Add illumination patterns and refine imaging modality examples in Jupyter notebooks

Author: alessandratrapani

examples/multi_plane_imaging_example.ipynb

@@ -33,6 +33,7 @@
     "\n",
     "from ndx_microscopy import (\n",
     "    Microscope,\n",
+    "    LineScan,\n",
     "    ExcitationLightPath,\n",
     "    EmissionLightPath,\n",
     "    PlanarImagingSpace,\n",
@@ -104,7 +105,8 @@
     "    name='etl-scope',\n",
     "    description='Two-photon microscope with electrically tunable lens',\n",
     "    manufacturer='Custom Build',\n",
-    "    model='ETL-Special'\n",
+    "    model='ETL-Special',\n",
+    "    technique='XY raster scanning combined with electrically tunable lens to control Z direction',    \n",
     ")\n",
     "nwbfile.add_device(microscope)\n",
     "\n",
@@ -261,6 +263,14 @@
     "response_series_list = []\n",
     "depths = [-100, -50, 0, 50, 100]  # Depths in µm\n",
     "\n",
+    "illumination_pattern = LineScan(\n",
+    "    name=\"line_scanning\",\n",
+    "    description=\"Line scanning two-photon microscopy\",\n",
+    "    scan_direction=\"horizontal\",\n",
+    "    line_rate_in_Hz=1000.0,\n",
+    "    dwell_time_in_s=1.0e-6,\n",
+    ")\n",
+    "\n",
     "for depth in depths:\n",
     "    # Create imaging space for this depth\n",
     "    plane_space = PlanarImagingSpace(\n",
@@ -270,7 +280,8 @@
     "        origin_coordinates=[-1.2, -0.6, depth/1000],  # Convert to mm\n",
     "        location='Visual cortex',\n",
     "        reference_frame='bregma',\n",
-    "        orientation='RAS'\n",
+    "        orientation='RAS',\n",
+    "        illumination_pattern=illumination_pattern\n",
     "    )\n",
     "\n",
     "    # Create example data for this plane\n",

examples/one-photon_calcium_imaging_example.ipynb

@@ -32,7 +32,7 @@
     "\n",
     "from ndx_microscopy import (\n",
     "    Microscope, \n",
-    "    ImagingModality,\n",
+    "    PlaneAcquisition,\n",
     "    ExcitationLightPath,\n",
     "    EmissionLightPath,\n",
     "    PlanarImagingSpace,\n",
@@ -98,7 +98,8 @@
     "    name='1p-scope',\n",
     "    description='Custom one-photon microscope for calcium imaging',\n",
     "    manufacturer='Custom Build',\n",
-    "    model='1P-Special'\n",
+    "    model='1P-Special',\n",
+    "    technique='widefield',\n",
     ")\n",
     "nwbfile.add_device(microscope)\n",
     "\n",
@@ -236,9 +237,10 @@
    "outputs": [],
    "source": [
     "# Define imaging space\n",
-    "imaging_modality = ImagingModality(\n",
-    "    name=\"widefield\",\n",
+    "illumination_pattern = PlaneAcquisition(\n",
+    "    name=\"plane_acquisition\",\n",
     "    description=\"Widefield fluorescence imaging\",\n",
+    "    plane_thickness_in_um=5.0,\n",
     ")\n",
     "imaging_space = PlanarImagingSpace(\n",
     "    name=\"hippo_plane1\",\n",
@@ -248,7 +250,7 @@
     "    location=\"Hippocampus, CA1 region\",\n",
     "    reference_frame=\"bregma\",\n",
     "    orientation=\"RAS\",  # Right-Anterior-Superior\n",
-    "    imaging_modality=imaging_modality,\n",
+    "    illumination_pattern=illumination_pattern,\n",
     ")\n",
     "\n",
     "# Create example imaging data\n",

examples/two-photon_calcium_imaging_example.ipynb

@@ -34,7 +34,7 @@
     "    Microscope, \n",
     "    ExcitationLightPath,\n",
     "    EmissionLightPath,\n",
-    "    LineScanning,\n",
+    "    LineScan,\n",
     "    PlanarImagingSpace,\n",
     "    PlanarMicroscopySeries,\n",
     "    Segmentation2D,\n",
@@ -104,7 +104,8 @@
     "    name='2p-scope',\n",
     "    description='Custom two-photon microscope for calcium imaging',\n",
     "    manufacturer='Custom Build',\n",
-    "    model='2P-Special'\n",
+    "    model='2P-Special',\n",
+    "    technique='mirror scanning',\n",
     ")\n",
     "nwbfile.add_device(microscope)\n",
     "\n",
@@ -245,22 +246,22 @@
    "outputs": [],
    "source": [
     "# Define imaging space\n",
-    "imaging_modality = LineScanning(\n",
-    "    name='line_scanning',\n",
-    "    description='Line scanning two-photon microscopy',\n",
-    "    scan_direction='horizontal',\n",
+    "illumination_pattern = LineScan(\n",
+    "    name=\"line_scanning\",\n",
+    "    description=\"Line scanning two-photon microscopy\",\n",
+    "    scan_direction=\"horizontal\",\n",
     "    line_rate_in_Hz=1000.0,\n",
     "    dwell_time_in_s=1.0e-6,\n",
     ")\n",
     "imaging_space = PlanarImagingSpace(\n",
-    "    name='cortex_plane1',\n",
-    "    description='Layer 2/3 of visual cortex',\n",
+    "    name=\"cortex_plane1\",\n",
+    "    description=\"Layer 2/3 of visual cortex\",\n",
     "    grid_spacing_in_um=[1.0, 1.0],\n",
     "    origin_coordinates=[-1.2, -0.6, -2.0],\n",
-    "    location='Visual cortex, layer 2/3',\n",
-    "    reference_frame='bregma',\n",
-    "    orientation='RAS',  # Right-Anterior-Superior\n",
-    "    imaging_modality=imaging_modality\n",
+    "    location=\"Visual cortex, layer 2/3\",\n",
+    "    reference_frame=\"bregma\",\n",
+    "    orientation=\"RAS\",  # Right-Anterior-Superior\n",
+    "    illumination_pattern=illumination_pattern,\n",
     ")\n",
     "\n",
     "# Create example imaging data\n",

examples/volumetric_imaging_example.ipynb

@@ -35,6 +35,7 @@
     "\n",
     "from ndx_microscopy import (\n",
     "    Microscope,\n",
+    "    LineScan,\n",
     "    ExcitationLightPath,\n",
     "    EmissionLightPath,\n",
     "    VolumetricImagingSpace,\n",
@@ -101,10 +102,11 @@
    "source": [
     "# Set up microscope\n",
     "microscope = Microscope(\n",
-    "    name='volume-scope',\n",
-    "    description='Custom volumetric imaging microscope',\n",
-    "    manufacturer='Custom Build',\n",
-    "    model='Volume-Special'\n",
+    "    name=\"volume-scope\",\n",
+    "    description=\"Custom volumetric imaging microscope\",\n",
+    "    manufacturer=\"Custom Build\",\n",
+    "    model=\"Volume-Special\",\n",
+    "    technique=\"XY raster scanning combined with acousto-optic deflectors (AODs)\",\n",
     ")\n",
     "nwbfile.add_device(microscope)\n",
     "\n",
@@ -246,14 +248,22 @@
    "outputs": [],
    "source": [
     "# Define volumetric imaging space\n",
+    "illumination_pattern = LineScan(\n",
+    "    name=\"line_scanning\",\n",
+    "    description=\"Line scanning two-photon microscopy\",\n",
+    "    scan_direction=\"horizontal\",\n",
+    "    line_rate_in_Hz=1000.0,\n",
+    "    dwell_time_in_s=1.0e-6,\n",
+    ")\n",
     "volume_space = VolumetricImagingSpace(\n",
     "    name='cortex_volume',\n",
     "    description='Visual cortex volume',\n",
     "    grid_spacing_in_um=[1.0, 1.0, 2.0],  # Higher spacing in z\n",
     "    origin_coordinates=[-1.2, -0.6, -2.0],\n",
     "    location='Visual cortex',\n",
     "    reference_frame='bregma',\n",
-    "    orientation='RAS'  # Right-Anterior-Superior\n",
+    "    orientation='RAS',  # Right-Anterior-Superior\n",
+    "    illumination_pattern=illumination_pattern,\n",
     ")\n",
     "\n",
     "# Create example volumetric data\n",
@@ -276,6 +286,7 @@
     "    rate=5.0,  # Lower rate for volumetric imaging\n",
     "    starting_time=0.0\n",
     ")\n",
+    "\n",
     "nwbfile.add_acquisition(volume_series)"
    ]
   },
@@ -412,7 +423,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "ndx-microscopy-env",
    "language": "python",
    "name": "python3"
   },
@@ -426,7 +437,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.0"
+   "version": "3.11.10"
   }
  },
  "nbformat": 4,