Autopatcher.orgIn Vivo Robotics, for Automatic
Recording of Neurons in the Live Brain
Welcome to the center for in-vivo neurorobotics!
Here you can find the relevant papers, devices, parts lists, manuals, software, best practices, and partners, involved with the effort to advance the development and use of robots to analyze the living brain.
Contact InformationPlease send inquiries to firstname.lastname@example.org
References and Links
- Kodandaramaiah, et al., Nature Protocols 2016 [Publisher link] [PDF] [Supplementary Material]
- Kodandaramaiah, et al., Nature Methods 2012 [Publisher link] [PDF] [Supplementary Material]
- Kodandaramaiah, et al. Annals of the New York Academy of Sciences 2013 (review) [Publisher link]
- Wikipedia (See the "In-Vivo" section) [Link]
Autopatching in the News
[MIT, Georgia Tech robot records brain cell information (Mass High Tech, 5/6/2012)] [Robotic probes plumb brain's circuitry (EETimes, 5/6/2012)] [Robots that reveal the inner workings of brain cells (R&D Magazine, 5/7/2012)] Robotic arm to reveal inner working of brain cells (New York Daily News, 5/7/2012)] [Robot brain scientists to learn how you think? (MSNBC, 5/7/2012)] [Bots beat humans probing brain's neural activity (CNET, 5/7/2012)] [MIT & Georgia Tech Researchers Develop Robots That Can Reveal the Inner Workings of Your Brain (BostInno, 5/7/2012)] Robotic probes plumb brain's circuitry (EDN, 5/7/2012)] [Researchers automate process of recording data from neurons (The Engineer, 5/8/2012)] [Robot That Connects to Neurons Could Provide Key to Understanding the Human Brain (TIME, 5/9/2012)] [Research Brief: Robots Trained in Patch-Clamp Experiments (Alzheimer Research Forum, 5/11/2012)] [Robot Reveals Inner Workings of Brain Cells (Photonics.com, 5/10/2012)]
Neuromatic Devices, Inc. is currently producing a commercial autopatcher robot. Full disclosure: I.R.W., S.B.K. and G.L.H. received financial remuneration from NeuromaticDevices for technical consulting services provided in 2012, 2013, and 2012-2015, respectively.
The Autopatcher hardware consists of electronic pressure regulators, digital controllers, precision actuators, and a data acquisition board. These, combined with the Autopatcher software, automate the process of patch clamping in-vivo.
Recent Publication in Nature Protocols!March 3rd, 2016
The newest versions of the hardware, software, and protocols were recently published in Nature Protocols in 2016 [Publisher's Link] [PDF] [Supplementary Material] with detailed instructions for building, configuring, and operating the autopatcher. The main control box hardware is also commercially available from Neuromatic Devices.
The information below represents the development of the previous version of the autopatcher from 2011 to 2015. Please refer to the 216 paper for the most up-to-date information.
Build Your Own (2011-2015 version)
This tutorial explains how to build your own robotic arm for the autopatcher. The Autopatcher User's Manual shows more detail about the function and how to build the pneumatic and electrical control systems
Step 1: Order Parts
This photograph shows, from left to right, the Molecular Devices Headstage, dovetail adapter plate that comes with the headstage, the Newport piezo motor attached to the linear stage, another dovetail adapter plate, and the Sutter 3 Axis Micromanipulator. The second dovetail adapter plate came with the Sutter manipulator. To assemble the arm, several holes must be drilled in the adapter plates or completely new plates can be manufactured.
Order these items for the autopatcher actuator. The following items assume the Imperial 1/4"-20 bolt hole convention. There are equivalent metric components available but they have different part numbers.
RS-485 to RS-232 adapter
USB to Serial (if you need it)
The above items are the bare essentials for actuation and they work with the Autopatcher 1500 software. If you have a Sutter 3 Axis Micromanipulator, you can order the following parts to build the complete arm.
A more detailed parts list is available here with metric and imperial part numbers.
If you don't have a different 3 axis manipulator, you will still need a way to mount the Newport stage vertically above the animal. The above parts are one example of how this can be done but you will need to make sure the hole patterns match the 3 axis actuator you are using. You will also need to design a custom adapter plate between your manipulator and the Newport stage.
The following items are necessary for controlling the pressure.
Large diameter syringes can be used with 3 solenoid valves from the Lee Company for an inexpensive pressure control system. See the Autopatcher User's Manual for more details.
3 Way Valves LHDA0533215H
In addition to these parts, there are other accessories that must be purchased to complete the Autopatcher. These are also discussed in the Autopatcher User's Manual.
Step 2: Build Adapters
The drawings and CAD for the adapter plates can be downloaded here. These are for the Newport stage mentioned above and the Sutter MPC-285. If you use different stages or manipulators, you will have to design your own adapter plates for them.
Step 3: Assembly
Assembly section is under construction!
The assembly steps above mainly cover the mechanical assembly of the autopatcher. There is also a pneumatic control system and electrical control system that must be constructed to complete the autopatcher. The details can be found in the Autopatcher User's Manual.
Parts Lists and Drawings
This tutorial assumes that the user has a functioning patch rig already built, using Axon headstages and Sutter manipulators. The choice of Imperial vs. Metric is governed by your existing optics table and hardware choices.[Detailed Parts List Excel]
ManualsAutopatcher User's Manual - [Word] [PDF]
A detailed description of how to build and operate an autopatcher like the one used to obtain the results in the Nature Methods paper . This tutorial is based on the Autopatch 1000 software available on the "Software" tab.
Modifying Autopatch 1500 for Custom Hardware - [Word] [PDF]
This manual describes how to set up the Autopatch 1500 series software to work with your DAQ if you are building your own autopatcher. It details the locations in the software where the autopatcher algorithm references the input and output pins on the DAQ and how to modify them to match your hardware.
Existing Control Box HardwareThese are the pneumatic and electronic control units that currently exist in different labs.
4 Channel, built in 2011
1 Channel, built in 2012
1 Channel V2, built in 2013
(SN# G00003 - G00007)
Boxes Built at MIT
(SN# 2013033101 - 2013033106)
Autopatch 1501 System
The autopatcher algorithm is implemented in NI Labview . Each version is designed to work with a specific hardware set so read the comments carefully to ensure they match your hardware. If you have built your own autopatcher, feel free to download and customize the code to match your hardware.
Published in Nature Protocols 2016. Written by: Michael McKinnon, 2013, based on the algorithm developed by Suhasa Kodandaramaiah, 2012.
This is the most up-to-date version of the autopatcher software. It is a major overhaul of the Autopatcher sofware including a modular backend that is easily reconfigured, stimulus generation and recording, and an updated interface. It was published in Nature Protocols in 2016 [PDF] [Supplementary Material]. We highly recommend referencing the paper and examining the supplementary material for the most up-to-date information. Depending on which version of the control box you have, you may need to reconfigure the hardware settings for it to work. If you build a control box using the instructions in the paper, it will work with this version without modification. It is also directly compatible with the boxes built at MIT (SN# 2013033101 - 2013033106).
If you have customized a version of Autopatch 2000 or new features that you'd like to make available to the community, feel free to send it to email@example.com and we'll post it here.
This is the in-vitro (IG: Image-Guided) version of the Autopatcher algorithm. It is used in the manuscript "Autopatcher IG: Image-assisted, automated patch-clamp electrophysiology in vitro." Download the installation and user manual here.
NOTE: Please install the latest QCam drivers before installing the Autopatcher IG executable to ensure proper function.
This version uses the same autopatching algorithm as Autopatch 1000 but has a more intuitive user interface. This version was in use between 2012 and 2015.
There are many custom versions of "Autopatch 1500" in circulation. Here are a few of the variants that are designed for a specific set of hardware. Some versions have additional features that haven't been incorporated into the main version.
Written by: Suhasa Kodandaramaiah 2012.
This 1st-generation version of the autopatcher software was used to obtain the original data in the Nature Methods paper (Kodandaramaiah et al., 2012). The user interface is a little rough but it is functional with the hardware described in the paper. This version is no longer updated.