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* Improve landing page - Simplify presentation - Remove warning as first thing you see - Tell people why we target bonsai * Address some review comments * Minor updates after merging * Remove breadcrumb attribute Co-authored-by: cjsha <[email protected]> Co-authored-by: bparks13 <[email protected]>
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| Original file line number | Diff line number | Diff line change |
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| --- | ||
| uid: index | ||
| title: OpenEphys.Onix1 | ||
| _disableBreadcrumb: true | ||
| --- | ||
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| > [!Warning] | ||
| > These docs are under active development, feel free to contribute by either [raising an issue](https://github.com/bonsai-rx/docs/issues) or following the links saying **Edit this page**. | ||
| `OpenEphys.Onix1` is a [Bonsai](https://bonsai-rx.org/) library that can be used to control the [ONIX PCIe Acquisition System](https://open-ephys.org/onix/oeps-9006), which provides: | ||
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| `OpenEphys.Onix1` is a library that can be used in [Bonsai](https://bonsai-rx.org/) to acquire data from ONIX devices, such as the [ONIX PCIe Acquisition System](https://open-ephys.org/onix/oeps-9006). For more details on the ONI specification, check out [this link](https://open-ephys.github.io/ONI/), and to learn more about ONIX devices and their implementation of ONI, click [here](https://open-ephys.github.io/onix-docs/). | ||
| * Support for a variety of tools such as [Neuropixels (all | ||
| variants)](https://www.neuropixels.org/), | ||
| [Miniscopes](https://open-ephys.org/miniscope-v4/miniscope-v4), [Intan-based | ||
| headstages](https://open-ephys.org/onix/oeps-7741), and more | ||
| * Automatic hardware synchronization of all data streams. | ||
| * Torque-free commutation of ultra-thin (down to ~0.2mm diameter) tethers | ||
| * High performance closed-loop control (100 usec feedback loop times) | ||
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| ## Advantages | ||
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| While data can be acquired using programs other than Bonsai, there are a number of advantages that come from building `OpenEphys.Onix1` as a Bonsai library. A major advantage is that it maintains maximal compatibility with open source programs, including [OpenCV](https://opencv.org/), [DeepLabCut](https://www.mackenziemathislab.org/deeplabcut), and many more. | ||
| <br> | ||
| <div class="quick-links"> | ||
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| Other major advantages include: | ||
| * Visual interface provided by building on top of Bonsai's foundation | ||
| * Time-stamped synchronization across multiple devices | ||
| * Combine data streams for real-time processing | ||
| | <xref:getting-started> | [Operator Reference](xref:OpenEphys.Onix1) | <xref:tutorials> | [Hardware Guide](https://open-ephys.github.io/onix-docs/) | | ||
| |:----:|:----:|:----:|:----:| | ||
| | [{width=150}](xref:getting-started) | [{width=150}](xref:OpenEphys.Onix1) | [{width=150}](xref:tutorials) |[{width=150}](https://open-ephys.github.io/onix-docs/)| | ||
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| </div> | ||
| <br> | ||
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| ### Quick Links | ||
| <br> | ||
| ### Why Bonsai? | ||
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| ONIX is built on the [ONI standard](https://open-ephys.github.io/ONI/), which is software | ||
| agnostic. Bonsai is the first software target pursued by the Open Ephys team for | ||
| ONIX hardware. There are three major reasons for this: | ||
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| 1. **Performance.** ONIX is a universal interface for neural recording instruments. It can | ||
| capture data produced by neural probes, cameras, high-speed ADCs, etc. In | ||
| general terms, ONIX can capture data from arbitrary mixtures of | ||
| asynchronous[^1] data sources. Bonsai provides an extremely powerful, | ||
| open-source software platform for elegantly collecting, combining, and | ||
| processing data from essentially any data source regardless of its sample | ||
| rate, sample regularity, packet size, and bandwidth. Bonsai accomplishes this | ||
| task in a fundamental manner: it explicitly models each data source as an | ||
| ordered temporal sequence with a start and end called an | ||
| [Observable](https://reactivex.io/documentation/observable.html). This is | ||
| analogous to how, for instance, | ||
| [Numpy](https://numpy.org/doc/stable/index.html) explicitly models fixed-size | ||
| multi-dimensional arrays as | ||
| [ndarrays](https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html#numpy.ndarray). | ||
| And, just like Numpy offers an extensive linear algebra toolkit | ||
| to operate on these arrays, Bonsai offers an analogous | ||
| [toolkit](https://reactivex.io/documentation/operators.html) | ||
| for operating on temporal sequences of data. Because Bonsai was created around this core | ||
| data model and operator library, it makes capturing, processing, and combining data | ||
| sequences from different hardware sources natural in Bonsai, whereas it is | ||
| bug prone and difficult in other software options. | ||
| 1. **Code quality.** Open Ephys has been developing open source hardware and | ||
| software for the Neuroscience community for over a decade. In terms of code | ||
| quality, Bonsai is excellent. Bonsai uses a modern language and build system, | ||
| has integrated package management, and an extremely clean, featureful, and well | ||
| maintained API. Given that Bonsai's development model perfectly aligns with our | ||
| values, we are very proud to be able to contribute to its growth in the | ||
| Neuroscience community. | ||
| 1. **Third party integration.** Bonsai provides support for | ||
| hundreds of pieces of open- and closed-source hardware and software that are | ||
| used extensively in neuroscience research. For instance: | ||
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| - The classic Open Ephys [acquisition system](https://open-ephys.org/acquisition-system) | ||
| - [Ucla Miniscope ecosystem](https://open-ephys.github.io/miniscope-docs/index.html) | ||
| - [National Instruments](https://bonsai-rx.org/daqmx/articles/intro.html) acquisition boards | ||
| - Virtually every machine-vision and sCMOS camera[^2] | ||
| - [Sanworks Bpod](https://sanworks.github.io/Bpod_Wiki/) | ||
| - [Harp](https://harp-tech.org/index.html) | ||
| - [Deeplabcut](https://github.com/bonsai-rx/deeplabcut) & [Sleap](https://github.com/bonsai-rx/sleap) | ||
| - And much more | ||
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| By targeting Bonsai, ONIX can be used seamlessly with these third party tools. | ||
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| > [!NOTE] | ||
| > We put a lot of effort into | ||
| > making these docs useful for everyone. If you have suggestions for making | ||
| > them even better, please contribute by either [raising an | ||
| > issue](https://github.com/bonsai-rx/docs/issues) or following the links saying | ||
| > **Edit this page**. We welcome all constructive feedback. As always, our goals | ||
| > are better performing tools, less redundant development, and more reproducible | ||
| > science. | ||
| > | ||
| > In addition to this library, we are currently developing ONIX support for the | ||
| [Open Ephys GUI](https://open-ephys.org/gui/). | ||
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| <div class="quick-links"> | ||
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| | <xref:getting-started> | <xref:OpenEphys.Onix1> | <xref:tutorials> | | ||
| |:--------------:|:-------------------:|:---------:| | ||
| | [{width=200}](xref:getting-started) | [{width=200}](xref:OpenEphys.Onix1) | [{width=200}](xref:tutorials) | | ||
| | [New to Bonsai or <br>OpenEphys.Onix? Start here!](xref:getting-started) | [Operator references here](xref:OpenEphys.Onix1) | [Check out our tutorials <br>for useful workflows](xref:tutorials) | | ||
| [^1]: Although physical data sources are asynchronous (e.g. a Neuropixels probe | ||
| runs on a distinct clock and produces data at a distinct rate compared to the | ||
| camera sensor on a Miniscope), all data is hardware-timestamped on a common | ||
| clock. No post-hoc data alignment is required. | ||
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| </div> | ||
| [^2]: [Flir](https://github.com/bonsai-rx/spinnaker), [Allied | ||
| Vision](https://github.com/bonsai-rx/vimba), | ||
| [Ximea](https://github.com/bonsai-rx/ximea), | ||
| [Basler](https://github.com/bonsai-rx/pylon), | ||
| [Excelitas](https://github.com/bonsai-rx/pco), etc. |