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[[File:miniscopev2.JPG|thumb|300px]]
 
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Welcome to Miniscope.org Wiki!
 
  
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The miniature fluorescence microscope described here is based on a design pioneered by Mark Schnitzer's Lab at Standford  and published in a [http://www.nature.com/nmeth/journal/v8/n10/full/nmeth.1694.html 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 [[Overview of System Components|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!
+
 
 +
  '''Quick Announcement:''' We have multiple Postdoc/Engineering/Researcher positions open within the Miniscope project! Looking for exceptional, creative 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 [https://www.nature.com/naturejobs/science/jobs/654273-postdoctoral-fellow-engineer here]. If interested please contact Daniel Aharoni, DBAharoni_at_gmail.com.
 +
 
 +
<br clear=all>
 +
 
 +
[[File:miniscopev4_render.png|thumb|300px]]
 +
 
 +
'''Welcome to Miniscope.org Wiki! Follow the project on Twitter: [https://twitter.com/MiniscopeTeam @MiniscopeTeam].'''
 +
 
 +
We are happy to announce the release of our next generation, open-source Miniscope platform, [[Miniscope V4]]. This new system is a substantial leap forward over previous designs and will serve as the base Miniscope platform for years to come. An overview of new features can be found below:
 +
 
 +
* >1mm diameter field of view
 +
* ~1mm working distance
 +
* +/-200um electronic focal adjustment
 +
* All achromatic optics
 +
* 2.6 grams
 +
* 22mm tall
 +
* Absolute head orientation sensor
 +
* Requires ~1/5th the excitation power of previous systems
 +
* No more soldering!
 +
* Still uses only a single coaxial cable (down to 0.3mm in diameter) for power, communication, and data.
 +
* New DAQ 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 no soldering and simple hands-on assembly. The Miniscope project and Miniscope.org are on going projects and will be routinely updated over the coming months and years.
  
 
== Current Status of Project ==
 
== Current Status of Project ==
−
The Miniscope project is now in its third year of development at UCLA and has gone through two major revisions. 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.
+
The Miniscope project is now in its 6th year of development at UCLA and in its third major revision. Miniscope developers have used Miniscopes to understand  [http://www.nature.com/nature/journal/v534/n7605/full/nature17955.html how the brain links memories across time in Nature, 2016] and how [https://www.nature.com/articles/s41593-019-0559-0 spatial coding breaks down in epilepsy in Nature Neuroscience, 2019]. 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. We encourage Miniscope users to 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.
 
Initial access to the miniscope.org wiki was enabled mid January, 2016.
  
−
'''Important:''' Using this system we have successfully imaged Hippocampal CA1, Subiculum, 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 [[GRIN Lens Information|here]]).
+
'''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 [[GRIN Lens Information|here]]).
 +
 
 +
{{#ev:youtube|https://youtu.be/xUf7HHiazEI|640|center}}
 +
 
 +
<br clear=all>
  
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== Links to information on miniscope subsystems ==
+
== Links to information on Miniscope subsystems ==
 
[[File:Overview_System.png|thumb|600px]]
 
[[File:Overview_System.png|thumb|600px]]
−
:[[Head Mounted Scope]]
 
  
−
:[[Data Acquisition Box]]
+
Information on the newest generation of the UCLA Miniscope platform can be found here:
 +
:[[Miniscope V4]]
 +
 
 +
Our currently release Wire-Free Miniscope (based on the Version 3 Miniscope platform can be found here:
 +
:[[Information on the Version 3 Wire-free Miniscope platform]]
 +
Information on the past Miniscope platforms(s) can be found here:
 +
:[[Information on the (previous Version 3) Miniscope platform]]
  
−
:[[Data Acquisition Software]]
+
Additional information relating to Miniscope imaging can be found below:
  
 
:[[Surgery Protocol]]
 
:[[Surgery Protocol]]
  
−
:[https://docs.google.com/spreadsheets/d/12H71DU2QX8d7efUE4yNuikBEiIzKaXjYqdc0A-oLNSw/edit?usp=sharing Master Parts List]
+
:[[Analysis Package]]
  
−
:[[Analysis Package]]
+
:[[GRIN Lens Information]]
  
 
<br clear=all>
 
<br clear=all>
 +
 
== Discussion Board and FAQ ==
 
== Discussion Board and FAQ ==
−
:[[Special:WikiForum|Discussion Board]]
+
:[https://groups.google.com/d/forum/miniscope Google Group and current Discussion Board]. Please post all new questions and discussions here!
 +
:(Our previous discussion boards can be found [http://miniscope.org/board here] and [[Special:WikiForum|here.]]. Please do not post to these)
 
:[[FAQs]]
 
:[[FAQs]]
  
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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.
 
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.
  
−
# [[Overview of System Components]]
+
Guides and tutorials for the current, Version 4, Miniscope platform:
−
# [[Part Procurement]]
+
:[[Miniscope V4]]
−
# [[System Assembly]]
 
−
# [[Recommended Computer Specs]]
 
−
# [[Software and Firmware Setup]]
 
−
# [[Surgery Protocol]]
 
−
# [[Animal Behavior Guide]]
 
  
−
Once you have built your system. This tutorial will explain how to use the different features of the scope.
+
Past guides and tutorials can be found here:
 +
:[[Information on the (previous Version 3) Miniscope platform]]
  
−
:[[Using Your Miniscope System For The First Time]]
+
== Workshop Resource ==
 +
We will be holding a pre-SfN workshop November 9th, 2017. For more information visit our [http://www.iclm.ucla.edu/page/MiniscopeWorkshopMCCS-ICLM.html 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 [https://goo.gl/forms/YXt8HeLpoeX2fVWz2 here] to request a spot in upcoming workshops.
 +
 
 +
<gallery widths=300px heights=200px mode="packed">
 +
Image:Workshop_Jan2016.jpg|January 2016 Workshop
 +
Image:Workshop_Mar2016.jpg|March 2016 Workshop
 +
Image:Workshop_April2016.JPG|April 2016 Workshop
 +
Image:UCLA_Worshop_June.JPG|UCLA Workshop, June 2016
 +
Image:MCCS_Workshop_Nov2016.JPG|MCCS Miniscope Workshop, November 2016
 +
Image:Workshop_April2017.jpg|April 2017 Workshop
 +
Image:Germany_Workshop.jpg|Munich, Germany Workshop, August 2017
 +
</gallery>
 +
 
 +
'''If you cannot attend one of our workshops, presentations, data files, and workshop videos can be found on our [[Online Workshop]] page.'''
 +
 
 +
<br clear=all>
 +
 
 +
== Miniscope Community Member Pages ==
 +
:[[Member Pages]]
  
 
== Update Log ==
 
== Update Log ==
 +
;01/31/2020
 +
:Added Miniscope V4 information, tutorials, design files, and source code
 +
;05/21/2019
 +
:Added [[Wire-free Miniscope]] tutorials, design files, and source code
 +
;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 [https://docs.google.com/spreadsheets/d/1eXogU7JdeuhMHnVIJBHvCVjgZ6e9KnxPGWvJEBK-eyw/edit?usp=sharing 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 [https://docs.google.com/spreadsheets/d/10_WgeJhZptxXbO2iEl93GyYGTDoEPvbrUjbIsegxpiI/edit?usp=sharing here].
 +
;04/13/2016
 +
:Updated the [https://github.com/daharoni/Miniscope_CMOS_Imaging_Sensor_PCB GitHub repository] to include the newer version of the CMOS Imaging Sensor PCB (v3.2).
 +
;03/25/2016
 +
:Updated the [https://drive.google.com/file/d/0ByUbjrn9MxK0TWdxUVVjakF3cDQ/view?usp=sharing| 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 [[Online Workshop|Workshop Resources]] page.
 +
;02/17/2016
 +
:Added a new way to connectorize the coaxial cable. This update includes a new PCB design on the [https://github.com/daharoni/Miniscope_Coax_2_SMA_PCB GitHub repository] as well as an assembly video on the [[System Assembly]] page.
 +
;02/10/2016
 +
:Started adding videos to the [[Online Workshop|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
 
;01/14/2016
 +
:Comments added to segmentation functions
 
:Added through-hole components for DAQ PCB on Master Parts List
 
:Added through-hole components for DAQ PCB on Master Parts List
 +
:Added additional soldering tools on Master Parts List
 
;01/13/2016
 
;01/13/2016
 
:Added basic surgery outline
 
:Added basic surgery outline
−
;01/13/2016
 
 
:Added a picture guide for scope and Baseplate assembly
 
:Added a picture guide for scope and Baseplate assembly
 
;01/12/2016
 
;01/12/2016

Revision as of 18:00, 12 August 2021


  Quick Announcement: We have multiple Postdoc/Engineering/Researcher positions open within the Miniscope project! Looking for exceptional, creative 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.


Miniscopev4 render.png

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

We are happy to announce the release of our next generation, open-source Miniscope platform, Miniscope V4. This new system is a substantial leap forward over previous designs and will serve as the base Miniscope platform for years to come. An overview of new features can be found below:

  • >1mm diameter field of view
  • ~1mm working distance
  • +/-200um electronic focal adjustment
  • All achromatic optics
  • 2.6 grams
  • 22mm tall
  • Absolute head orientation sensor
  • Requires ~1/5th the excitation power of previous systems
  • No more soldering!
  • Still uses only a single coaxial cable (down to 0.3mm in diameter) for power, communication, and data.
  • New DAQ 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 no soldering and simple hands-on assembly. The Miniscope project and Miniscope.org are on going projects and will be routinely updated over the coming months and years.

Current Status of Project

The Miniscope project is now in its 6th year of development at UCLA and in its third major revision. Miniscope developers have used Miniscopes to understand how the brain links memories across time in Nature, 2016 and how spatial coding breaks down in epilepsy in Nature Neuroscience, 2019. 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. We encourage Miniscope users to 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

Overview System.png

Information on the newest generation of the UCLA Miniscope platform can be found here:

Miniscope V4

Our currently release Wire-Free Miniscope (based on the Version 3 Miniscope platform can be found here:

Information on the Version 3 Wire-free Miniscope platform

Information on the past Miniscope platforms(s) can be found here:

Information on the (previous Version 3) Miniscope platform

Additional information relating to Miniscope imaging can be found below:

Surgery Protocol
Analysis Package
GRIN Lens Information


Discussion Board and FAQ

Google Group and current Discussion Board. Please post all new questions and discussions here!
(Our previous discussion boards can be found here and here.. Please do not post to these)
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.

Guides and tutorials for the current, Version 4, Miniscope platform:

Miniscope V4

Past guides and tutorials can be found here:

Information on the (previous Version 3) Miniscope platform

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.

  • January 2016 Workshop

  • March 2016 Workshop

  • April 2016 Workshop

  • UCLA Workshop, June 2016

  • MCCS Miniscope Workshop, November 2016

  • April 2017 Workshop

  • 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

01/31/2020
Added Miniscope V4 information, tutorials, design files, and source code
05/21/2019
Added Wire-free Miniscope tutorials, design files, and source code
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
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