General Miniscope Workshop

Day 1 Recordings

General Miniscope Workshop

Day 2 Recordings

Hands-On Analysis Tutorial

Day 3 Recordings

Keep Learning

  • Please select "One-on-one support" on this form if you would like to get personalized help for your calcium imaging data analysis. We’ll follow up with you to set up a call to discuss your needs;

  • Select "Free Trial" (same form) if you would like to interactively run the same notebook used in the Hands-On Analysis Workshop Demo, with zero local setup. You’ll receive a login to a duplicate environment of the one used in the workshop;

  • Select "Training workspace" (same form) if you are interested in running a workshop that includes a hands-on component using zero setup data analysis environments like the one we created for the Virtual Miniscope Hands-on Tutorial.

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!


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

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


Paolo Bazzigaluppi

Senior Consultant


Previous Miniscope Workshops

Any questions? Please email