Difference between revisions of "Main Page"

Revision as of 14:36, 29 November 2018

  Quick Announcement: We are excited to announce we have multiple Postdoc/Engineering/Researcher positions open within the Miniscope project! Looking for exceptional people interested in instrumentation/tool/software development and who can effectively communicate in both the fields of engineering and neuroscience. A job listing for one of the open positions can be found here. If interested please contact Daniel Aharoni, DBAharoni_at_gmail.com.

Welcome to Miniscope.org Wiki! Follow the project on Twitter: @MiniscopeTeam.

The miniature fluorescence microscope described here is based on a design pioneered by Mark Schnitzer's Lab at Stanford and published in a paper in Nature Methods in 2011. It uses wide-field fluorescence imaging to record neural activity in awake, freely moving mice. The microscope introduced here (Miniscope) has a mass of 3 grams and uses a single, flexible coaxial cable (0.3mm to 1.5mm diameter) to carry power, control signals, and imaging data to custom open source Data Acquisition (DAQ) hardware and software. This wiki site provides a centralized location for sharing design files, source code, and other relevant information so that a community of users can share ideas and developments related to this important imaging technique. Our goal is to help disseminate this technology to the larger neuroscience community and build a foundation of users that will continue advancing this technology and contribute back to the project. While the Miniscope system described here is not an off-the-shelf commercial solution, we have focused on making it as easy as possible for the average neuroscience lab to build and modify, requiring minimal soldering and hands on assembly. For more information please visit the Project Overview page. The Miniscope project and Miniscope.org are still works in progress and will be routinely updated over the coming months and years. We hope you will contribute to this important process!

Current Status of Project

The Miniscope project is now in its third year of development at UCLA and has gone through two major revisions. Miniscopes were used to understand how the brain links memories across time, with the findings published in Nature, 2016. The work and files available on this site are the most up-to-date public version of our system and will be updated frequently with improvements and new system features. Again, we hope that you will contribute to this development process! This wiki is designed for this very purpose.

Initial access to the miniscope.org wiki was enabled mid January, 2016.

Important: Using this system we have successfully imaged Hippocampal CA1, Subiculum, Dorsal Striatum, Parietal Cortex, Prefrontal Cortex, and Visual Cortex using 0.5mm, 1mm, 1.8mm, and 2mm diameter GRIN lenses from either Grintech or GoFoton. (More information on GRIN lenses can be found here).

Links to information on miniscope subsystems

Head Mounted Scope

Data Acquisition Box

Data Acquisition Software

Surgery Protocol

Master Parts List

Analysis Package

GRIN Lens Information

Discussion Board and FAQ

Discussion Board (Our previous discussion board can be found here.. Please do not post here)

FAQs

Guides and Tutorials

A key feature of this effort is to design miniscope systems that are easy to build and use. The guides below will walk you through component procurement, scope assembly, and software installation.

1. Overview of System Components
2. Part Procurement
3. System Assembly
4. Recommended Computer Specs
5. Software and Firmware Setup
6. Initial Testing of Assembled Miniscopes
7. Imaging With Thin GRIN Lenses
8. Surgery Protocol
9. Animal Behavior Guide

Workshop Resource

We will be holding a pre-SfN workshop November 9th, 2017. For more information visit our MCCS/ICLM Workshop Page.

The Golshani, Silva, and Khakh labs will be hosting free, two-day long Miniscope workshops here at UCLA. We are currently planning at least 3 workshops for 2018. Please enter your information here to request a spot in upcoming workshops.

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  January 2016 Workshop

• 

  March 2016 Workshop

• 

  April 2016 Workshop

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  UCLA Workshop, June 2016

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  MCCS Miniscope Workshop, November 2016

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  April 2017 Workshop

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  Munich, Germany Workshop, August 2017

If you cannot attend one of our workshops, presentations, data files, and workshop videos can be found on our Online Workshop page.

Miniscope Community Member Pages

Member Pages

Update Log

11/29/2018

Updated GoFoton GRIN lens information

06/21/2018

Added link and information to MIN1PIPE analysis package on the Analysis Package page and Other_Open_Source_Projects page

05/24/2018

Updated the Analysis Package page and Other_Open_Source_Projects page

04/14/2018

Updated the Master Parts List for more up-to-date information and comments

01/27/2018

Added Miniscope Gripper by Bastijn van den Boom at NIN

11/6/2017

Added Miniscope Baseplate and Protective Cone for Rats by Bastijn van den Boom at NIN

5/2/2017

Updated 'Additional Open Source Resources' to include CNMF-E from the Paninski Lab and an open source miniature microscope from the Gardner Lab.

2/01/2017

Added additional assembly and surgery tutorial videos.

11/29/2016

Added a link on the front page to request a spot in upcoming Miniscope workshops.

10/28/2016

Added version 3.2 of the DAQ PCB to the GitHub repository.

07/28/2016

Added a new group PCB order signup sheet here.

07/21/2016

Fixed bug that would crash the Miniscope DAQ software when using the 'Trigger Ext' option. This option is now fully functional and allows one to remotely trigger the Miniscope to record using a LVTTL or TTL high signal.

04/20/2016

Added Initial Testing of Assembled Miniscopes which outlines the process of testing new Miniscope systems.

04/16/2016

Added Imaging With Thin GRIN Lenses describing how to use Miniscopes to image with GRIN lenses 1mm diameter and thinner.

04/12/2016

Added a new group PCB order signup sheet here.

04/13/2016

Updated the GitHub repository to include the newer version of the CMOS Imaging Sensor PCB (v3.2).

03/25/2016

Updated the Surgery and Baseplating Presentation link.

Updated the Recommended Computer Specs page... Apparently a MacBook Pro running Windows 8 doesn't always agree with the Miniscope system.

03/18/2016

Added the DAQ housing design files to our GitHub repository.

03/16/2016

Added a Member Pages page for sharing miniscope.org member created pages.

02/24/2016

Added a set of example Miniscope data to the Workshop Resources page.

02/17/2016

Added a new way to connectorize the coaxial cable. This update includes a new PCB design on the GitHub repository as well as an assembly video on the System Assembly page.

02/10/2016

Started adding videos to the Workshop Resource and System Assembly page

02/05/2016

Updated the DAQ Software and Firmware to support FPS adjustment. The source code and compiled files can be found on our GitHub repository.

02/03/2016

Updated Surgery Tools on Miniscope Master Parts List

01/28/2016

Added PCB price quotes to reference when ordering PCB fabrication and assembly through Sierra Circuits. They can be found on the Part Procurement page.

01/27/2016

IMPORTANT: Updated CMOS Imaging Sensor PCB Fabrication file to newest version

01/20/2016

Updated Surgery Tools on Miniscope Master Parts List

Added GRIN lens specifications on GRIN Lens Information page

Updated the PCB Assembly documents on Github will a more detailed description of SMD LED orientation

Slight modification to the Baseplate 3D model on Github

01/14/2016

Comments added to segmentation functions

Added through-hole components for DAQ PCB on Master Parts List

Added additional soldering tools on Master Parts List

01/13/2016

Added basic surgery outline

Added a picture guide for scope and Baseplate assembly

01/12/2016

Finalizing of Miniscope Master Parts List

01/10/2016

Upload of current version of all files and documents to Github

01/09/2016

Added guide to programming firmware to DAQ PCB