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

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 around 3 grams and uses only a single, flexible coaxial cable (0.3mm to 1.5mm diameter) to carry power, control signals, and imaging data. The goal of this wiki site is to provide 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 technology. The initial goal is to help disseminate this technology to the larger neuroscience community so that we can build a community of users that will continue to develop this technology and share on these developments. 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 a standard 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, and Visual Cortex using 1.8mm and 2mm diameter GRIN lenses from Grintech. While thinner GRIN lenses should theoretically be compatible with our system we have limited our initial development to larger lenses due to supply and experimental constraints. We are now actively testing thinner lenses as well as pursuing multiple avenues of GRIN lens production (More information on GRIN lenses can be found here).

Links to information on miniscope subsystems

Overview System.png
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

The Golshani, Silva, and Khakh labs will be hosting free, two-day long miniscope workshops here at UCLA. The next scheduled UCLA workshop is completely full but we are working on setting up more in the near future. We will update this page when more information is available.

A free one-day workshop will be held at this year's Molecular Cellular Cognition Society Meeting in San Diego on November 10th. You can register for the workshop here. Space is limited.

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

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