Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Improve software section headings #68

Closed
wants to merge 1 commit into from
Closed
Show file tree
Hide file tree
Changes from all commits
Commits
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 1 addition & 1 deletion source/Hardware Guide/Headstages/tether-voltage.rst
Original file line number Diff line number Diff line change
Expand Up @@ -20,7 +20,7 @@ host computer will not be able to detect the headstage. A borderline
voltage can still cause connectivity issues as the headstage occasionally dips
below the level it needs to function properly.

.. attention:: The :ref:`openephys_onix1ref` Bonsai package automatically sets the
.. attention:: The :ref:`Bonsai package <openephys_onix1ref>` automatically sets the
headstage port voltage by default, but allows the user to override the
voltage setting as well. The documentation linked shows how to use this
functionality and what valid voltage ranges are for each headstage. This
Expand Down
4 changes: 2 additions & 2 deletions source/Hardware Guide/Miniscopes/index.rst
Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,7 @@ UCLA Miniscope V3
:Design Repository: https://github.com/daharoni/Miniscope_CMOS_Imaging_Sensor_PCB
:Documentation: http://miniscope.org/index.php/Guides_and_Tutorials
:Compatibility: :ref:`pcie_host`, :ref:`breakout`
:Software: :ref:`openephys_onix1ref` Bonsai package
:Software: :ref:`openephys_onix1ref`

.. figure:: /_static/images/miniscopes/ucla-miniscope-v3-render.jpg
:align: center
Expand All @@ -21,7 +21,7 @@ UCLA Miniscope V4
:Design Repository: https://github.com/Aharoni-Lab/Miniscope-v4
:Documentation: https://github.com/Aharoni-Lab/Miniscope-v4/wiki
:Compatibility: :ref:`pcie_host`, :ref:`breakout`
:Software: :ref:`openephys_onix1ref` Bonsai package
:Software: :ref:`openephys_onix1ref`

.. figure:: /_static/images/miniscopes/ucla-miniscope-v4-render.png
:align: center
Expand Down
4 changes: 1 addition & 3 deletions source/Hardware Guide/PCIe Host/setup-windows.rst
Original file line number Diff line number Diff line change
Expand Up @@ -117,7 +117,5 @@ Install Device Driver

Install Software
---------------------------------------
Have a look at the :ref:`software_guide` page for open-source software options. We
recommend using :ref:`bonsairef` and the :ref:`openephys_onix1ref` Bonsai package because it provides first class
support for all ONIX hardware features.
Have a look at the :ref:`software_guide` page for software options.

6 changes: 3 additions & 3 deletions source/Software Guide/Open Ephys GUI/index.rst
Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
.. _open_ephys_gui:

Open Ephys GUI
Open Ephys GUI ONIX Plugin
--------------------------------------------

The `Open Ephys GUI <https://open-ephys.github.io/gui-docs/index.html>`__ is an
Expand All @@ -10,8 +10,8 @@ experiments more flexible and enjoyable. It works equally well on macOS, Linux,
and Windows.

.. note:: An ONIX plugin for the Open Ephys is in development. To access all of
ONIX's capabilities right now, have a look at the :ref:`openephys_onix1ref` Bonsai package.
**You can still take advantage of the GUI's excellent
ONIX's capabilities right now, have a look at the :ref:`openephys_onix1ref`.
**In the meantime, you can still take advantage of the GUI's excellent
ephys visualizaiton tools by streaming data from Bonsai to the GUI using
the** `Ephys Socket Plugin <https://open-ephys.github.io/gui-docs/User-Manual/Plugins/Ephys-Socket.html>`__.

Expand Down
53 changes: 26 additions & 27 deletions source/Software Guide/OpenEphys.Onix1/index.rst
Original file line number Diff line number Diff line change
@@ -1,41 +1,21 @@
.. _bonsairef:

Bonsai
========================

`Bonsai <https://bonsai-rx.org/>`__ is a visual programming language (think
LabView) for `reactive programming
<https://en.wikipedia.org/wiki/Reactive_programming>`__ with features such as:

- Real-time compilation of workflows to machine code as they are edited
(zero-overhead).
- A large array of operators for combining and sychronizing asynchronous data
streams, which is a major issue in other software.
- Lots of support for all sorts of hardware outside of ONIX.

Bonsai is ideal for accessing the full power of ONIX hardware and combining it
with third-party data sources (e.g. machine vision cameras,
behavioral hardware, etc.), and for real-time processing and manipulation of
data streams.

.. _openephys_onix1ref:

OpenEphys.Onix1
----------------
Bonsai ONIX Package
=================================

`OpenEphys.Onix1
<https://open-ephys.github.io/onix1-bonsai-docs/index.html>`__ is the Bonsai
<https://open-ephys.github.io/onix1-bonsai-docs/index.html>`__ is the `Bonsai <https://bonsai-rx.org/>`__
package for ONIX hardware. This package contains `Bonsai Operators
<https://bonsai-rx.org/docs/articles/operators.html>`__ for acquiring and
sending data to ONIX hardware.

:Code: https://github.com/open-ephys/onix-bonsai-onix1
:Compatibility: ONIX Hardware, UCLA miniscopes & variants
:Documentation: https://open-ephys.github.io/onix1-bonsai-docs/index.html
:Code: https://github.com/open-ephys/bonsai-onix1
:Compatibility: All ONIX hardware, Neuropixels, UCLA miniscopes & variants
:Documentation: https://open-ephys.github.io/bonsai-onix1-docs/index.html

.. raw:: html

<a href="https://open-ephys.github.io/onix1-bonsai-docs/index.html"><span class="std std-ref custom-card">
<a href="https://open-ephys.github.io/bonsai-onix1-docs/index.html"><span class="std std-ref custom-card">
<div class="card text-center page-card">

<header>
Expand All @@ -46,3 +26,22 @@ sending data to ONIX hardware.
package documentation">

</div>

What is Bonsai?
------------------------------
`Bonsai <https://bonsai-rx.org/>`__ is a visual programming language (think
LabView) for `reactive programming
<https://en.wikipedia.org/wiki/Reactive_programming>`__ with features such as:

- Real-time compilation of workflows to machine code as they are edited
(zero-overhead).
- A large array of operators for combining and sychronizing asynchronous data
streams, which is a major issue in other software.
- Lots of support for all sorts of hardware outside of ONIX.

Bonsai is A good choice for accessing the full power of ONIX hardware and
combining it with third-party data sources (e.g. machine vision cameras,
behavioral hardware, etc.), and for real-time processing and manipulation of
data streams. The documentation linked above contains detailed instructions on
how to use Bonsai with ONIX hardware along with fully useable example workflows,
data loading scripts, etc.
14 changes: 8 additions & 6 deletions source/Software Guide/index.rst
Original file line number Diff line number Diff line change
Expand Up @@ -14,13 +14,15 @@
oni-repl/index
Bonsai.ONIX (DEPRECATED) <Bonsai.ONIX/index>

:ref:`Bonsai <bonsairef>`
:ref:`openephys_onix1ref` is a :ref:`bonsairef` package for acquiring data from ONIX
hardware for real-time experiments. Bonsai is very good at processing the
:ref:`Bonsai ONIX Package <openephys_onix1ref>`
:ref:`OpenEphys.Onix1 <openephys_onix1ref>` is a `Bonsai
<https://bonsai-rx.org/>`__ package for acquiring data from ONIX hardware
for real-time experiments. Bonsai is very good at processing the
heterogeneous data streams produced by ONIX hardware.

:ref:`Open Ephys GUI <open_ephys_gui>`
The Open Ephys GUI can be used for ONIX data visualization.
:ref:`Open Ephys GUI ONIX Plugin<open_ephys_gui>`
The `Open Ephys GUI <https://open-ephys.github.io/gui-docs/> excels at
electrophysiology data visualization and recording.

:ref:`oni-repl <oni_repl>`
A simple command-line application that can be used for debugging and basic
Expand All @@ -35,5 +37,5 @@ Deprecated Software
___________________________________

- The :ref:`bonsai_onixref` pages provide information about the original Bonsai
package, which has been superseded by :ref:`openephys_onix1ref`
package, which has been superseded by :ref:`OpenEphys.Onix1 <openephys_onix1ref>`.

Loading