From 80dcfb5ad9e248f0dece075307d899e820db6f13 Mon Sep 17 00:00:00 2001 From: GitHub Action Date: Fri, 9 Aug 2024 18:56:43 +0000 Subject: [PATCH] Update documentation --- Getting Started/index.html | 18 +- Getting Started/troubleshooting.html | 2 +- Getting Started/warnings.html | 105 +-- Getting Started/whatisonix.html | 73 +- .../Adapters & EIBs/eib-64-large.html | 6 +- Hardware Guide/Adapters & EIBs/eib-64.html | 6 +- Hardware Guide/Adapters & EIBs/index.html | 6 +- .../Adapters & EIBs/nano-z-adapter-64.html | 6 +- .../Adapters & EIBs/omnetics-adapter-64.html | 6 +- Hardware Guide/Breakout Board/index.html | 6 +- Hardware Guide/Breakout Board/setup.html | 6 +- .../updating-breakout-firmware.html | 6 +- Hardware Guide/Commutators/index.html | 31 +- .../Connections & Cables/index.html | 6 +- Hardware Guide/Datasheets/bno055.html | 6 +- Hardware Guide/Datasheets/ds90ub9x-raw.html | 6 +- Hardware Guide/Datasheets/estim-hs64.html | 6 +- Hardware Guide/Datasheets/fmc-analog-io.html | 6 +- Hardware Guide/Datasheets/fmc-clock-out.html | 6 +- Hardware Guide/Datasheets/fmc-digital-io.html | 6 +- .../Datasheets/fmc-link-control.html | 10 +- Hardware Guide/Datasheets/heartbeat.html | 6 +- Hardware Guide/Datasheets/index.html | 6 +- Hardware Guide/Datasheets/load-test.html | 6 +- Hardware Guide/Datasheets/memory-usage.html | 6 +- Hardware Guide/Datasheets/neuropixels-v1.html | 6 +- Hardware Guide/Datasheets/ostim-hs64.html | 6 +- Hardware Guide/Datasheets/rhd2164.html | 6 +- .../Datasheets/rhs2116-trigger.html | 6 +- Hardware Guide/Datasheets/rhs2116.html | 6 +- Hardware Guide/Datasheets/test-0.html | 6 +- .../Datasheets/ts4231-v1-array.html | 6 +- .../Headstages/headstage-64/index.html | 16 +- .../headstage-64/test-board-64.html | 6 +- .../Headstages/headstage-neuropix-1.html | 6 +- .../Headstages/headstage-neuropix-1e.html | 8 +- .../headstage-neuropix-2e-beta.html | 8 +- .../Headstages/headstage-neuropix-2e.html | 12 +- .../{rhs2116.html => headstage-rhs2116.html} | 93 +-- Hardware Guide/Headstages/index.html | 10 +- Hardware Guide/Headstages/serialization.html | 6 +- Hardware Guide/Headstages/setup.html | 13 +- Hardware Guide/Headstages/tether-voltage.html | 97 ++- Hardware Guide/Headstages/tethers.html | 12 +- Hardware Guide/Lighthouses/index.html | 6 +- Hardware Guide/Lighthouses/setup.html | 6 +- Hardware Guide/Miniscopes/index.html | 36 +- .../PCIe Host/bracket-assembly.html | 2 +- Hardware Guide/PCIe Host/index.html | 6 +- .../PCIe Host/multi-board-sync.html | 6 +- Hardware Guide/PCIe Host/overview.html | 25 +- .../PCIe Host/programming-with-jtag.html | 2 +- Hardware Guide/PCIe Host/setup-windows.html | 37 +- .../PCIe Host/updating-firmware.html | 6 +- Hardware Guide/index.html | 6 +- Resources/downloads.html | 2 +- Resources/faq.html | 5 +- Resources/index.html | 8 +- Resources/support.html | 2 +- .../Bonsai Examples/CameraSync.html | 14 +- .../Bonsai Examples/Commutator.html | 20 +- .../Bonsai Examples/Headstage64.html | 14 +- .../Bonsai Examples/HeadstageNP1e.html | 14 +- .../Bonsai Examples/LatencyTest.html | 14 +- .../Bonsai.ONIX/Bonsai Examples/index.html | 14 +- .../Bonsai.ONIX/GettingStarted.html | 16 +- Software Guide/Bonsai.ONIX/Installation.html | 18 +- .../Bonsai.ONIX/Nodes/AnalogIODevice.html | 14 +- .../Bonsai.ONIX/Nodes/BNO055Device.html | 14 +- .../Bonsai.ONIX/Nodes/ClockOutputDevice.html | 14 +- .../Bonsai.ONIX/Nodes/DigitalIODevice.html | 14 +- .../Nodes/ElectricalStimulationDevice.html | 14 +- .../Nodes/HeadstagePortControlDevice.html | 14 +- .../Bonsai.ONIX/Nodes/HeartbeatDevice.html | 14 +- .../Bonsai.ONIX/Nodes/MemoryUsageDevice.html | 14 +- .../Bonsai.ONIX/Nodes/MiniscopeV3Device.html | 14 +- .../Nodes/MiniscopeV4BNO055Device.html | 14 +- .../Bonsai.ONIX/Nodes/MiniscopeV4Device.html | 14 +- .../Nodes/NeuropixelsV1Device.html | 16 +- .../Nodes/NeuropixelsV1eDevice.html | 16 +- .../Bonsai.ONIX/Nodes/ONIContext.html | 18 +- .../Nodes/OpticalStimulationDevice.html | 14 +- .../Bonsai.ONIX/Nodes/RHD2164Device.html | 14 +- .../Bonsai.ONIX/Nodes/RHS2116Device.html | 16 +- .../Nodes/RHS2116TriggerDevice.html | 14 +- .../Bonsai.ONIX/Nodes/TS4231V1Device.html | 14 +- Software Guide/Bonsai.ONIX/Nodes/index.html | 14 +- .../Bonsai.ONIX/deprecation-notice.html | 522 ++++++++++++++ Software Guide/Bonsai.ONIX/index.html | 24 +- Software Guide/Open Ephys GUI/index.html | 76 +-- Software Guide/OpenEphys.Onix1/index.html | 635 ++++++++++++++++++ Software Guide/index.html | 66 +- Software Guide/oni-repl/index.html | 14 +- Software Guide/oni-repl/usage.html | 8 +- ...re.jpg => bonsai-package-architecture.jpg} | Bin _images/bonsai-start-menu.png | Bin 22997 -> 0 bytes _images/todo.jpg | Bin 95258 -> 0 bytes _sources/Getting Started/index.rst.txt | 9 +- _sources/Getting Started/warnings.rst.txt | 83 +-- _sources/Getting Started/whatisonix.rst.txt | 63 +- .../Hardware Guide/Commutators/index.rst.txt | 24 +- .../Datasheets/fmc-link-control.rst.txt | 4 +- .../Headstages/headstage-rhs2116.rst.txt | 97 +++ .../Hardware Guide/Headstages/index.rst.txt | 4 +- .../Hardware Guide/Headstages/rhs2116.rst.txt | 130 ---- .../Hardware Guide/Headstages/setup.rst.txt | 10 +- .../Headstages/tether-voltage.rst.txt | 76 +-- .../Hardware Guide/Miniscopes/index.rst.txt | 11 +- .../Hardware Guide/PCIe Host/overview.rst.txt | 18 +- .../PCIe Host/setup-windows.rst.txt | 24 +- _sources/Resources/faq.rst.txt | 7 +- .../Bonsai Examples/CameraSync.rst.txt | 2 + .../Bonsai Examples/Commutator.rst.txt | 2 + .../Bonsai Examples/Headstage64.rst.txt | 2 + .../Bonsai Examples/HeadstageNP1e.rst.txt | 2 + .../Bonsai Examples/LatencyTest.rst.txt | 3 + .../Bonsai.ONIX/Bonsai Examples/index.rst.txt | 2 + .../Bonsai.ONIX/GettingStarted.rst.txt | 4 +- .../Bonsai.ONIX/Installation.rst.txt | 6 +- .../Bonsai.ONIX/Nodes/AnalogIODevice.rst.txt | 2 + .../Bonsai.ONIX/Nodes/BNO055Device.rst.txt | 2 + .../Nodes/ClockOutputDevice.rst.txt | 2 + .../Bonsai.ONIX/Nodes/DigitalIODevice.rst.txt | 2 + .../Nodes/ElectricalStimulationDevice.rst.txt | 2 + .../Nodes/HeadstagePortControlDevice.rst.txt | 2 + .../Bonsai.ONIX/Nodes/HeartbeatDevice.rst.txt | 2 + .../Nodes/MemoryUsageDevice.rst.txt | 2 + .../Nodes/MiniscopeV3Device.rst.txt | 2 + .../Nodes/MiniscopeV4BNO055Device.rst.txt | 2 + .../Nodes/MiniscopeV4Device.rst.txt | 2 + .../Nodes/NeuropixelsV1Device.rst.txt | 4 +- .../Nodes/NeuropixelsV1eDevice.rst.txt | 4 +- .../Bonsai.ONIX/Nodes/ONIContext.rst.txt | 6 +- .../Nodes/OpticalStimulationDevice.rst.txt | 2 + .../Bonsai.ONIX/Nodes/RHD2164Device.rst.txt | 2 + .../Bonsai.ONIX/Nodes/RHS2116Device.rst.txt | 4 +- .../Nodes/RHS2116TriggerDevice.rst.txt | 2 + .../Bonsai.ONIX/Nodes/TS4231V1Device.rst.txt | 2 + .../Bonsai.ONIX/Nodes/index.rst.txt | 2 + .../Bonsai.ONIX/deprecation-notice.rst.txt | 5 + .../Software Guide/Bonsai.ONIX/index.rst.txt | 12 +- .../Open Ephys GUI/index.rst.txt | 46 +- .../OpenEphys.Onix1/index.rst.txt | 48 ++ _sources/Software Guide/index.rst.txt | 49 +- ...re.jpg => bonsai-package-architecture.jpg} | Bin ...re.pdf => bonsai-package-architecture.pdf} | Bin _static/images/bonsai-lettering.svg | 258 +++++++ _static/images/onix1-example.svg | 3 + _static/theme_overrides.css | 26 +- genindex.html | 2 +- index.html | 2 +- objects.inv | Bin 4623 -> 4696 bytes search.html | 2 +- searchindex.js | 2 +- 154 files changed, 2529 insertions(+), 1155 deletions(-) rename Hardware Guide/Headstages/{rhs2116.html => headstage-rhs2116.html} (84%) create mode 100644 Software Guide/Bonsai.ONIX/deprecation-notice.html create mode 100644 Software Guide/OpenEphys.Onix1/index.html rename _images/{bonsai-library-architecture.jpg => bonsai-package-architecture.jpg} (100%) delete mode 100644 _images/bonsai-start-menu.png delete mode 100644 _images/todo.jpg create mode 100644 _sources/Hardware Guide/Headstages/headstage-rhs2116.rst.txt delete mode 100644 _sources/Hardware Guide/Headstages/rhs2116.rst.txt create mode 100644 _sources/Software Guide/Bonsai.ONIX/deprecation-notice.rst.txt create mode 100644 _sources/Software Guide/OpenEphys.Onix1/index.rst.txt rename _static/bonsai/{bonsai-library-architecture.jpg => bonsai-package-architecture.jpg} (100%) rename _static/bonsai/{bonsai-library-architecture.pdf => bonsai-package-architecture.pdf} (100%) create mode 100644 _static/images/bonsai-lettering.svg create mode 100644 _static/images/onix1-example.svg diff --git a/Getting Started/index.html b/Getting Started/index.html index e30b0d28..70cd2870 100644 --- a/Getting Started/index.html +++ b/Getting Started/index.html @@ -30,7 +30,7 @@ - + @@ -450,8 +450,8 @@

Usage WarningsUsage Warnings before starting to work with the system to avoid causing damage to system components.

-
-

Setting up ONIX#

+
+

Setting up your system#

  1. Check that you have all the necessary hardware. A full ONIX setup consists of:

    Hardware

    @@ -484,18 +484,12 @@

    Setting up ONIXfollowing these steps. Be sure to read this page on the voltage supplied to the headstage to prevent damaging your headstage.

    2. -

  2. Test the installation.

    -
    -

    Todo

    -

    Bonsai workflows for testing each component

    -
    -

Using ONIX#

-

ONIX uses Bonsai for data acquisition. See the Getting Started -page to learn how to install Bonsai and use it to acquire from ONIX.

+

Have a look at the Software Guide page to explore +software options and for intefacing with ONIX hardware.

@@ -554,7 +548,7 @@

Using ONIX
  • Understanding the System
  • Usage Warnings
    • -
  • Setting up ONIX
    • +
  • Setting up your system
  • Using ONIX
    • diff --git a/Getting Started/troubleshooting.html b/Getting Started/troubleshooting.html index 28e720ee..fac52714 100644 --- a/Getting Started/troubleshooting.html +++ b/Getting Started/troubleshooting.html @@ -30,7 +30,7 @@ - + diff --git a/Getting Started/warnings.html b/Getting Started/warnings.html index 3117a4a2..9a3c08b6 100644 --- a/Getting Started/warnings.html +++ b/Getting Started/warnings.html @@ -30,7 +30,7 @@ - + @@ -431,96 +431,33 @@

    Usage Warnings

    Warning

    Improper setup and usage can cause damage to system components.

    - -
      -

    • Read the following warnings before starting to work with your system. These are crucial -aspects to consider during setup and usage that are included in the documentation but -are listed here for your convenience.

      • -

    • Read the complete documentation carefully to understand how the system works and refer -back to these warnings before using it.

      • -
    -
    -

    Hardware#

      -

    • Connecting or disconnecting the breakout board while the PC is on causes damage to the -FMChost. For more details, see Breakout Board Guide.

      • +

    • Read the following warnings before starting to work with your system. These +are crucial aspects to consider during setup and usage that are included in +the documentation but are listed here for your convenience.

      • +

    • Read the complete documentation carefully to understand how the system works +and refer back to these warnings before using it.

    -
    -

    Warning

    -

    Power off the PC before connecting/disconnecting the breakout board.

    -
      -

    • Headstage voltage must be configured correctly for operation. The voltage that works -for one headstage can damage another, and depends on your hardware configuration such -as tether length. For more details, see Tethered Headstage Voltages.

      • -
    +
    +

    Breakout Board#

    Warning

    -

    Ensure each headstage is configured with the correct voltage according to its -specification before connecting and switching on the headstage port switch.

    +

    Connecting or disconnecting the Breakout Board while the PC is on +can damage to the PCIe Host. For more details, see +Breakout Board Guide. Power off the PC before connecting/disconnecting the +breakout board.

    -
    -

    Software#

    -

    For the current Bonsai.ONIX library which is being revised to improve usability

    -
      -

    • Headstage port voltage configuration is managed via the ONIContext node -or the HeadstagePortControlDevice node. The changes you make using these -nodes apply immediately and persist in hardware even if the Bonsai workflow is not -running. Headstage port voltage is reset to the default 4.9V only on a power cycle -(power off and on — not reboot).

      • -
    -
    -

    Warning

    -

    Keep the headstage port switches off until you have configured each port correctly.

    -
    -
    -

    Warning

    -

    Remember to set the headstage voltage to the desired value after a power cycle.

    -
    -
      -

    • The ONIContext provides a dynamic window to read and write to hardware, -but parameters such as device voltage are not saved in the node when the workflow is -saved. The HeadstagePortControlDevice node also reads and writes to hardware, -but parameters are saved with the workflow. On loading a workflow, Bonsai writes the -parameter values set when the workflow was last saved.

      • -
    -
    -

    Warning

    -

    When you configure the voltage, the ONIContext node shows that value -and when you save the workflow this value is not saved. Therefore, that value will -not be set to hardware when you load the workflow again. On loading the workflow, -the ONIContext node will be reading the voltage that is already set -on the hardware and showing this in the LinkVoltage field.

    -
    -
    -

    Warning

    -

    When you configure the voltage, the HeadstagePortControlDevice node shows -that value and when you save the workflow this value is saved. Therefore, that value -will be set to hardware when you load the workflow again. If you make changes to the -voltage value (with any node) and save the workflow, they will be saved in the -LinkVoltage property of the HeadstagePortControlDevice node.

    -
    - -
    -

    Warning

    -

    Check that the voltage set to the headstage port is correct for the -Neuropixels-1.0e Headstage by using a workflow of a single ONIContext -node to configure it before connecting the headstage in order to open a workflow that -contains the NeuropixelsV1eDevice node.

    -
    -
      -

    • An ONIContext node or any device node in a workflow can override device -settings in another workflow if device addresses are not distinct, because these nodes -read/write directly to hardware.

      • -
    +
    +

    Headstage Voltages#

    Warning

    -

    Only have one workflow open at a time.

    +

    Ensure each headstage is configured with the correct voltage. Although +headstages are quite tolerate of over-voltage and under-voltage conditions, +they are only guaranteed to function within a specified range. When using +long and/or thin tethers, the voltage drop across the cable can become +significant. For more details, see Headstage Voltages.

    @@ -578,8 +515,8 @@

    Software diff --git a/Getting Started/whatisonix.html b/Getting Started/whatisonix.html index 234528a9..33cde121 100644 --- a/Getting Started/whatisonix.html +++ b/Getting Started/whatisonix.html @@ -30,7 +30,7 @@ - + @@ -429,9 +429,9 @@

    What is ONIX?#

    ONIX is a data acquisition system for neuroscience, composed of various pieces -of hardware. ONIX differs from other acquisition systems in three major points:

    -
    -

    1. Standards#

    +of hardware. ONIX differs from other acquisition systems in three ways:

    +
    +

    1. Standards & Interoperability#

    All acquisition systems follow specific sets of rules that outline how data is structured and transmitted between parts of the system. For instance, Intan headstages and the classic Open Ephys Board use a Serial Peripheral Interface (SPI) @@ -452,19 +452,19 @@

    1. Standards -

    2. Tethers#

    +
    +

    2. Thin Tethers & Zero Torque Commutation#

    There is a growing appreciation of experiments that examine the natural behaviours of animals. This often means using larger and more intricate (perhaps 3D) experimental setups. It also means that the animal should be impaired as little as possible by the recording setup. To achieve this it is of course important to reducing the weight of the headstage, but the weight of the tether that connects the headstage to the acquisition system is often -overlooked. As the animal explores the arena, the centre of mass of the tether +overlooked. As the animal explores the arena, the center of mass of the tether is rarely directly above the animal. Instead, it is off to one side, -introducing a rotational force on the animal. The animal must compensate for -this torque in order to keep its head up straight. Because the ONI -specification allows communication over a single wire, ONIX uses a single +introducing a rotational force (torque) on the animal. The animal must +compensate for this torque in order to keep its head up straight. Because the +ONI specification allows communication over a single wire, ONIX uses a single coaxial cable, making ONIX tethers lighter and thinner compared to classic acquisition systems. ONIX tethers are 0.1 to 0.4 mm in diameter and are extremely flexible.

    @@ -473,30 +473,39 @@

    2. Tethers +motor to actively rotate the tether, preventing twisting. Importantly, this +process is driven by real-time measurement of headstage rotation, not by +torque transmitted by the tether. This allows nearly zero-torque commutation +and the use of tethers that are so thin, they would not not function in systems +that require torque measurements to drive active commutation.

    -
    -

    3. Latencies#

    +
    +

    3. Low Latencies#

    In closed-loop experiments, data is not only acquired, but also processed and acted upon. For instance, one can provide optogenetic stimulation to a brain area every time a certain type of event is detected by an extracellular probe. The closed-loop latency of the acquisition system describes how much time -passes between the initial event and the response of the system. In classic -acquisition systems, this time is primarily spent on transmitting and -processing acquired data, which becomes more and more challenging as the number -of channels on a probe increases. A short latency allows the user to respond on -the timescale of the biological event; for instance, within the integration -window of a neuron.

    -

    Many classic acquisition systems rely on a USB connection between the -acquisition board and PC. The slower transfer characteristics of USB means that -a typical closed-loop latency would be in the range of several to tens of -milliseconds. This is a considerable duration for the brain, as it is notably -longer than the average action potential duration of around 1 ms. ONIX has much -shorter latencies, of around 150 microseconds, because the host board of ONIX -is directly connected to the acquisition PC, in a PCIe slot. This means that -the system can respond quickly to detected events. It also means that time is -freed up for this detection itself; by reducing the overhead time, more complex -analysis can be run to extract the phenomenon you are interested in.

    +passes between the physical event and the response of the real-time system. A +short latency allows the user to respond on the timescale of the biological +event; for instance, within the integration window of a neuron.

    +

    Many acquisition systems rely on a USB connection between the acquisition board +and PC. Or, they rely on closed-source 3rd-party drivers and APIs that are not +optimized for low response latencies. The slower transfer characteristics of +USB means that a typical closed-loop latency is in the range of several +to tens of milliseconds. This is a considerable duration for the brain, as it +is notably longer than the average action potential duration of around 1 ms. On +average, ONIX provides much shorter latencies, of around 150 microseconds, because:

    +
      +

    • ONIX is transfers data to the host computer without the CPU via DMA over PCIe.

      • +

    • ONIX uses a custom device driver optimized for low latency.

      • +

    • The ONI API allows explicit control over a single parameter to governs the +trade off between data latency and overall bandwidth.

      • +
    +

    This permits the user to optimize their system’s response time for a given +experiment. In all, this means that the system can respond quickly to detected +events. It also means that time is freed up for this detection itself; by +reducing the overhead time, more complex analysis can be run to extract the +phenomenon you are interested in.

    @@ -553,9 +562,9 @@

    3. Latencies diff --git a/Hardware Guide/Adapters & EIBs/eib-64-large.html b/Hardware Guide/Adapters & EIBs/eib-64-large.html index e99c3ed8..61473029 100644 --- a/Hardware Guide/Adapters & EIBs/eib-64-large.html +++ b/Hardware Guide/Adapters & EIBs/eib-64-large.html @@ -30,7 +30,7 @@ - + @@ -381,6 +381,7 @@
  • Setup
  • Coaxial Data Serialization & Power
  • Making Coaxial Tethers
    • +
  • Headstage Voltages
  • Headstage-64 @@ -389,8 +390,7 @@
  • Neuropixels-1.0e Headstage
  • Neuropixels-2.0eBeta Headstage
  • Neuropixels-2.0e Headstage
    • -
  • RHS2116 Headstage
    • -
  • Tethered Headstage Voltages
    • +
  • RHS2116 Headstage
  • Miniscopes
    • diff --git a/Hardware Guide/Adapters & EIBs/eib-64.html b/Hardware Guide/Adapters & EIBs/eib-64.html index 49d52d87..70aa9605 100644 --- a/Hardware Guide/Adapters & EIBs/eib-64.html +++ b/Hardware Guide/Adapters & EIBs/eib-64.html @@ -30,7 +30,7 @@ - + @@ -381,6 +381,7 @@
  • Setup
  • Coaxial Data Serialization & Power
  • Making Coaxial Tethers
    • +
  • Headstage Voltages
  • Headstage-64 @@ -389,8 +390,7 @@
  • Neuropixels-1.0e Headstage
  • Neuropixels-2.0eBeta Headstage
  • Neuropixels-2.0e Headstage
    • -
  • RHS2116 Headstage
    • -
  • Tethered Headstage Voltages
    • +
  • RHS2116 Headstage
  • Miniscopes
    • diff --git a/Hardware Guide/Adapters & EIBs/index.html b/Hardware Guide/Adapters & EIBs/index.html index 3b0bbed1..89abe598 100644 --- a/Hardware Guide/Adapters & EIBs/index.html +++ b/Hardware Guide/Adapters & EIBs/index.html @@ -30,7 +30,7 @@ - + @@ -381,6 +381,7 @@
  • Setup
  • Coaxial Data Serialization & Power
  • Making Coaxial Tethers
    • +
  • Headstage Voltages
  • Headstage-64 @@ -389,8 +390,7 @@
  • Neuropixels-1.0e Headstage
  • Neuropixels-2.0eBeta Headstage
  • Neuropixels-2.0e Headstage
    • -
  • RHS2116 Headstage
    • -
  • Tethered Headstage Voltages
    • +
  • RHS2116 Headstage
  • Miniscopes
    • diff --git a/Hardware Guide/Adapters & EIBs/nano-z-adapter-64.html b/Hardware Guide/Adapters & EIBs/nano-z-adapter-64.html index b3776c62..04e4a8c7 100644 --- a/Hardware Guide/Adapters & EIBs/nano-z-adapter-64.html +++ b/Hardware Guide/Adapters & EIBs/nano-z-adapter-64.html @@ -30,7 +30,7 @@ - + @@ -381,6 +381,7 @@
  • Setup
  • Coaxial Data Serialization & Power
  • Making Coaxial Tethers
    • +
  • Headstage Voltages
  • Headstage-64 @@ -389,8 +390,7 @@
  • Neuropixels-1.0e Headstage
  • Neuropixels-2.0eBeta Headstage
  • Neuropixels-2.0e Headstage
    • -
  • RHS2116 Headstage
    • -
  • Tethered Headstage Voltages
    • +
  • RHS2116 Headstage
  • Miniscopes
    • diff --git a/Hardware Guide/Adapters & EIBs/omnetics-adapter-64.html b/Hardware Guide/Adapters & EIBs/omnetics-adapter-64.html index 6c4344eb..f400fbbf 100644 --- a/Hardware Guide/Adapters & EIBs/omnetics-adapter-64.html +++ b/Hardware Guide/Adapters & EIBs/omnetics-adapter-64.html @@ -30,7 +30,7 @@ - + @@ -381,6 +381,7 @@
  • Setup
  • Coaxial Data Serialization & Power
  • Making Coaxial Tethers
    • +
  • Headstage Voltages
  • Headstage-64 @@ -389,8 +390,7 @@
  • Neuropixels-1.0e Headstage
  • Neuropixels-2.0eBeta Headstage
  • Neuropixels-2.0e Headstage
    • -
  • RHS2116 Headstage
    • -
  • Tethered Headstage Voltages
    • +
  • RHS2116 Headstage
  • Miniscopes
    • diff --git a/Hardware Guide/Breakout Board/index.html b/Hardware Guide/Breakout Board/index.html index f795cb24..128440dc 100644 --- a/Hardware Guide/Breakout Board/index.html +++ b/Hardware Guide/Breakout Board/index.html @@ -30,7 +30,7 @@ - + @@ -381,6 +381,7 @@
  • Setup
  • Coaxial Data Serialization & Power
  • Making Coaxial Tethers
    • +
  • Headstage Voltages
  • Headstage-64 @@ -389,8 +390,7 @@
  • Neuropixels-1.0e Headstage
  • Neuropixels-2.0eBeta Headstage
  • Neuropixels-2.0e Headstage
    • -
  • RHS2116 Headstage
    • -
  • Tethered Headstage Voltages
    • +
  • RHS2116 Headstage
  • Miniscopes
    • diff --git a/Hardware Guide/Breakout Board/setup.html b/Hardware Guide/Breakout Board/setup.html index 7a7d9b08..679b110a 100644 --- a/Hardware Guide/Breakout Board/setup.html +++ b/Hardware Guide/Breakout Board/setup.html @@ -30,7 +30,7 @@ - + @@ -381,6 +381,7 @@
  • Setup
  • Coaxial Data Serialization & Power
  • Making Coaxial Tethers
    • +
  • Headstage Voltages
  • Headstage-64 @@ -389,8 +390,7 @@
  • Neuropixels-1.0e Headstage
  • Neuropixels-2.0eBeta Headstage
  • Neuropixels-2.0e Headstage
    • -
  • RHS2116 Headstage
    • -
  • Tethered Headstage Voltages
    • +
  • RHS2116 Headstage
  • Miniscopes
    • diff --git a/Hardware Guide/Breakout Board/updating-breakout-firmware.html b/Hardware Guide/Breakout Board/updating-breakout-firmware.html index 4fc2bc4c..47113dd8 100644 --- a/Hardware Guide/Breakout Board/updating-breakout-firmware.html +++ b/Hardware Guide/Breakout Board/updating-breakout-firmware.html @@ -30,7 +30,7 @@ - + @@ -381,6 +381,7 @@
  • Setup
  • Coaxial Data Serialization & Power
  • Making Coaxial Tethers
    • +
  • Headstage Voltages
  • Headstage-64 @@ -389,8 +390,7 @@
  • Neuropixels-1.0e Headstage
  • Neuropixels-2.0eBeta Headstage
  • Neuropixels-2.0e Headstage
    • -
  • RHS2116 Headstage
    • -
  • Tethered Headstage Voltages
    • +
  • RHS2116 Headstage
  • Miniscopes
    • diff --git a/Hardware Guide/Commutators/index.html b/Hardware Guide/Commutators/index.html index 794cb8c8..6822c28b 100644 --- a/Hardware Guide/Commutators/index.html +++ b/Hardware Guide/Commutators/index.html @@ -30,7 +30,7 @@ - + @@ -381,6 +381,7 @@
  • Setup
  • Coaxial Data Serialization & Power
  • Making Coaxial Tethers
    • +
  • Headstage Voltages
  • Headstage-64 @@ -389,8 +390,7 @@
  • Neuropixels-1.0e Headstage
  • Neuropixels-2.0eBeta Headstage
  • Neuropixels-2.0e Headstage
    • -
  • RHS2116 Headstage
    • -
  • Tethered Headstage Voltages
    • +
  • RHS2116 Headstage
  • Miniscopes
    • @@ -486,17 +486,20 @@

    Coaxial Commutators#

    -

    Active, near-zero torque commutators to prevent tether twisting during -freely moving recordings with headstages and/or miniscopes. -This page provides a very brief overview of the commutators; for a more extensive -walkthrough, please follow the documentation link for Commutators.

    +

    Active, near-zero torque commutators prevent tether twisting during freely +moving recordings with headstages and/or miniscopes. This page provides a very +brief overview of the commutators; for a more extensive walkthrough, please +follow the documentation link for Commutators.

    Design Repository:

    open-ephys/commutators

    Compatibility:
    -

    PCIe Host, Headstage-64, -Neuropixels-1.0 Headstage, Miniscopes

    +

    All coaxial headstags (e.g. Headstage-64, +Neuropixels-2.0e Headstage, Miniscopes)

    +
    +
    Documentation:
    +

    https://open-ephys.github.io/commutator-docs/index.html

    @@ -510,11 +513,11 @@

    ONIX uses an active commutator to prevents tether twisting during freely moving recordings. A inertial measurement unit (IMU) on the headstage or miniscope sends orientation data to the host computer. Because the real-time orientation -of the animal is known, software (e.g. Bonsai) can be used to send commands to -the commutator via its USB interface, and the motor in the commutator will turn -when the animal does. A high-quality radio-frequency rotary joint inside the -commutator maintains electrical connectivity for both power and high-frequency -data signals between the tether leading to the headstage and the coaxial cable +of the animal is known, software can be used to send commands to the commutator +via its USB interface, and the motor in the commutator will turn when the +animal does. A high-quality radio-frequency rotary joint inside the commutator +maintains electrical connectivity for both power and high-frequency data +signals between the tether leading to the headstage and the coaxial cable leading to the PCIe host board while turning.

    Features#

    diff --git a/Hardware Guide/Connections & Cables/index.html b/Hardware Guide/Connections & Cables/index.html index 3f75d452..b5a3f024 100644 --- a/Hardware Guide/Connections & Cables/index.html +++ b/Hardware Guide/Connections & Cables/index.html @@ -30,7 +30,7 @@ - + @@ -381,6 +381,7 @@
  • Setup
  • Coaxial Data Serialization & Power
  • Making Coaxial Tethers
    • +
  • Headstage Voltages
  • Headstage-64 @@ -389,8 +390,7 @@
  • Neuropixels-1.0e Headstage
  • Neuropixels-2.0eBeta Headstage
  • Neuropixels-2.0e Headstage
    • -
  • RHS2116 Headstage
    • -
  • Tethered Headstage Voltages
    • +
  • RHS2116 Headstage
  • Miniscopes
    • diff --git a/Hardware Guide/Datasheets/bno055.html b/Hardware Guide/Datasheets/bno055.html index abb741de..79b141ba 100644 --- a/Hardware Guide/Datasheets/bno055.html +++ b/Hardware Guide/Datasheets/bno055.html @@ -30,7 +30,7 @@ - + @@ -382,6 +382,7 @@
  • Setup
  • Coaxial Data Serialization & Power
  • Making Coaxial Tethers
    • +
  • Headstage Voltages
  • Headstage-64 @@ -390,8 +391,7 @@
  • Neuropixels-1.0e Headstage
  • Neuropixels-2.0eBeta Headstage
  • Neuropixels-2.0e Headstage
    • -
  • RHS2116 Headstage
    • -
  • Tethered Headstage Voltages
    • +
  • RHS2116 Headstage
  • Miniscopes
    • diff --git a/Hardware Guide/Datasheets/ds90ub9x-raw.html b/Hardware Guide/Datasheets/ds90ub9x-raw.html index fb7e6c06..edcac7e8 100644 --- a/Hardware Guide/Datasheets/ds90ub9x-raw.html +++ b/Hardware Guide/Datasheets/ds90ub9x-raw.html @@ -30,7 +30,7 @@ - + @@ -381,6 +381,7 @@
  • Setup
  • Coaxial Data Serialization & Power
  • Making Coaxial Tethers
    • +
  • Headstage Voltages
  • Headstage-64 @@ -389,8 +390,7 @@
  • Neuropixels-1.0e Headstage
  • Neuropixels-2.0eBeta Headstage
  • Neuropixels-2.0e Headstage
    • -
  • RHS2116 Headstage
    • -
  • Tethered Headstage Voltages
    • +
  • RHS2116 Headstage
  • Miniscopes
    • diff --git a/Hardware Guide/Datasheets/estim-hs64.html b/Hardware Guide/Datasheets/estim-hs64.html index 50a7b770..c25b8516 100644 --- a/Hardware Guide/Datasheets/estim-hs64.html +++ b/Hardware Guide/Datasheets/estim-hs64.html @@ -30,7 +30,7 @@ - + @@ -382,6 +382,7 @@
  • Setup
  • Coaxial Data Serialization & Power
  • Making Coaxial Tethers
    • +
  • Headstage Voltages
  • Headstage-64 @@ -390,8 +391,7 @@
  • Neuropixels-1.0e Headstage
  • Neuropixels-2.0eBeta Headstage
  • Neuropixels-2.0e Headstage
    • -
  • RHS2116 Headstage
    • -
  • Tethered Headstage Voltages
    • +
  • RHS2116 Headstage
  • Miniscopes
    • diff --git a/Hardware Guide/Datasheets/fmc-analog-io.html b/Hardware Guide/Datasheets/fmc-analog-io.html index 2ff8493d..757bf1f7 100644 --- a/Hardware Guide/Datasheets/fmc-analog-io.html +++ b/Hardware Guide/Datasheets/fmc-analog-io.html @@ -30,7 +30,7 @@ - + @@ -382,6 +382,7 @@
  • Setup
  • Coaxial Data Serialization & Power
  • Making Coaxial Tethers
    • +
  • Headstage Voltages
  • Headstage-64 @@ -390,8 +391,7 @@
  • Neuropixels-1.0e Headstage
  • Neuropixels-2.0eBeta Headstage
  • Neuropixels-2.0e Headstage
    • -
  • RHS2116 Headstage
    • -
  • Tethered Headstage Voltages
    • +
  • RHS2116 Headstage
  • Miniscopes
    • diff --git a/Hardware Guide/Datasheets/fmc-clock-out.html b/Hardware Guide/Datasheets/fmc-clock-out.html index 1cdd66d1..8c68a5c7 100644 --- a/Hardware Guide/Datasheets/fmc-clock-out.html +++ b/Hardware Guide/Datasheets/fmc-clock-out.html @@ -30,7 +30,7 @@ - + @@ -381,6 +381,7 @@
  • Setup
  • Coaxial Data Serialization & Power
  • Making Coaxial Tethers
    • +
  • Headstage Voltages
  • Headstage-64 @@ -389,8 +390,7 @@
  • Neuropixels-1.0e Headstage
  • Neuropixels-2.0eBeta Headstage
  • Neuropixels-2.0e Headstage
    • -
  • RHS2116 Headstage
    • -
  • Tethered Headstage Voltages
    • +
  • RHS2116 Headstage
  • Miniscopes
    • diff --git a/Hardware Guide/Datasheets/fmc-digital-io.html b/Hardware Guide/Datasheets/fmc-digital-io.html index 6583c0a4..f3f1ea25 100644 --- a/Hardware Guide/Datasheets/fmc-digital-io.html +++ b/Hardware Guide/Datasheets/fmc-digital-io.html @@ -30,7 +30,7 @@ - + @@ -381,6 +381,7 @@
  • Setup
  • Coaxial Data Serialization & Power
  • Making Coaxial Tethers
    • +
  • Headstage Voltages
  • Headstage-64 @@ -389,8 +390,7 @@
  • Neuropixels-1.0e Headstage
  • Neuropixels-2.0eBeta Headstage
  • Neuropixels-2.0e Headstage
    • -
  • RHS2116 Headstage
    • -
  • Tethered Headstage Voltages
    • +
  • RHS2116 Headstage
  • Miniscopes
    • diff --git a/Hardware Guide/Datasheets/fmc-link-control.html b/Hardware Guide/Datasheets/fmc-link-control.html index 7bc69ce7..4283b82e 100644 --- a/Hardware Guide/Datasheets/fmc-link-control.html +++ b/Hardware Guide/Datasheets/fmc-link-control.html @@ -30,7 +30,7 @@ - + @@ -381,6 +381,7 @@
  • Setup
  • Coaxial Data Serialization & Power
  • Making Coaxial Tethers
    • +
  • Headstage Voltages
  • Headstage-64 @@ -389,8 +390,7 @@
  • Neuropixels-1.0e Headstage
  • Neuropixels-2.0eBeta Headstage
  • Neuropixels-2.0e Headstage
    • -
  • RHS2116 Headstage
    • -
  • Tethered Headstage Voltages
    • +
  • RHS2116 Headstage
  • Miniscopes
    • @@ -510,8 +510,8 @@

    Description#

    The FMC Host Link Controller is used to control and monitor DS90UB9x-based serialized connections to hubs connected to a host such as headstages and -miniscopes. It can control power provided to those hubs and receives RF lock, -CRC error, and other information.

    +miniscopes. It can control the voltage provided to those hubs and receives RF +lock, CRC error, and other diagnostic information.

    Note

    Typical inplementaitons will default link voltages to 0. Often the link diff --git a/Hardware Guide/Datasheets/heartbeat.html b/Hardware Guide/Datasheets/heartbeat.html index 08fb897f..7042bb3a 100644 --- a/Hardware Guide/Datasheets/heartbeat.html +++ b/Hardware Guide/Datasheets/heartbeat.html @@ -30,7 +30,7 @@ - + @@ -381,6 +381,7 @@

  • Setup
  • Coaxial Data Serialization & Power
  • Making Coaxial Tethers
    • +
  • Headstage Voltages
  • Headstage-64 @@ -389,8 +390,7 @@
  • Neuropixels-1.0e Headstage
  • Neuropixels-2.0eBeta Headstage
  • Neuropixels-2.0e Headstage
    • -
  • RHS2116 Headstage
    • -
  • Tethered Headstage Voltages
    • +
  • RHS2116 Headstage
  • Miniscopes
    • diff --git a/Hardware Guide/Datasheets/index.html b/Hardware Guide/Datasheets/index.html index 55e57cc6..a39fd72b 100644 --- a/Hardware Guide/Datasheets/index.html +++ b/Hardware Guide/Datasheets/index.html @@ -30,7 +30,7 @@ - + @@ -381,6 +381,7 @@
  • Setup
  • Coaxial Data Serialization & Power
  • Making Coaxial Tethers
    • +
  • Headstage Voltages
  • Headstage-64 @@ -389,8 +390,7 @@
  • Neuropixels-1.0e Headstage
  • Neuropixels-2.0eBeta Headstage
  • Neuropixels-2.0e Headstage
    • -
  • RHS2116 Headstage
    • -
  • Tethered Headstage Voltages
    • +
  • RHS2116 Headstage
  • Miniscopes
    • diff --git a/Hardware Guide/Datasheets/load-test.html b/Hardware Guide/Datasheets/load-test.html index c5d5ebb3..bcec7f1c 100644 --- a/Hardware Guide/Datasheets/load-test.html +++ b/Hardware Guide/Datasheets/load-test.html @@ -30,7 +30,7 @@ - + @@ -382,6 +382,7 @@
  • Setup
  • Coaxial Data Serialization & Power
  • Making Coaxial Tethers
    • +
  • Headstage Voltages
  • Headstage-64 @@ -390,8 +391,7 @@
  • Neuropixels-1.0e Headstage
  • Neuropixels-2.0eBeta Headstage
  • Neuropixels-2.0e Headstage
    • -
  • RHS2116 Headstage
    • -
  • Tethered Headstage Voltages
    • +
  • RHS2116 Headstage
  • Miniscopes
    • diff --git a/Hardware Guide/Datasheets/memory-usage.html b/Hardware Guide/Datasheets/memory-usage.html index 18f90958..b4d25e03 100644 --- a/Hardware Guide/Datasheets/memory-usage.html +++ b/Hardware Guide/Datasheets/memory-usage.html @@ -30,7 +30,7 @@ - + @@ -381,6 +381,7 @@
  • Setup
  • Coaxial Data Serialization & Power
  • Making Coaxial Tethers
    • +
  • Headstage Voltages
  • Headstage-64 @@ -389,8 +390,7 @@
  • Neuropixels-1.0e Headstage
  • Neuropixels-2.0eBeta Headstage
  • Neuropixels-2.0e Headstage
    • -
  • RHS2116 Headstage
    • -
  • Tethered Headstage Voltages
    • +
  • RHS2116 Headstage
  • Miniscopes
    • diff --git a/Hardware Guide/Datasheets/neuropixels-v1.html b/Hardware Guide/Datasheets/neuropixels-v1.html index e0567c3f..9fb6a2de 100644 --- a/Hardware Guide/Datasheets/neuropixels-v1.html +++ b/Hardware Guide/Datasheets/neuropixels-v1.html @@ -30,7 +30,7 @@ - + @@ -381,6 +381,7 @@
  • Setup
  • Coaxial Data Serialization & Power
  • Making Coaxial Tethers
    • +
  • Headstage Voltages
  • Headstage-64 @@ -389,8 +390,7 @@
  • Neuropixels-1.0e Headstage
  • Neuropixels-2.0eBeta Headstage
  • Neuropixels-2.0e Headstage
    • -
  • RHS2116 Headstage
    • -
  • Tethered Headstage Voltages
    • +
  • RHS2116 Headstage
  • Miniscopes
    • diff --git a/Hardware Guide/Datasheets/ostim-hs64.html b/Hardware Guide/Datasheets/ostim-hs64.html index 63e099d7..86005b76 100644 --- a/Hardware Guide/Datasheets/ostim-hs64.html +++ b/Hardware Guide/Datasheets/ostim-hs64.html @@ -30,7 +30,7 @@ - + @@ -381,6 +381,7 @@
  • Setup
  • Coaxial Data Serialization & Power
  • Making Coaxial Tethers
    • +
  • Headstage Voltages
  • Headstage-64 @@ -389,8 +390,7 @@
  • Neuropixels-1.0e Headstage
  • Neuropixels-2.0eBeta Headstage
  • Neuropixels-2.0e Headstage
    • -
  • RHS2116 Headstage
    • -
  • Tethered Headstage Voltages
    • +
  • RHS2116 Headstage
  • Miniscopes
    • diff --git a/Hardware Guide/Datasheets/rhd2164.html b/Hardware Guide/Datasheets/rhd2164.html index 0f341555..c095d05e 100644 --- a/Hardware Guide/Datasheets/rhd2164.html +++ b/Hardware Guide/Datasheets/rhd2164.html @@ -30,7 +30,7 @@ - + @@ -381,6 +381,7 @@
  • Setup
  • Coaxial Data Serialization & Power
  • Making Coaxial Tethers
    • +
  • Headstage Voltages
  • Headstage-64 @@ -389,8 +390,7 @@
  • Neuropixels-1.0e Headstage
  • Neuropixels-2.0eBeta Headstage
  • Neuropixels-2.0e Headstage
    • -
  • RHS2116 Headstage
    • -
  • Tethered Headstage Voltages
    • +
  • RHS2116 Headstage
  • Miniscopes
    • diff --git a/Hardware Guide/Datasheets/rhs2116-trigger.html b/Hardware Guide/Datasheets/rhs2116-trigger.html index 098eef78..a7fa8eb0 100644 --- a/Hardware Guide/Datasheets/rhs2116-trigger.html +++ b/Hardware Guide/Datasheets/rhs2116-trigger.html @@ -30,7 +30,7 @@ - + @@ -381,6 +381,7 @@
  • Setup
  • Coaxial Data Serialization & Power
  • Making Coaxial Tethers
    • +
  • Headstage Voltages
  • Headstage-64 @@ -389,8 +390,7 @@
  • Neuropixels-1.0e Headstage
  • Neuropixels-2.0eBeta Headstage
  • Neuropixels-2.0e Headstage
    • -
  • RHS2116 Headstage
    • -
  • Tethered Headstage Voltages
    • +
  • RHS2116 Headstage
  • Miniscopes
    • diff --git a/Hardware Guide/Datasheets/rhs2116.html b/Hardware Guide/Datasheets/rhs2116.html index e7bced56..9a6cf2eb 100644 --- a/Hardware Guide/Datasheets/rhs2116.html +++ b/Hardware Guide/Datasheets/rhs2116.html @@ -30,7 +30,7 @@ - + @@ -381,6 +381,7 @@
  • Setup
  • Coaxial Data Serialization & Power
  • Making Coaxial Tethers
    • +
  • Headstage Voltages
  • Headstage-64 @@ -389,8 +390,7 @@
  • Neuropixels-1.0e Headstage
  • Neuropixels-2.0eBeta Headstage
  • Neuropixels-2.0e Headstage
    • -
  • RHS2116 Headstage
    • -
  • Tethered Headstage Voltages
    • +
  • RHS2116 Headstage
  • Miniscopes
    • diff --git a/Hardware Guide/Datasheets/test-0.html b/Hardware Guide/Datasheets/test-0.html index 04546437..33e5f3c1 100644 --- a/Hardware Guide/Datasheets/test-0.html +++ b/Hardware Guide/Datasheets/test-0.html @@ -30,7 +30,7 @@ - + @@ -381,6 +381,7 @@
  • Setup
  • Coaxial Data Serialization & Power
  • Making Coaxial Tethers
    • +
  • Headstage Voltages
  • Headstage-64 @@ -389,8 +390,7 @@
  • Neuropixels-1.0e Headstage
  • Neuropixels-2.0eBeta Headstage
  • Neuropixels-2.0e Headstage
    • -
  • RHS2116 Headstage
    • -
  • Tethered Headstage Voltages
    • +
  • RHS2116 Headstage
  • Miniscopes
    • diff --git a/Hardware Guide/Datasheets/ts4231-v1-array.html b/Hardware Guide/Datasheets/ts4231-v1-array.html index 98f287b1..8d1a1776 100644 --- a/Hardware Guide/Datasheets/ts4231-v1-array.html +++ b/Hardware Guide/Datasheets/ts4231-v1-array.html @@ -30,7 +30,7 @@ - + @@ -381,6 +381,7 @@
  • Setup
  • Coaxial Data Serialization & Power
  • Making Coaxial Tethers
    • +
  • Headstage Voltages
  • Headstage-64 @@ -389,8 +390,7 @@
  • Neuropixels-1.0e Headstage
  • Neuropixels-2.0eBeta Headstage
  • Neuropixels-2.0e Headstage
    • -
  • RHS2116 Headstage
    • -
  • Tethered Headstage Voltages
    • +
  • RHS2116 Headstage
  • Miniscopes
    • diff --git a/Hardware Guide/Headstages/headstage-64/index.html b/Hardware Guide/Headstages/headstage-64/index.html index c68deecc..ccc01ddc 100644 --- a/Hardware Guide/Headstages/headstage-64/index.html +++ b/Hardware Guide/Headstages/headstage-64/index.html @@ -30,7 +30,7 @@ - + @@ -47,7 +47,7 @@ - + @@ -381,6 +381,7 @@
  • Setup
  • Coaxial Data Serialization & Power
  • Making Coaxial Tethers
    • +
  • Headstage Voltages
  • Headstage-64 @@ -389,8 +390,7 @@
  • Neuropixels-1.0e Headstage
  • Neuropixels-2.0eBeta Headstage
  • Neuropixels-2.0e Headstage
    • -
  • RHS2116 Headstage
    • -
  • Tethered Headstage Voltages
    • +
  • RHS2116 Headstage
  • Miniscopes
    • @@ -570,7 +570,7 @@

    Data Link Serialization

    Warning

    *Do not exceed 6.3 VDC at the coaxial input to the headstage. Make -sure you make this measurement at the headstage (see Measuring headstage voltage) to +sure you make this measurement at the headstage (see Measuring Headstage Voltage) to account for a potential voltage drop in the tether. Exceeding this voltage can permanently damage the headstage.

    @@ -717,7 +717,7 @@

    Bill of Materials

    Note

    -

    Have a look at the Tethered Headstage Voltages page for more details on probing and verifying headstage power voltages

    +

    Have a look at the Headstage Voltages page for more details on probing and verifying headstage power voltages

    @@ -740,12 +740,12 @@

    Bill of Materials

    previous

    -

    Making Coaxial Tethers

    +

    Headstage Voltages

     - + @@ -381,6 +381,7 @@
  • Setup
  • Coaxial Data Serialization & Power
  • Making Coaxial Tethers
    • +
  • Headstage Voltages
  • Headstage-64 @@ -389,8 +390,7 @@
  • Neuropixels-1.0e Headstage
  • Neuropixels-2.0eBeta Headstage
  • Neuropixels-2.0e Headstage
    • -
  • RHS2116 Headstage
    • -
  • Tethered Headstage Voltages
    • +
  • RHS2116 Headstage
  • Miniscopes
    • diff --git a/Hardware Guide/Headstages/headstage-neuropix-1.html b/Hardware Guide/Headstages/headstage-neuropix-1.html index 148ee153..5921a955 100644 --- a/Hardware Guide/Headstages/headstage-neuropix-1.html +++ b/Hardware Guide/Headstages/headstage-neuropix-1.html @@ -30,7 +30,7 @@ - + @@ -381,6 +381,7 @@
  • Setup
  • Coaxial Data Serialization & Power
  • Making Coaxial Tethers
    • +
  • Headstage Voltages
  • Headstage-64 @@ -389,8 +390,7 @@
  • Neuropixels-1.0e Headstage
  • Neuropixels-2.0eBeta Headstage
  • Neuropixels-2.0e Headstage
    • -
  • RHS2116 Headstage
    • -
  • Tethered Headstage Voltages
    • +
  • RHS2116 Headstage
  • Miniscopes
    • diff --git a/Hardware Guide/Headstages/headstage-neuropix-1e.html b/Hardware Guide/Headstages/headstage-neuropix-1e.html index 18d028f4..7e6c8c4f 100644 --- a/Hardware Guide/Headstages/headstage-neuropix-1e.html +++ b/Hardware Guide/Headstages/headstage-neuropix-1e.html @@ -30,7 +30,7 @@ - + @@ -381,6 +381,7 @@
  • Setup
  • Coaxial Data Serialization & Power
  • Making Coaxial Tethers
    • +
  • Headstage Voltages
  • Headstage-64 @@ -389,8 +390,7 @@
  • Neuropixels-1.0e Headstage
  • Neuropixels-2.0eBeta Headstage
  • Neuropixels-2.0e Headstage
    • -
  • RHS2116 Headstage
    • -
  • Tethered Headstage Voltages
    • +
  • RHS2116 Headstage
  • Miniscopes
    • @@ -551,7 +551,7 @@

    Coaxial Link

    Important

    -

    *If your headstage is misbehaving, have a look at the Tethered Headstage Voltages page to confirm headstage power voltages

    +

    *If your headstage is misbehaving, have a look at the Headstage Voltages page to confirm headstage power voltages

    diff --git a/Hardware Guide/Headstages/headstage-neuropix-2e-beta.html b/Hardware Guide/Headstages/headstage-neuropix-2e-beta.html index af0a312c..455ee028 100644 --- a/Hardware Guide/Headstages/headstage-neuropix-2e-beta.html +++ b/Hardware Guide/Headstages/headstage-neuropix-2e-beta.html @@ -30,7 +30,7 @@ - + @@ -381,6 +381,7 @@
  • Setup
  • Coaxial Data Serialization & Power
  • Making Coaxial Tethers
    • +
  • Headstage Voltages
  • Headstage-64 @@ -389,8 +390,7 @@
  • Neuropixels-1.0e Headstage
  • Neuropixels-2.0eBeta Headstage
  • Neuropixels-2.0e Headstage
    • -
  • RHS2116 Headstage
    • -
  • Tethered Headstage Voltages
    • +
  • RHS2116 Headstage
  • Miniscopes
    • @@ -550,7 +550,7 @@

    Coaxial Link

    Important

    -

    *If your headstage is misbehaving, have a look at the Tethered Headstage Voltages page to confirm headstage power voltages

    +

    *If your headstage is misbehaving, have a look at the Headstage Voltages page to confirm headstage power voltages

    diff --git a/Hardware Guide/Headstages/headstage-neuropix-2e.html b/Hardware Guide/Headstages/headstage-neuropix-2e.html index 2972f1f6..c910ae2a 100644 --- a/Hardware Guide/Headstages/headstage-neuropix-2e.html +++ b/Hardware Guide/Headstages/headstage-neuropix-2e.html @@ -30,7 +30,7 @@ - + @@ -46,7 +46,7 @@ - + @@ -381,6 +381,7 @@
  • Setup
  • Coaxial Data Serialization & Power
  • Making Coaxial Tethers
    • +
  • Headstage Voltages
  • Headstage-64 @@ -389,8 +390,7 @@
  • Neuropixels-1.0e Headstage
  • Neuropixels-2.0eBeta Headstage
  • Neuropixels-2.0e Headstage
    • -
  • RHS2116 Headstage
    • -
  • Tethered Headstage Voltages
    • +
  • RHS2116 Headstage
  • Miniscopes
    • @@ -551,7 +551,7 @@

    Coaxial Link

    Important

    -

    *If your headstage is misbehaving, have a look at the Tethered Headstage Voltages page to confirm headstage power voltages

    +

    *If your headstage is misbehaving, have a look at the Headstage Voltages page to confirm headstage power voltages

    @@ -588,7 +588,7 @@

    Probe connector identification

    next

    diff --git a/Hardware Guide/Headstages/rhs2116.html b/Hardware Guide/Headstages/headstage-rhs2116.html similarity index 84% rename from Hardware Guide/Headstages/rhs2116.html rename to Hardware Guide/Headstages/headstage-rhs2116.html index 959bef17..50ddea86 100644 --- a/Hardware Guide/Headstages/rhs2116.html +++ b/Hardware Guide/Headstages/headstage-rhs2116.html @@ -30,7 +30,7 @@ - + @@ -42,11 +42,11 @@ - + - + @@ -381,6 +381,7 @@
  • Setup
  • Coaxial Data Serialization & Power
  • Making Coaxial Tethers
    • +
  • Headstage Voltages
  • Headstage-64 @@ -390,7 +391,6 @@
  • Neuropixels-2.0eBeta Headstage
  • Neuropixels-2.0e Headstage
  • RHS2116 Headstage
    • -
  • Tethered Headstage Voltages
  • Miniscopes
    • @@ -493,16 +493,16 @@

    RHS2116 Headstage

    -

    The RHS2116 Headstage is a serialized headstage for small animals with 32 channels which can independently be configured as stimulator outputs or amplifier inputs. The RHS2116 can be used with passive probes (e.g. silicon arrays, EEG/ECOG arrays, etc) using a 36-Channel Omnetics EIB. To learn how to use the RHS2116 headstage in software, refer to the RHS2116Device software guide. For technical information, refer to the RHS2116 datasheet.

    -
    -

    Warning

    -

    There are multiple headstage hardware revisions. The revision number is printed on the PCB. You can use the compatibility matrix to find host hardware for your headstage.

    -
    +

    The RHS2116 Headstage is a serialized headstage for small animals with 32 +bi-direcional channels which each can be used to deliver electrical stimuli. +The RHS2116 Headstage can be used with passive probes (e.g. silicon arrays, EEG/ECOG +arrays, etc) using a 36-Channel Omnetics EIB.

    Features#

    Electrophysiology#

    RHS2116 headstage uses two 16-channel Intan RHS2116 bioamplifier chip. The chip is operated at a fixed -sampling rate of 30 kHz/channel. These 32 ephys channels are exposed via a 36 pin Omnetics connector at the edge of the headstage and can record from most passive probes (e.g. tetrodes, silicon probe arrays, tungsten microwires, steel EEG wires, etc.) as well as stimulate.

    -
    -

    Getting Started#

    -
      -

    1. Install Bonsai and Install Bonsai.ONIX

      2. -

    2. Get Started with Bonsai

      3. -

    3. Establish hardware connections

      -
        -

      1. Gather Materials

        -
          -

        • RHS2116 headstage

          • -

        • ONIX acquisition system

          • -

        • Coaxial tether

          • -
        -
        2. -

      2. Set the ONIX headstage switch off

        3. -

      3. Connect RHS2116 headstage using the coaxial tether

        -
          -

        1. Gently thread on the SMA connector into the ONIX headstage port

          2. -

        2. Gently press the x.fl coax connector onto the RHS2116 headstage

          3. -
        -
        4. -

      4. Set the correct voltage according to the table in the Data Link Serialization section

        5. -

      5. Set the ONIX headstage switch on

        6. -
      -
      4. -

    4. Either:

      -
        -

      • Configure the RHS2116Device node properties and run the workflow on the RHS2116Device page if you want to collect data

        • -

      • Configure the RHS2116TriggerDevice node properties and run the workflow on the RHS2116TriggerDevice page if you want to trigger stimulus

        -
          -

        • Stimulus trains can be parameterized in a similar way to the master-8 or pulse pal. Refer to the Configuration GUI section of the documentation for more info.

          • -
        -
        • -
      -
      5. -
    -
    +sampling rate of ~30 kHz/channel. These 32 ephys channels are exposed via a 36 +pin Omnetics connector at the +edge of the headstage and can record from most passive probes (e.g. tetrodes, +silicon probe arrays, tungsten microwires, steel EEG wires, etc.) as well as +stimulate.

    Bill of Materials#

    @@ -618,7 +586,7 @@

    Bill of Materials

    Note

    -

    Have a look at the Tethered Headstage Voltages page for more details on probing and verifying headstage power voltages

    +

    Have a look at the Headstage Voltages page for more details on probing and verifying headstage power voltages

    @@ -650,11 +618,11 @@

    Bill of Materials

    next

    -

    Tethered Headstage Voltages

    +

    Miniscopes

     @@ -678,10 +646,7 @@

    Bill of Materials
  • Features
  • Data Link Serialization
    • -
  • Electrophysiology -
    • +
  • Electrophysiology
  • Bill of Materials
    • @@ -689,7 +654,7 @@

    Bill of Materials
    - + @@ -703,7 +668,7 @@

    Bill of Materials
    - + Show Source
    diff --git a/Hardware Guide/Headstages/index.html b/Hardware Guide/Headstages/index.html index d9037a36..adca642f 100644 --- a/Hardware Guide/Headstages/index.html +++ b/Hardware Guide/Headstages/index.html @@ -30,7 +30,7 @@ - + @@ -381,6 +381,7 @@
  • Setup
  • Coaxial Data Serialization & Power
  • Making Coaxial Tethers
    • +
  • Headstage Voltages
  • Headstage-64 @@ -389,8 +390,7 @@
  • Neuropixels-1.0e Headstage
  • Neuropixels-2.0eBeta Headstage
  • Neuropixels-2.0e Headstage
    • -
  • RHS2116 Headstage
    • -
  • Tethered Headstage Voltages
    • +
  • RHS2116 Headstage
  • Miniscopes
    • @@ -492,13 +492,13 @@
  • Setup
  • Coaxial Data Serialization & Power
  • Making Coaxial Tethers
    • +
  • Headstage Voltages
  • Headstage-64
  • Neuropixels-1.0 Headstage
  • Neuropixels-1.0e Headstage
  • Neuropixels-2.0eBeta Headstage
  • Neuropixels-2.0e Headstage
    • -
  • RHS2116 Headstage
    • -
  • Tethered Headstage Voltages
    • +
  • RHS2116 Headstage

    • diff --git a/Hardware Guide/Headstages/serialization.html b/Hardware Guide/Headstages/serialization.html index 0dcc37ef..64d168fc 100644 --- a/Hardware Guide/Headstages/serialization.html +++ b/Hardware Guide/Headstages/serialization.html @@ -30,7 +30,7 @@ - + @@ -381,6 +381,7 @@
  • Setup
  • Coaxial Data Serialization & Power
  • Making Coaxial Tethers
    • +
  • Headstage Voltages
  • Headstage-64 @@ -389,8 +390,7 @@
  • Neuropixels-1.0e Headstage
  • Neuropixels-2.0eBeta Headstage
  • Neuropixels-2.0e Headstage
    • -
  • RHS2116 Headstage
    • -
  • Tethered Headstage Voltages
    • +
  • RHS2116 Headstage
  • Miniscopes
    • diff --git a/Hardware Guide/Headstages/setup.html b/Hardware Guide/Headstages/setup.html index d8b70313..7537b8ea 100644 --- a/Hardware Guide/Headstages/setup.html +++ b/Hardware Guide/Headstages/setup.html @@ -30,7 +30,7 @@ - + @@ -381,6 +381,7 @@
  • Setup
  • Coaxial Data Serialization & Power
  • Making Coaxial Tethers
    • +
  • Headstage Voltages
  • Headstage-64 @@ -389,8 +390,7 @@
  • Neuropixels-1.0e Headstage
  • Neuropixels-2.0eBeta Headstage
  • Neuropixels-2.0e Headstage
    • -
  • RHS2116 Headstage
    • -
  • Tethered Headstage Voltages
    • +
  • RHS2116 Headstage
  • Miniscopes
    • @@ -490,9 +490,10 @@

    Setup#

      -

    • Connect the headstages either directly to host or through the breakout board (see Headstage Link).

      • -

    • The LED on the breakout board (and the PCIe board itself, if visible) should turn purple when the link is made between the headstage and the PCIe host board.

      • -

    • Double-clicking on the OniContext node in Bonsai should now show an additional tab, labelled with the type of headstage.

      • +

    • Connect the headstage to one of the Ports on the Breakout Board by screwing +in the SMA connector. Alternatively, the headstage can be pluged directly +into port A or B on the PCIe control board using an SMA to MMCX adapter (see +Headstage Link).

    diff --git a/Hardware Guide/Headstages/tether-voltage.html b/Hardware Guide/Headstages/tether-voltage.html index 53f59d78..58eaae77 100644 --- a/Hardware Guide/Headstages/tether-voltage.html +++ b/Hardware Guide/Headstages/tether-voltage.html @@ -8,7 +8,7 @@ - Tethered Headstage Voltages — ONIX Docs + Headstage Voltages — ONIX Docs @@ -30,7 +30,7 @@ - + @@ -46,8 +46,8 @@ - - + + @@ -381,6 +381,7 @@
  • Setup
  • Coaxial Data Serialization & Power
  • Making Coaxial Tethers
    • +
  • Headstage Voltages
  • Headstage-64 @@ -389,8 +390,7 @@
  • Neuropixels-1.0e Headstage
  • Neuropixels-2.0eBeta Headstage
  • Neuropixels-2.0e Headstage
    • -
  • RHS2116 Headstage
    • -
  • Tethered Headstage Voltages
    • +
  • RHS2116 Headstage
  • Miniscopes
    • @@ -470,7 +470,7 @@
  • Headstages
    • -
  • Tethered Headstage Voltages
    • +
  • Headstage Voltages
    • @@ -487,42 +487,44 @@
    -
    -

    Tethered Headstage Voltages#

    -

    The voltage on the headstage must be carefully regulated: if its too low the -headstage will not function reliably. If the voltage is too high sensitive -components could be damaged. Many issues with the system can be traced back to -inadequate headstage voltage supply.

    +
    +

    Headstage Voltages#

    +

    Each ONIX headstage has a required operating voltage that is specified on its +documentation page. Because ONIX hardware supports headstages that have +different voltage requirements, it must be changed to match the requirements +of the headstage that is plugged into a port. If the headstage voltage is too +low, it will not function reliably. If the voltage is too high, the headstage +will dissipate excess heat and it may be damaged.

    -

    Setting headstage voltage#

    -

    Each headstage has a minimum and maximum voltage requirement (e.g. 5.3 to 5.7 -Volts for Headstage-64) circuits on the board to function properly. If -the voltage is far too low, the green LED on the headstage will be dim and -Bonsai will not detect the headstage. Even if the LED is bright, a borderline +

    Setting Headstage Voltage#

    +

    The headstage voltage is set using FMC Link Controller devices +on the PCIe Host. Each headstage has a minimum and maximum voltage +requirement (e.g. 5.3 to 5.7 Volts for Headstage-64) in order for +circuits on the board to function properly. If the voltage is far too low, the +host computer will not be able to detect the headstage. A borderline voltage can still cause connectivity issues as the headstage occasionally dips -beneath the power it needs to function properly.

    -
    -

    The voltage output at the FMC-host can be set in Bonsai:

    -
    - -

    Default headstage voltage is 4.9 V

    +below the level it needs to function properly.

    +
    +

    Attention

    +

    The OpenEphys.Onix1 Bonsai package 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 +functionality has been been tuned for the tethers that are shipped with each +headstage. The voltage override is available when custom tethers are used +(see Measuring Headstage Voltage).

    -
    - -

    Increasing the voltage to 7V in Bonsai (measured as 5V at the headstage) allows the second headstage to connect.

    -
    -

    The voltage set in Bonsai is not identical to the voltage supplied to the -headstage, as some voltage drop will occur over the coaxial cable tether that -connects them. The amount of voltage drop will depend on the cable properties -(e.g. thickness) and even the temperature of the cable. These very thin tethers -can cause large voltage drops, so that even when the voltage setting in Bonsai -seems high, the headstage is only seeing 3 or 4 Volts and becomes unreliable. -Voltage should therefore always be measured on the headstage itself. The -voltage setting is persistent until computer power off. It gets stored in the -hardware, so even after a reboot, it will be set to the latest value.

    +

    The voltage set in software is not identical to the voltage supplied to the +headstage, as some voltage drop will occur over the tether that connects them. The +amount of voltage drop is proportional to the current draw of the headstage and +inversely proportional to the thickness of the tether. The thin tethers used +with ONIX headstages can result in significant voltage drops that need to be +compensated for. For very long (5 to 10m) and thin (diameter of 0.2mm) coaxial +tethers, the voltage drop can be on the order of 2 volts. For this reason, the +headstage voltage must be measured on the headstage itself.

    -

    Measuring headstage voltage#

    +

    Measuring Headstage Voltage#

    Use a multimeter to probe the headstage at the two points marked below: the ground pin and either terminal of the large inductor on the headstage.

    @@ -580,12 +582,6 @@

    Setting headstage voltage -

    Rebooting#

    -

    If you have slowly increased the voltage supplied to a headstage, but it does -not appear as a tab in the ONI-Context, try turning the voltage supply to 0 and -back to the higher value before refreshing the ONI-Context.

    - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    +
    +
    + + + Ctrl+K +
    +
    + + + +
    +
    + +
    + + + +
    + + +
    + +
    + +
    + + + +
    + +
    + +
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    +
    + +
    +
    + +
    + +
    + + + + +
    + +
    + + +
    +
    + + + + + +
    + +
    +

    Deprecated since version 1.2.13: Bonsai.ONIX is deprecated.

    +

    To use ONIX with Bonsai, refer to the documentation for OpenEphys.Onix1.

    +
    + + + +
    + + + +
    + +
    + +
    +
    +
    + +
    + +
    + +
    + + + +
    + +
    +
    + On this page +
    +
    + +
    + +
    + + + + + + Edit on GitHub + + + +
    +
    + +
    +
    + + Show Source + +
    +
    + +
    + + +
    +
    + +
    + +
    +
    +
    + + + + + +
    +
    + +
    + +
    +

    + + © Copyright 2010-2024, Open Ephys & Contributors. +
    + +

    +
    + +
    + + +
    + +

    + Built with the PyData Sphinx Theme 0.13.3. +

    + +
    + +
    + +
    + + \ No newline at end of file diff --git a/Software Guide/Bonsai.ONIX/index.html b/Software Guide/Bonsai.ONIX/index.html index af2c9e32..ee55bd53 100644 --- a/Software Guide/Bonsai.ONIX/index.html +++ b/Software Guide/Bonsai.ONIX/index.html @@ -30,7 +30,7 @@ - + @@ -365,11 +365,13 @@ aria-label="Section Navigation">

    Section Navigation

    @@ -463,16 +463,20 @@
    -
    +
    +

    Deprecated since version 1.2.13: Bonsai.ONIX is deprecated.

    +

    To use ONIX with Bonsai, refer to the documentation for OpenEphys.Onix1.

    +
    +

    Bonsai.ONIX#

    -

    Bonsai.ONIX is a Bonsai library for ONIX hardware. This library contains +

    Bonsai.ONIX is a Bonsai package for ONIX hardware. This package contains Bonsai Operators for -acquiring and sending data to ONIX hardware. An additional library, -Bonsai.ONIX.Design, contains GUI elements for the core library. Although it -is possible to use Bonsai.ONIX without the GUI library, it is not -recommended. There are three major classes of operators in the library:

    +acquiring and sending data to ONIX hardware. An additional package, +Bonsai.ONIX.Design, contains GUI elements for the core package. Although it +is possible to use Bonsai.ONIX without the GUI package, it is not +recommended. There are three major classes of operators in the package:

    1. ONIContext - This operator wraps the underlying Acquisition Context and provides access to the device table for a hardware slot. At least one of these diff --git a/Software Guide/Open Ephys GUI/index.html b/Software Guide/Open Ephys GUI/index.html index 4daa30e2..d49b834d 100644 --- a/Software Guide/Open Ephys GUI/index.html +++ b/Software Guide/Open Ephys GUI/index.html @@ -30,7 +30,7 @@ - + @@ -46,8 +46,8 @@ - - + + @@ -365,11 +365,13 @@ aria-label="Section Navigation">

      Section Navigation

      @@ -465,43 +465,19 @@

      Open Ephys GUI#

      -

      There is currently no dedicated ONIX plugin available for the Open Ephys GUI. The Open Ephys GUI is -built primarily for multichannel electrophysiology using an audio processing -library that makes it difficult to deal with multiple asynchronous data -streams.

      -
      -

      Note

      -

      Have a look at the Open Ephys GUI documentation -for information on the GUI’s design.

      -
      -

      This is fine when the data being processed is synchronized ephys and auxiliary -data. However, by design, ONIX hardware makes no such guarantees about the -nature of the data it produces. On the contrary, an -Acquisition Context manages a table of devices that are -potentially all asynchronous from one another. Even though each sample from -these devices is individually time-stamped in hardware, there is no guarantee -of when they will arrive or in what order. This necessitates the use of -event-driven acquisition software that only propagates data when its received, -and this is where Bonsai really shines. For this -reason, we have dedicated the majority of our development effort toward the -Bonsai.ONIX library.

      -
      -
      -

      Using the Open Ephys GUI for ONIX Data Visualization#

      -

      Bonsai provides advanced access to GPU visualization capabilities, but has to -be manually programmed to generate high performance real-time plotting. This can -be a hurdle for those that just want to see if they have their probe in the -right spot. In the future, we aim to change this situation, and eventually -provide first-class native ephys visualization capabilities in the Bonsai -Editor.

      +

      The Open Ephys GUI is an +open-source, plugin-based application for acquiring extracellular +electrophysiology data. It was designed by neuroscientists to make their +experiments more flexible and enjoyable. It works equally well on macOS, Linux, +and Windows.

      Note

      -

      If you want to help improve Bonsai’s Ephys visualization capabilites, -get in touch.

      +

      An ONIX plugin for the Open Ephys is in development. To access all of +ONIX’s capabilities right now, have a look at the OpenEphys.Onix1 Bonsai package. +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.

      -

      In the meantime we can take advantage of the Ephys GUI’s visualization and -audio streaming by the Ephys Socket Plugin -to receive data from Bonsai.

      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      +
      +
      +
      + + + Ctrl+K +
      +
      + + + +
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      + +
      +

      Bonsai#

      +

      Bonsai is a visual programming language (think +LabView) for 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.Onix1#

      +

      OpenEphys.Onix1 is the Bonsai +package for ONIX hardware. This package contains Bonsai Operators for acquiring and +sending data to ONIX hardware.

      +
      +
      Code:
      +

      open-ephys/onix-bonsai-onix1

      +
      +
      Compatibility:
      +

      ONIX Hardware, UCLA miniscopes & variants

      +
      +
      Documentation:
      +

      https://open-ephys.github.io/onix1-bonsai-docs/index.html

      +
      +
      + +
      + +
      +

      Go to the OpenEphys.Onix1 Docs

      +
      + OpenEphys.Onix1 bonsai + package documentation + +
      +
      + + + +
      + + + + + +
      + + + +
      + +
      +
      + On this page +
      +
      + +
      + +
      + + + + + + Edit on GitHub + + + +
      +
      + +
      +
      + + Show Source + +
      +
      + +
      + + +
      +
      + +
      + +
      +
      +
      + + + + + +
      +
      + +
      + +
      +

      + + © Copyright 2010-2024, Open Ephys & Contributors. +
      + +

      +
      + +
      + + +
      + +

      + Built with the PyData Sphinx Theme 0.13.3. +

      + +
      + +
      + +
      + + \ No newline at end of file diff --git a/Software Guide/index.html b/Software Guide/index.html index e6debd01..cc66ae6a 100644 --- a/Software Guide/index.html +++ b/Software Guide/index.html @@ -30,7 +30,7 @@ - + @@ -46,7 +46,7 @@ - + @@ -365,11 +365,13 @@ aria-label="Section Navigation">

      Section Navigation

      @@ -460,28 +460,34 @@
      -
      +
      +

      software_logo Software Guide#

      +
      -
      -

      software_logo Software Guide#

      -

      Although ONIX is software agnostic, we have focused our development efforts on Bonsai for data acquisition. Bonsai is -very good at dealing with the asynchronous and heterogeneous data that ONIX -hardware produces.

      -
        -

      • The oni-repl pages document a low-level C program that -can be used for debugging and basic streaming IO with ONIX -hardware.

        • -

      • The Bonsai.ONIX pages provide detailed information about the ONIX -Bonsai library.

        • -

      • The Open Ephys GUI page shows how ephys data can be streamed the Open -Ephys GUI to take advantage of its excellent visualization capabilities.

        • -
      +
      +
      Bonsai

      OpenEphys.Onix1 is a Bonsai 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.

      +
      +
      Open Ephys GUI

      The Open Ephys GUI can be used for ONIX data visualization.

      +
      +
      oni-repl

      A simple command-line application that can be used for debugging and basic +streaming IO with ONIX hardware.

      +
      +

      Tip

      -

      If you want to use ONIX hardware with your acquisition software, -please get in touch. It’s not as hard as you might think -:).

      +

      ONIX uses an ONI-compliant API that is software +agnostic. If you want to use ONIX hardware with your acquisition software, +please get in touch.

      +
      +

      Deprecated Software#

      + +