General Miniscope Workshop

Day 1 Recordings


General Miniscope Workshop

Day 2 Recordings


Hands-On Analysis Tutorial

Day 3 Recordings

If you would like to interactively run the same notebook used in the Hands-On Analysis Workshop Demo, with zero local setup, sign up for a trial of MetaCell Cloud Workspaces. Just select "Free Trial" on this form in order to receive a login to a duplicate environment of the one used in the workshop. Alternately, if your lab ever runs virtual workshops or virtual group trainings that you think could benefit from our Cloud Workspaces, please select "Training Workspace".


About the 2021 Virtual Miniscope Workshop

Welcome to the 2021 Virtual Miniscope Workshop! We are excited to be hosting a virtual workshop with lectures and hands-on tutorials that will teach participants how to use open-source Miniscopes for in vivo calcium imaging. This workshop is designed to introduce all aspects of using Miniscopes, including basic principles of Miniscope design and imaging, how to build and attach a Miniscope, how to implant a GRIN lens for imaging deep structures, and how to analyze imaging data. The workshop will also cover the most recent developments in Miniscope technology and highlight some of the best advances in this exciting and growing field.

We are offering two separate tracks for this workshop:

  1. A comprehensive 2-day Miniscope workshop (November 29-30) will cover all aspects of Miniscope imaging, from hardware development to implementation, and include a lecture introducing recent advances in data analysis. This workshop is appropriate for all experience levels and participants should leave the workshop with enough knowledge to begin building and performing imaging in their own lab. This workshop is open to everyone and space will not be limited, but registration is required.

  2. A hands-on analysis tutorial (November 30-December 1) will go in-depth into how to analyze data using Minian, a python-based analysis package developed by the Cai, Aharoni, and Shuman Labs. Participants will walk through the analysis of demo data through a cloud platform and then work to analyze their own data, or additional provided data. To ensure adequate interaction with instructors, this track is limited to 25 participants, so you must apply for this track.

Participants can choose to register/apply for both tracks, or can choose a single track. Both tracks are entirely free to attend and will take place on November 29 - December 1, 2021. This event is organized by Daniel Aharoni, Denise Cai, and Tristan Shuman, and it is hosted at MetaCell's Workspace for Calcium Imaging Analysis.


Virtual Workshop Structure

General Miniscope Workshop
Days 1-2


  • Learn basic principles of imaging with Miniscopes, how to build a Miniscope, perform GRIN lens implants, and acquire data during behavior

  • Learn about the Minian analysis pipeline and other calcium imaging analysis tools

  • Learn about the latest Miniscope developments, ongoing projects, and future directions of Miniscopes

  • See how investigators across the world are using Miniscopes and developing new innovations in miniature microscopy

  • Connect with other scientists and developers during the various interactive break out sessions

  • Open to everyone, but registration is required

Hands-on Analysis Tutorial
Days 2-3


  • In-depth tutorial on using Minian to analyze Miniscope calcium imaging data

  • Learn how to interface with Minian in the cloud to perform analysis on analysis servers

  • Each participant will run the Minian pipeline on demo data, then can conduct analysis using their own data, or additional provided data sets

  • Network with the community of researchers working to analyze calcium imaging data in a small group setting

  • Space is limited to 25 participants, so apply early!


Speakers

Denise Cai


Assistant Professor, Icahn School of Medicine at Mount Sinai

Cai Lab

Daniel Aharoni


Assistant Professor, University of California, Los Angeles

Aharoni Lab

Tristan Shuman


Assistant Professor, Icahn School of Medicine at Mount Sinai

Shuman Lab

Tycho Hoogland


Senior Scientist, Netherlands Institute for Neuroscience

De Zeeuw Lab

Caleb Kemere


Associate Professor, Rice University

Kemere Lab

Andrea Giovannucci


Assistant Professor, University of North Carolina at Chapel Hill

Neural Engineering Lab

Laura Waller


Associate Professor, UC Berkeley

Computational Imaging Lab

Yaniv Ziv


Assistant Professor, Weizmann Institute of Science

Yaniv Ziv Lab

Lingxuan Chen


Postdoctoral Fellow

Cai Lab

Zachary Pennington


Postdoctoral Fellow

zachpenn.github.io

William Mau


Postdoctoral Fellow

Cai Lab

Phil (Zhe) Dong


Graduate Student

Cai Lab

Joe (Yosif) Zaki


Graduate Student

Cai Lab

Susie (Yu) Feng


Graduate Student

Shuman Lab

Federico Sangiuliano


Lab Technician

Aharoni Lab

Stephen Larson


Co-founder & CEO

MetaCell

Paolo Bazzigaluppi


Senior Consultant

MetaCell


Previous Miniscope Workshops

Carousel imageCarousel imageCarousel imageCarousel imageCarousel imageCarousel imageCarousel imageAugust 2017 | Munich (Germany) WorkshopCarousel imageApril 2017November 2016 | MCCS WorkshopJune 2016 | UCLA WorkshopApril 2016March 2016January 2016

Any questions? Please email workshop@metacell.us