update tutorials

Author: alessandratrapani

examples/multi_plane_imaging_example.ipynb

@@ -36,6 +36,7 @@
     "    MicroscopeModel,\n",
     "    Microscope,\n",
     "    MicroscopyRig,\n",
+    "    MicroscopyExperimentMetadata,\n",
     "    LineScan,\n",
     "    MicroscopyChannel,\n",
     "    PlanarImagingSpace,\n",
@@ -113,7 +114,7 @@
     "    model_number='etl-001',\n",
     "    manufacturer='Custom Build'\n",
     ")\n",
-    "nwbfile.add_device(microscope_model)\n",
+    "nwbfile.add_device_model(microscope_model)\n",
     "\n",
     "# Set up microscope with ETL technique\n",
     "microscope = Microscope(\n",
@@ -142,7 +143,7 @@
     "    excitation_mode=\"two-photon\",\n",
     "    wavelength_range_in_nm=[800.0, 1000.0]\n",
     ")\n",
-    "nwbfile.add_device(excitation_source_model)\n",
+    "nwbfile.add_device_model(excitation_source_model)\n",
     "\n",
     "laser = PulsedExcitationSource(\n",
     "    name='laser',\n",
@@ -172,7 +173,7 @@
     "    center_wavelength_in_nm=920.0,\n",
     "    bandwidth_in_nm=80.0\n",
     ")\n",
-    "nwbfile.add_device(excitation_filter_model)\n",
+    "nwbfile.add_device_model(excitation_filter_model)\n",
     "\n",
     "excitation_filter = BandOpticalFilter(\n",
     "    name='excitation_filter',\n",
@@ -192,7 +193,7 @@
     "    reflection_band_in_nm=(400.0, 750.0),\n",
     "    angle_of_incidence_in_degrees=45.0\n",
     ")\n",
-    "nwbfile.add_device(dichroic_mirror_model)\n",
+    "nwbfile.add_device_model(dichroic_mirror_model)\n",
     "\n",
     "dichroic = DichroicMirror(\n",
     "    name=\"primary_dichroic\",\n",
@@ -210,7 +211,7 @@
     "    center_wavelength_in_nm=510.0,\n",
     "    bandwidth_in_nm=84.0\n",
     ")\n",
-    "nwbfile.add_device(emission_filter_model)\n",
+    "nwbfile.add_device_model(emission_filter_model)\n",
     "\n",
     "emission_filter = BandOpticalFilter(\n",
     "    name='emission_filter',\n",
@@ -228,7 +229,7 @@
     "    gain=70.0,\n",
     "    gain_unit=\"dB\"\n",
     ")\n",
-    "nwbfile.add_device(photodetector_model)\n",
+    "nwbfile.add_device_model(photodetector_model)\n",
     "\n",
     "detector = Photodetector(\n",
     "    name='pmt',\n",
@@ -251,8 +252,6 @@
     "    label='GCaMP6f',\n",
     "    description='Calcium indicator for multi-plane imaging',\n",
     "    manufacturer='Addgene',\n",
-    "    injection_brain_region='Visual cortex',\n",
-    "    injection_coordinates_in_mm=[-2.5, 3.2, 0.5]\n",
     ")"
    ]
   },
@@ -282,6 +281,19 @@
     "    photodetector=detector,\n",
     "    emission_filter=emission_filter\n",
     ")\n",
+    "microscopy_experiment_metadata = MicroscopyExperimentMetadata(\n",
+    "    indicators=[indicator],\n",
+    "    microscopy_rigs=[microscopy_rig],\n",
+    ")\n",
+    "nwbfile.add_lab_meta_data(microscopy_experiment_metadata)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
     "\n",
     "# Create microscopy channel\n",
     "microscopy_channel = MicroscopyChannel(\n",
@@ -290,7 +302,8 @@
     "    excitation_wavelength_in_nm=920.0,\n",
     "    emission_wavelength_in_nm=510.0,\n",
     "    indicator=indicator\n",
-    ")"
+    ")\n",
+    "\n"
    ]
   },
   {
@@ -442,13 +455,29 @@
     "    name='multi_plane_data',\n",
     "    planar_microscopy_series=planar_series_list\n",
     ")\n",
-    "nwbfile.add_acquisition(multi_plane_container)\n",
+    "nwbfile.add_acquisition(multi_plane_container)\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
     "\n",
     "segmentation_container = SegmentationContainer(\n",
     "    name='plane_segmentations',\n",
     "    segmentations=segmentation_list\n",
     ")\n",
-    "ophys_module.add(segmentation_container)\n",
+    "ophys_module.add(segmentation_container)\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
     "\n",
     "response_container = MicroscopyResponseSeriesContainer(\n",
     "    name='plane_responses',\n",
@@ -468,7 +497,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 9,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -502,7 +531,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "ndx-microscopy-env",
+   "display_name": "ndx-ophys-devices-env",
    "language": "python",
    "name": "python3"
   },
@@ -516,7 +545,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.10"
+   "version": "3.13.0"
   }
  },
  "nbformat": 4,