Autopatcher.org

In Vivo Robotics, for Automatic

Recording of Neurons in the Live Brain



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Read the autopatcher papers, etc.
Hardware
DIY / Build it yourself
Software
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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.

This is a joint production between




Contact Information

Please send inquiries to info@autopatcher.org

References and Links

Kodandaramaiah, et al., Nature Methods 2012 [Publisher link]
Kodandaramaiah, et al. Annals of the New York Academy of Sciences 2013 (review) [Publisher link]
Autopatching tutorial, with best experimental practices, Sept. 3, 2013 version.
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)]

Commercial Partners

Neuromatic Devices, Inc. is currently producing a commercial autopatcher robot. (Anti-disclaimer: none of the authors of the Nature Methods 2012 paper are owners or otherwise financially linked to this company.)

Introduction


The Autopatcher hardware consists of electronic pressure regulators, digital controllers, precision microactuators, and a data acquisition board. These, combined with the Autopatcher software, automate the process of patch clamping in-vivo.

There are several incarnations of the autopatcher software as it has been developed and distributed to many labs around the country and internationally. This tutorial explains how to assemble your own robotic arm and includes documentation on how to build the pressure and electrical control system as well. A commercial version of the electrical and pneumatic control box is also available from Neuromatic Devices.


Build Your Own

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

Assembly Photograph of Robotic Arm
(click for larger image)



Actuation

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.

Quantity
1
1
1
1
1
Vendor
Newport
Newport
Newport
Newport
Newegg

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.

Quantity
1
1
1
1
1
Vendor
ThorLabs
ThorLabs
ThorLabs
ThorLabs
ThorLabs

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.


Pressure Control

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.

Quantity
3
Vendor
Lee Company

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

Adapter Plate Construction



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]

Manuals

Autopatcher 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 Hardware

These are the pneumatic and electronic control units that currently exist in different labs.

Georgia Tech


4 Channel, built in 2011

(SN# G00001)

1 Channel, built in 2012

(SN# G00002)

1 Channel V2, built in 2013

(SN# G00003 - G00007)










MIT


Boxes Built at MIT

(SN# 2013033101 - 2013033106)











Neuromatic Devices


Autopatch 1501 System

(SN# N00001)

Autopatch 1506 System

(SN# N00002 through N00100)










FAQ
Please send your hardware questions to info@autopatcher.org and we will build a collection of FAQs to post here.


Introduction


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. The Hardware section explains how to do this in the [Modifying Autopatch 1500 for Custom Hardware" manual.


Autopatch 2000
[Currently in Beta testing...]

Written by: Michael McKinnon, 2013, based on the algorithm developed by Suhasa Kodandaramaiah, 2012.

This version is a major overhaul of the Autopatcher 1500 software to include data logging, manual controls, and a modular design interface so new experimental steps can be added to the autopatching algorithm and distributed to other users in the community. This version is not yet stable and there are some known issues. We recommend using Autopatch 1500 until a fully tested version of Autopatch 2000 is posted here.


Autopatch 1500

Written by: Suhasa Kodandaramaiah, 2012


This version uses the same autopatching algorithm as Autopatch 1000 and has a more intuitive user interface. This is the tried-and-true, stable version of the software and is currently in use in many labs.

This version is also recommended for anyone building their own autopatcher. If you are building your own system, this software must be modified to match your configuration. Specifically, the DAQ input and output pins will need to be changed in the "Autopatch1500_ver1.04" VI inside the "Autopatcher_Labview_Software v1500" LLB file. There is a GUIDE that shows how this is done.


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.

Autopatch 1501
This version is compatible with the single channel control box (SN# N00001) installed by Neuromatic Devices in the Montreal Heart Institute.


Autopatch 1502
This version is compatible with the 4 channel control box (SN# G00001) in the PBL at Georgia Tech. Only 1 channel is currently implemented. Modified by Gregory Holst 2012, Ilya Kolb 2013.


Autopatch 1503
This version is compatible with the single channel control box (SN# G00002) in the PBL at Georgia Tech. It also includes a feature that automatically saves screen shots of all the plots for every trial after control is transfered to pClamp. Modified by Gregory Holst 2013.


Autopatch 1504
[ Under Development ]
This version is compatible with the single channel control boxes (SN# G00003 through G00007) built and distributed by the PBL at Georgia Tech. Modified by Gregory Holst 2013.


Autopatch 1505
This version is compatible with the single channel control boxes (SN# 2013033101 through 2013033106) built in the Media Lab at MIT . Also contains standalone VIs for switching the BNC relay and pressure valves. Modified by Ian Wickersham 2013.


Autopatch 1506
version 1506.1
[LV 2011] [MANUAL]
This version is compatible with single channel control boxes (SN# N00002 through N00100) built by Neuromatic Devices. The original version was 1506; the current version, 1506.1 (uploaded 1/10/2014), contains bug fixes over version 1506.





Autopatch 1000

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.


FAQ
Please send your software questions to info@autopatcher.org and we will build a collection of FAQs to post here.