Autopatcher.org

In Vivo Robotics, for Automatic

Recording of Neurons in the Live Brain



Explore
Read the autopatcher papers, etc.
Hardware
DIY / Build it yourself
Software
Download the latest version
 
 
 

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






Commercial Partners

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.

Introduction


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 Neuron!

August 30th, 2017

The newest version of the Autopatcher, the Imagepatcher, capable of targeting and recording from specific individual cells in vivo, was recently published in Neuron [Publisher's Link] [PDF] [Supplementary Material].

Please refer to section 1 of the Imagepatcher User Manual for the information on hardware requirements for the Imagepatcher.

The Imagepatcher described in the paper operates on a conventional two-photon image-guided patch-clamp rig with the autopatcher control box (built using the Autopatcher control box assembly manual in our 2016 Nature Protocols paper) slightly modified for additional functions.

Please refer to sections 1.C-D of the Imagepatcher User Manual for step-by-step instructions on how to modify an existing autopatcher control box and how to calibrate it. Please also download the modification parts list and the pressure calibration files that are required for the modification and calibration respectively.

Note: the modification of the autopatcher control box described in the Imagepatcher User Manual has been tested on the boxes that were built using the Autopatcher control box assembly manual in our 2016 Nature Protocols paper, but not on those that are commercially available from Neuromatic Devices.


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 2016 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

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 Control Box 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)










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


Software For The Imagepatcher

The Imagepatcher algorithm is implemented in MATLAB and operates in parallel with ScanImage. The current version of the Imagepatcher software is designed to work on specific versions of MATLAB and ScanImage. Please refer to section 2 of the Imagepatcher User Manual for the detailed information on the software requirements.

If you have different versions of ScanImage, feel free to download and customize the code to match your software version. It is possible that you may NOT need to modify the code, if the ScanImage function names and the file responsible for frame generation (makeFrameByStripes.m) have stayed the same over all ScanImage versions.


Imagepatcher v.1

Published in Neuron 2017.

Written by: Ho-Jun Suk, 2017.

This is the first version of the Imagepatcher software. Please refer to the Imagepatcher User Manual for detailed insturctions on how to install the software on your computer and use it for automated image-guided patching experiments.

If you have customized this version of the Imagepatcher software or new features that you'd like to make available to the community, feel free to send it to info@autopatcher.org and we'll post it here.


Software For The Autopatcher

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.


Autopatch 2000

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 info@autopatcher.org and we'll post it here.


Autopatcher IG

Written by: Ilya Kolb, 2016.


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.


Autopatch 1500

Written by: Suhasa Kodandaramaiah, 2012


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.

Autopatch 1501
This version is compatible with the single channel control box (SN# N00001).


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. Arduino drivers are required for Neuromatic Devices control boxes [DOWNLOAD]


Autopatch 1508
This version is compatible with single channel control boxes (SN# N00002 through N00100) built by Neuromatic Devices. This version is compatible with THORlabs Z825 series motors. Arduino drivers are required for Neuromatic Devices control boxes [DOWNLOAD]





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.