Guides

Tutorials, assembly guides, and how-tos contributed by the community.

18

Guides

8

Distinct topics

List

Getting Started with Miniscopes Introduction

Jun 2026 · Beginner

Converting a Miniscope V4 to Image a Different Fluorophore Tutorial

May 2026 · Advanced

A walkthrough of what considerations and adjustments need to be made to modify or purchase a Miniscope V4 designed to image something other than GCaMP such as rCaMP or PinkyCaMP

Calcium imaging, Imaging, Optics

UCLA 2P Miniscope Assembly Tutorial

May 2026 · Beginner

Mechanics, Optogenetics

A Test Suite for Working with Miniscope Data Tutorial

May 2026 · Intermediate

Calcium imaging, Data analysis, Data management, Data processing

Common Pitfalls and FAQs Troubleshooting

May 2026 · Beginner

A discussion of common issues and where to access additional guides and FAQs on the most reoccurring questions around Miniscopes.

Fundamentals of Miniscope Optoelectronics and Imaging Introduction

May 2026 · Beginner

Calcium imaging, Imaging, Mechanics, Optics

How (and Why) to Submit an Issue Introduction

May 2026 · Beginner

Miniscope tools are driven by the community. When issues, bugs, or challenges come up, it is extremely helpful to us to know about them. This guide will walk you through the how, and why, of submitting problem/bug/issue to the Miniscope Project.

How to Test and Debug your Miniscope V4 Maintenance

May 2026 · Intermediate

A walk through of considerations when first testing a Miniscope V4 and some tips and tricks for debugging common issues that might come up across use.

Electronics, Imaging, Mechanics, Optics, Software

Introduction to Open-Source Contribution and Project Standardization of Testing and Validation Introduction

May 2026 · Intermediate

Miniscope V4 Part Procurement Tutorial

May 2026 · Beginner

Surgery and Baseplating Tutorial

May 2026 · Intermediate

A workflow for cortical and deep region surgery and baseplating

Workflow for Freely Behaving Animal Experiments Tutorial

May 2026 · Beginner

An overview and workflow for thinking through and implementing freely behaving animals experiments

Working with One-Photon Miniscope Calcium Imaging Data: A Practical Walkthrough Troubleshooting

May 2026 · Intermediate

This document walks through the typical analysis pipeline, what the dominant algorithms (especially CNMF-E variants) actually do, what one-photon (1p) data can and cannot tell you, and how to assess single-cell calcium activity quality.

Calcium imaging, Imaging, Software, Data processing

Initial testing of assembled Miniscope Tutorial

May 2026 · Beginner

A walkthrough of steps to validate the functionality of a newly assembled Miniscope on the bench before moving to animal experiments.

Electronics, Imaging, Optics, Software

Miniscope V3 Surgery and Baseplating Tutorial

Oct 2019 · Intermediate

A basic outline of our procedure for implanting a GRIN lens above the hippocampus for CA1 imaging written for the Miniscope V3.

Animal Behavior Introduction

Nov 2016 · Beginner

Reference procedures for animal and imaging preparation, and experimental setup using legacy Miniscope systems.

Behavior