Create new ndx-holographic-stimulation extension

ndx-holographic-stimulation/README.md

@@ -0,0 +1,276 @@
+# ndx-holographic-stimulation Extension for NWB
+![extension schema](./schema.png)
+
+
+## Installation
+
+To install the extension, first clone the `ndx_holographic_stimulation` repository to the desired folder using the command
+```angular2svg
+git clone https://github.com/catalystneuro/ndx-holographic-stimulation.git
+```
+Then, to install the requisite python packages and extension, run:
+```angular2svg
+python -m pip install -r requirements.txt -r requirements-dev.txt
+python setup.py install
+```
+The extension can then be imported into python scripts via `import ndx_holographic_stimulation`.
+
+## Usage
+
+```python
+
+import datetime
+import numpy as np
+from pynwb import NWBFile, NWBHDF5IO
+from ndx_holographic_stimulation import (
+    PatternedOptogeneticSeries,
+    PatternedOptogeneticStimulusSite,
+    OptogeneticStimulusPatternTable,
+    OptogeneticStimulusPattern,
+    SpiralScanning,
+    TemporalFocusing,
+    SpatialLightModulator,
+    LightSource,
+)
+from pynwb.ophys import PlaneSegmentation, ImageSegmentation, OpticalChannel
+
+nwbfile = NWBFile(
+    session_description="session_description",
+    identifier="identifier",
+    session_start_time=datetime.datetime.now(datetime.timezone.utc),
+)
+```
+We need to define a `roi_table_region` in the imaging acquisition system, to link the holographic stimulus to a set of ROIs,
+
+```python
+recording_device = nwbfile.create_device(
+    name="2P_microscope",
+    description="My two-photon microscope",
+    manufacturer="The best microscope manufacturer",
+)
+
+optical_channel = OpticalChannel(
+    name="OpticalChannel",
+    description="an optical channel",
+    emission_lambda=500.0,
+)
+imaging_plane = nwbfile.create_imaging_plane(
+    name="ImagingPlane",
+    optical_channel=optical_channel,
+    imaging_rate=30.0,
+    description="a very interesting part of the brain",
+    device=recording_device,
+    excitation_lambda=600.0,
+    indicator="GFP",
+    location="V1",
+    grid_spacing=[0.01, 0.01],
+    grid_spacing_unit="meters",
+    origin_coords=[1.0, 2.0, 3.0],
+    origin_coords_unit="meters",
+)
+
+n_rois = 2
+plane_segmentation = PlaneSegmentation(
+    name="PlaneSegmentation",
+    description="output from segmenting my favorite imaging plane",
+    imaging_plane=imaging_plane,
+)
+for _ in range(n_rois):
+    plane_segmentation.add_roi(image_mask=np.zeros((10, 10)))
+
+if nwbfile is not None:
+    if "ophys" not in nwbfile.processing:
+        nwbfile.create_processing_module("ophys", "ophys")
+    nwbfile.processing["ophys"].add(plane_segmentation)
+
+roi_table_region = plane_segmentation.create_roi_table_region(
+    region=[0, 1], description="the first of two ROIs"
+)
+
+```
+Define optical device that provide the stimulus
+```python
+# metadata for spiatial light modulator
+slm_name = "spatial_light_modulator"
+slm_description = "Generic description for the slm"
+slm_model = "model"
+slm_resolution = 1.0
+
+spatial_light_modulator = SpatialLightModulator(
+    name=slm_name,
+    description=slm_description,
+    model=slm_model,
+    resolution=slm_resolution,
+)
+nwbfile.add_device(spatial_light_modulator)
+
+# metadata for the light source
+light_source_name = "light_source"
+light_source_description = "Generic description for the laser"
+light_source_manifacturer = "manifacturer"
+stimulation_wavelength = 600.0
+filter_description = "600/50"
+power = 8.0
+intensity = 100.0
+exposure_time = 1e-6
+pulse_rate = 1 / exposure_time
+
+light_source = LightSource(
+    name=light_source_name,
+    stimulation_wavelength=stimulation_wavelength,  # nm
+    description=light_source_description,
+    filter_description=filter_description,
+    power=power,
+    intensity=intensity,
+    exposure_time=exposure_time,
+    pulse_rate=pulse_rate,
+)
+nwbfile.add_device(light_source)
+
+# metadata for the stimulating device
+stimulating_device = nwbfile.create_device(
+    name="device",
+    description="Microsope used for optogenetic stimulation",
+)
+```
+Define the stimulus pattern and pattern table:
+```python
+# metadata for  stimulus pattern
+pattern_name = "generic_stimulus_pattern"
+pattern_description = "beam pattern"
+duration = 10e-3
+number_of_stimulus_presentation = 10
+inter_stimulus_interval = 0.02
+# metadata for spiral scanning pattern
+spiral_scanning_name = "spiral_scanning"
+spiral_diameter = 15e-6
+spiral_height = 10e-6
+num_revolutions = 5
+# metadata for temporal focusing pattern
+temporal_focusing_name = "temporal_focusing"
+lateral_psf = "9e-6 m ± 0.7e-6 m"
+axial_psf = "32e-6 m ± 1.6e-6 m"
+
+spiral_scanning = SpiralScanning(
+    name=spiral_scanning_name,
+    diameter=spiral_diameter,
+    height=spiral_height,
+    number_of_revolutions=num_revolutions,
+    description=pattern_description,
+    duration=duration,
+    number_of_stimulus_presentation=number_of_stimulus_presentation,
+    inter_stimulus_interval=inter_stimulus_interval,
+)
+
+nwbfile.add_lab_meta_data(spiral_scanning)
+
+temporal_focusing = TemporalFocusing(
+    name=temporal_focusing_name,
+    description=pattern_description,
+    lateral_point_spread_function=lateral_psf,
+    axial_point_spread_function=axial_psf,
+    duration=duration,
+    number_of_stimulus_presentation=number_of_stimulus_presentation,
+    inter_stimulus_interval=inter_stimulus_interval,
+)
+
+nwbfile.add_lab_meta_data(temporal_focusing)
+
+generic_pattern = OptogeneticStimulusPattern(
+    name=pattern_name,
+    description=pattern_description,
+    duration=duration,
+    number_of_stimulus_presentation=number_of_stimulus_presentation,
+    inter_stimulus_interval=inter_stimulus_interval,
+)
+
+nwbfile.add_lab_meta_data(generic_pattern)
+
+stimulus_pattern_table = OptogeneticStimulusPatternTable(
+    name="stimulus_pattern_table",
+    description=pattern_description,
+)
+stimulus_pattern_table.add_row(stimulus_pattern=generic_pattern)
+stimulus_pattern_table.add_row(stimulus_pattern=spiral_scanning)
+stimulus_pattern_table.add_row(stimulus_pattern=temporal_focusing)
+
+stimulus_pattern_ids = np.random.choice([0, 1, 2], size=[100, n_rois])
+
+```
+Define the stimulus site: specify the effector and the stimulus pattern used
+```python
+# metadata for Patterned stimulus site
+site_name = "site"
+site_description = "This is an example Patterned site."
+effector = "ChR2"
+location = "VISrl"
+
+stim_site = PatternedOptogeneticStimulusSite(
+    name=site_name,
+    device=stimulating_device,
+    description=site_description,
+    excitation_lambda=stimulation_wavelength,  # nm
+    effector=effector,
+    location=location,
+)
+nwbfile.add_ogen_site(stim_site)
+```
+Define the stimulus sequence on the ROIs previously defined in the imaging frame coordinates
+```python
+# metadata for Patterned series
+series_name = "PatternedOptogeneticSeries"
+series_description = "Patterned stimulus on 2 rois"
+unit = "watts"
+data = np.random.rand(100, n_rois)  # ntime x nroi
+timestamps = np.linspace(0, 10, num=100)  # a timestamp for every frame
+
+photostimulation = PatternedOptogeneticSeries(
+    name=series_name,
+    description=series_description,
+    data=data,
+    unit=unit,
+    timestamps=timestamps,
+    rois=roi_table_region,
+    stimulus_pattern_ids=stimulus_pattern_ids,
+    stimulus_pattern_table=stimulus_pattern_table,
+    site=stim_site,
+    device=stimulating_device,
+    light_source=light_source,
+    spatial_light_modulator=spatial_light_modulator,
+)
+
+nwbfile.add_stimulus(photostimulation)
+
+```
+Write and read the NWBFile 
+```python
+
+nwbfile_path = "test_photostimulation_nwb.nwb"
+with NWBHDF5IO(nwbfile_path, mode="w") as io:
+    io.write(nwbfile)
+
+with NWBHDF5IO(nwbfile_path, mode="r") as io:
+    nwbfile_in = io.read()
+
+```
+## Running tests
+
+<a href="https://pynwb.readthedocs.io/en/stable/software_process.html#continuous-integration">Unit and integration
+tests</a> are implemented using <a href="https://docs.pytest.org/en/7.2.x/">pytest</a>, and can be run via the command 
+`pytest` from the root of the extension directory (i.e., inside `ndx-holographi-stimulation/src`).
+
+### Specification
+
+Documentation for the extension's <a href="https://schema-language.readthedocs.io/en/latest/">specification</a>, which is based on the YAML files, is generated and stored in
+the `./docs` folder. To create it, run the following from the home directory:
+```angular2svg
+cd docs
+make fulldoc
+```
+This will save documentation to the `./docs/build` folder, and can be accessed via the 
+`./docs/build/html/index.html` file.
+
+
+
+
+This extension was created using [ndx-template](https://github.com/nwb-extensions/ndx-template).

ndx-holographic-stimulation/ndx-meta.yaml

@@ -0,0 +1,8 @@
+name: ndx-holographic-stimulation
+version: 0.1.0
+src: https://github.com/catalystneuro/ndx-holographic-stimulation
+pip: https://pypi.org/project/ndx-holographic-stimulation/
+license: BSD-3
+maintainers: 
+  - alessandratrapani
+

ndx_bipolar_referencing/README.md

@@ -0,0 +1,71 @@
+# ndx-bipolar-referencing Extension for NWB:N
+
+Structure for storing the bipolar schema of a recording in an NWB file.
+
+![schema schema](https://github.com/ben-dichter-consulting/ndx-bipolar-referencing/blob/master/docs/media/bipolar_reference_schema_schema.png?raw=true)
+
+## python installation
+```bash
+$ pip install ndx-bipolar-referencing
+```
+
+## python usage
+
+```python
+from pynwb import NWBHDF5IO, NWBFile
+from pynwb.file import DynamicTable, DynamicTableRegion
+from datetime import datetime
+from ndx_bipolar_referencing import EcephysExt
+from pynwb.ecephys import ElectricalSeries
+
+import numpy as np
+
+nwbfile = NWBFile('description', 'id', datetime.now().astimezone())
+
+device = nwbfile.create_device('device_name')
+
+electrode_group = nwbfile.create_electrode_group('electrode_group',
+                                                 'desc', 'loc', device=device)
+
+for _ in range(20):
+    nwbfile.add_electrode(np.nan, np.nan, np.nan, np.nan, 'loc', 'filt',
+                          electrode_group)
+
+positive_electrodes = DynamicTableRegion('positive_electrodes',
+                                         np.arange(0, 20, 2),
+                                         'desc',
+                                         nwbfile.electrodes)
+negative_electrodes = DynamicTableRegion('negative_electrodes',
+                                         np.arange(1, 20, 2),
+                                         'desc',
+                                         nwbfile.electrodes)
+
+bipolar_reference_scheme = DynamicTable(name='bipolar_reference_scheme',
+                                        description='desc',
+                                        columns=[positive_electrodes,
+                                                 negative_electrodes])
+
+ecephys_ext = EcephysExt(bipolar_reference_scheme=bipolar_reference_scheme)
+nwbfile.add_lab_meta_data(ecephys_ext)
+
+bipolar_scheme = DynamicTableRegion(
+    name='electrodes',
+    data=np.arange(0, 10),
+    description='desc',
+    table=nwbfile.lab_meta_data['extracellular_electrophysiology_extensions'].bipolar_reference_scheme)
+
+ec_series = ElectricalSeries(name='test_ec_series',
+                             description='desc',
+                             data=np.random.rand(100, 10),
+                             rate=1000.,
+                             electrodes=bipolar_scheme)
+
+nwbfile.add_acquisition(ec_series)
+
+with NWBHDF5IO('test_nwb.nwb', 'w') as io:
+    io.write(nwbfile)
+
+with NWBHDF5IO('test_nwb.nwb', 'r', load_namespaces=True) as io:
+    nwbfile = io.read()
+    print(nwbfile.acquisition['test_ec_series'].electrodes.table['positive_electrodes'].data)
+```

ndx_bipolar_referencing/ndx-meta.yaml

@@ -0,0 +1,8 @@
+name: ndx-bipolar-referencing
+version: 0.1.2
+src: https://github.com/ben-dichter-consulting/ndx-bipolar-referencing
+pip: https://pypi.org/project/ndx-bipolar-referencing/
+license: BSD
+maintainers:
+  - bendichter
+