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# ndx-photostim Extension for NWB | ||
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<div style="display:inline"> | ||
<img src="https://github.com/histedlab/ndx-photostim/blob/main/docs/images/ext.png?raw=True" height="50em" style="margin: 0em 0em 0em 0em;" align="right"> | ||
<img src="https://github.com/histedlab/ndx-photostim/blob/main/docs/images/nwb.png?raw=True" height="50em" style="margin: 0em 0em 0em 0em; " align="right"> | ||
This is a <a href="https://www.nwb.org/">NeuroData Without Borders (NWB)</a> extension for storing data and metadata from <a href="https://www.nature.com/articles/nmeth.3217">holographic photostimulation</a> | ||
methods. It includes containers for storing photostimulation-specific device parameters, holographic patterns | ||
(either 2D or 3D), and time series data related to photostimulation. | ||
</div> | ||
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<br>We release six <a href="https://pynwb.readthedocs.io/en/stable/">PyNWB</a> containers as part of this extension (we currently only have a Python implementation, rather than both Python and a MATLAB ones -- this is why the `matnwb` directory is empty): | ||
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* The `SpatialLightModulator` and `Laser` containers store metadata about the spatial light modulator and laser used in the photostimulation, respectively. These containers are then stored within the `PhotostimulationMethod` parent container, which stores the remaining photostimulation method-specifici metadata. | ||
* `HolographicPattern` stores the **holographic pattern** used in stimulation. | ||
* `PhotostimulationSeries` contains the **time series data** corresponding to the presentation of a given stimulus (where the stimulus is represented by a `HolographicPattern` container linked to the `PhotostimulationSeries`). | ||
* We group **all time series & patterns for a given experiment** together using the `PhotostimulationTable` container. This object is a dynamic table, where each row in the table corresponds to a single `PhotostimulationSeries`. Additionally, the table links to the `StimulationDevice` used in the experiment. | ||
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## Background | ||
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<img src="https://github.com/histedlab/ndx-photostim/blob/main/docs/images/Cap1.PNG?raw=True" width="225em" align="left" style=" margin:0.5em 0.5em 0.5em 0.5em;"> | ||
State-of-the-art <a href="https://www.nature.com/articles/s41467-017-01031-3">holographic photostimulation methods</a>, used in concert with <a href="https://www.nature.com/articles/nmeth818">two-photon imaging</a>, | ||
allow unprecedented | ||
control and measurement of cell activity in the living brain. Methods for managing data for two-photon imaging | ||
experiments are improving, but there is little to no standardization of data for holographic stimulation methods. | ||
Stimulation in vivo depends on fine-tuning many experimental variables, which poses a challenge for reproducibility | ||
and data sharing between researchers. To improve <a href="https://www.sciencedirect.com/science/article/pii/S0896627321009557">standardization</a> of photostimulation data storage and processing, | ||
we release this extension as a generic data format for simultaneous holographic stimulation experiments, | ||
using the NWB format to store experimental details and data relating to both acquisition | ||
and photostimulation. | ||
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## Installation | ||
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To install the extension, first clone the `ndx_photostim` repository to the desired folder using the command | ||
```angular2svg | ||
git clone https://github.com/histedlab/ndx-photostim.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_photostim`. | ||
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## Usage | ||
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**For full example usage, see [tutorial.ipynb](https://github.com/histedlab/ndx-photostim/blob/main/tutorial.ipynb)** | ||
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Below is example code to: | ||
1. Create a device used in photostimulation | ||
2. Simulate and store photostimulation ROIs | ||
3. Store the time series corresponding to each stimulation | ||
4. Record all time series and patterns used in an experiment in a table | ||
5. Write the above to an NWB file and read it back | ||
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```python | ||
import numpy as np | ||
from dateutil.tz import tzlocal | ||
from datetime import datetime | ||
from pynwb import NWBFile, NWBHDF5IO | ||
from ndx_photostim import SpatialLightModulator, Laser, PhotostimulationMethod, HolographicPattern, \ | ||
PhotostimulationSeries, PhotostimulationTable | ||
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# create an example NWB file | ||
nwbfile = NWBFile('ndx-photostim_example', 'EXAMPLE_ID', datetime.now(tzlocal())) | ||
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# store the spatial light modulator used | ||
slm = SpatialLightModulator(name='slm', | ||
model='Meadowlark', | ||
size=np.array([512, 512])) | ||
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# store the laser used | ||
laser = Laser(name='laser', | ||
model='Coherent Monaco', | ||
wavelength=1030, | ||
power=8, | ||
peak_pulse_energy=20, | ||
pulse_rate=500) | ||
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# create a container for the method used for photostimulation, and link the SLM and laser to it | ||
ps_method = PhotostimulationMethod(name="methodA", | ||
stimulus_method="scanless", | ||
sweep_pattern="none", | ||
sweep_size=0, | ||
time_per_sweep=0, | ||
num_sweeps=0) | ||
ps_method.add_slm(slm) | ||
ps_method.add_laser(laser) | ||
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# define holographic pattern | ||
hp = HolographicPattern(name='pattern1', | ||
image_mask_roi=np.round(np.random.rand(5, 5)), | ||
stim_duration=0.300, | ||
power_per_target=8) | ||
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# show the mask | ||
hp.show_mask() | ||
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# define stimulation time series using holographic pattern | ||
ps_series = PhotostimulationSeries(name="series_1", | ||
format='interval', | ||
data=[1, -1, 1, -1], | ||
timestamps=[0.5, 1, 2, 4], | ||
pattern=hp, | ||
method=ps_method) | ||
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# add the stimulus to the NWB file | ||
nwbfile.add_stimulus(ps_series) | ||
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# create a table to store the time series/patterns for all stimuli together, along with experiment-specific | ||
# parameters | ||
stim_table = PhotostimulationTable(name='test', description='...') | ||
stim_table.add_series(ps_series) | ||
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# plot the timestamps when the stimulus was presented | ||
stim_table.plot_presentation_times() | ||
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# create a processing module and add the PresentationTable to it | ||
module = nwbfile.create_processing_module(name="photostimulation", description="example photostimulation table") | ||
module.add(stim_table) | ||
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# write to an NWB file and read it back | ||
with NWBHDF5IO("example_file.nwb", "w") as io: | ||
io.write(nwbfile) | ||
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with NWBHDF5IO("example_file.nwb", "r", load_namespaces=True) as io: | ||
read_nwbfile = io.read() | ||
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# Check the file & processing module | ||
print(read_nwbfile) | ||
print(read_nwbfile.processing['photostimulation']) | ||
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if os.path.exists("example_file.nwb"): | ||
os.remove("example_file.nwb") | ||
``` | ||
## Running tests | ||
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<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-photostim/src`). In addition, the | ||
`pytest` command will also run a test of the example code above. | ||
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## Documentation | ||
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### Specification | ||
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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. | ||
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### API | ||
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To generate documentation for the Python API (stores in `./api_docs`), we use <a href="https://www.sphinx-doc.org/en/master/">Sphinx</a> | ||
and a template from <a href="https://readthedocs.org/">ReadTheDocs</a>. API documentation can | ||
be created by running | ||
```angular2svg | ||
sphinx-build -b html api_docs/source/ api_docs/build/ | ||
``` | ||
from the home folder. Similar to the specification docs, API documentation is stored in `./api_docs/build`. Select | ||
`./api_docs/build/index.html` to access the API documentation in a website format. | ||
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## Credit | ||
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Code by Carl Harris and Paul LaFosse (equal contribution). Collaboration between the NIMH's [Data Science and Sharing Team](https://cmn.nimh.nih.gov/dsst) and [Histed Lab](https://www.nimh.nih.gov/research/research-conducted-at-nimh/research-areas/clinics-and-labs/ncb). | ||
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This extension was created using [ndx-template](https://github.com/nwb-extensions/ndx-template). | ||
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name: ndx-photostim | ||
version: 0.0.3 | ||
src: https://github.com/histedlab/ndx-photostim | ||
pip: https://pypi.org/project/ndx-photostim | ||
license: BSD3 | ||
maintainers: | ||
- lafosse | ||
- histed |