diff --git a/docfx.json b/docfx.json index da22edb..46be3ab 100644 --- a/docfx.json +++ b/docfx.json @@ -59,7 +59,8 @@ "markdownEngineProperties": { "markdigExtensions": [ "attributes", - "customcontainers" + "customcontainers", + "footnotes" ], "alerts": { "TODO": "alert alert-secondary" diff --git a/images/beaker.svg b/images/beaker.svg new file mode 100644 index 0000000..8a5b29a --- /dev/null +++ b/images/beaker.svg @@ -0,0 +1,119 @@ + + + + diff --git a/images/screwdriver.svg b/images/screwdriver.svg new file mode 100644 index 0000000..cd3f76a --- /dev/null +++ b/images/screwdriver.svg @@ -0,0 +1,61 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/index.md b/index.md index ac55a48..f1e0cb4 100644 --- a/index.md +++ b/index.md @@ -1,33 +1,97 @@ --- uid: index title: OpenEphys.Onix1 -_disableBreadcrumb: true --- -> [!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: -`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) -## Advantages - -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. +
+
-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 +| | [Operator Reference](xref:OpenEphys.Onix1) | | [Hardware Guide](https://open-ephys.github.io/onix-docs/) | +|:----:|:----:|:----:|:----:| +| [![User Guide](images/running.svg){width=150}](xref:getting-started) | [![Operator Reference](images/books.svg){width=150}](xref:OpenEphys.Onix1) | [![Tutorials](images/beaker.svg){width=150}](xref:tutorials) |[![Tutorials](images/screwdriver.svg){width=150}](https://open-ephys.github.io/onix-docs/)| +

-### Quick Links -
+### Why Bonsai? + +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: + +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: + + - 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 + + By targeting Bonsai, ONIX can be used seamlessly with these third party tools. + +> [!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/). -
-| | | | -|:--------------:|:-------------------:|:---------:| -| [![User Guide](images/macbook.svg){width=200}](xref:getting-started) | [![Operator Guide](images/books.svg){width=200}](xref:OpenEphys.Onix1) | [![Tutorials](images/running.svg){width=200}](xref:tutorials) | -| [New to Bonsai or
OpenEphys.Onix? Start here!](xref:getting-started) | [Operator references here](xref:OpenEphys.Onix1) | [Check out our tutorials
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. -
\ No newline at end of file +[^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. \ No newline at end of file