices import Indicator, ViralVector, ViralVectorInjection
+
     # 1. Set up microscope model and instance
     microscope_model = MicroscopeModel(
         name='2p-model',
@@ -388,8 +390,6 @@ Basic workflow for 2D imaging:
     )
 
     # 4. Create experiment metadata with indicators and rig
-    from ndx_ophys_devices import Indicator, ViralVector, ViralVectorInjection
-
     viral_vector = ViralVector(
         name="viral_vector",
         description="AAV viral vector for optogenetic stimulation",
@@ -420,7 +420,7 @@ Basic workflow for 2D imaging:
     indicator = Indicator(
         name="indicator",
         description="Green indicator",
-        label="GCamp6f",
+        label="GCaMP6f",
         viral_vector_injection=viral_vector_injection,
     )
 
@@ -455,8 +455,8 @@ Basic workflow for 2D imaging:
     microscopy_channel = MicroscopyChannel(
         name='gcamp_channel',
         description='GCaMP6f channel',
-        excitation_wavelength_in_nm=488.0,
-        emission_wavelength_in_nm=520.0,
+        excitation_wavelength_in_nm=920.0,
+        emission_wavelength_in_nm=510.0,
         indicator=indicator  # Link to indicator from MicroscopyExperimentMetadata
     )
 
@@ -481,6 +481,8 @@ Workflow for one-photon widefield imaging:
 
 .. code-block:: python
 
+    from ndx_ophys_devices import Indicator, ViralVector, ViralVectorInjection
+
     # 1. Set up microscope model and instance
     microscope_model = MicroscopeModel(
         name='1p-model',
@@ -512,8 +514,6 @@ Workflow for one-photon widefield imaging:
     )
 
     # 4. Create experiment metadata with indicators and rig
-    from ndx_ophys_devices import Indicator, ViralVector, ViralVectorInjection
-
     viral_vector = ViralVector(
         name="viral_vector",
         description="AAV viral vector for optogenetic stimulation",
@@ -544,7 +544,7 @@ Workflow for one-photon widefield imaging:
     indicator = Indicator(
         name="indicator",
         description="Green indicator",
-        label="GCamp6f",
+        label="GCaMP6f",
         viral_vector_injection=viral_vector_injection,
     )
 
@@ -604,6 +604,8 @@ Workflow for volumetric imaging with targeted scanning:
 
 .. code-block:: python
 
+    from ndx_ophys_devices import Indicator, ViralVector, ViralVectorInjection
+
     # 1. Set up microscope model and instance
     microscope_model = MicroscopeModel(
         name='volume-model',
@@ -635,8 +637,6 @@ Workflow for volumetric imaging with targeted scanning:
     )
 
     # 4. Create experiment metadata with indicators and rig
-    from ndx_ophys_devices import Indicator, ViralVector, ViralVectorInjection
-
     viral_vector = ViralVector(
         name="viral_vector",
         description="AAV viral vector for optogenetic stimulation",
@@ -667,7 +667,7 @@ Workflow for volumetric imaging with targeted scanning:
     indicator = Indicator(
         name="indicator",
         description="Green indicator",
-        label="GCamp6f",
+        label="GCaMP6f",
         viral_vector_injection=viral_vector_injection,
     )
 
@@ -944,7 +944,7 @@ Data Organization
 1. **Naming Conventions**
    - Use descriptive, consistent names
    - Include relevant metadata in descriptions
-   - Document coordinate systems and reference frames
+   - Use ``anatomical_target`` to document the brain region being imaged
 
 2. **Data Structure**
    - Group related data appropriately