Light-Sheet Microscopy for Neuroscientists





Course Directors: Aurelien Begue, PhD (HMS) and Jason DeBruyne, PhD (MSM)

Course Description: Fluorescent light-sheet microscopy is a versatile microscopy technique that has diverse applications to neuroscience research and offers many advantages to other imaging methods. This nanocourse, offered as part of the MAHPING collaboration between Harvard Medical School and Morehouse School of Medicine, will introduce neuroscientists who have little or no experience with light-sheet microscopy to the scientific rationale and possible applications for the technique, foundational concepts that underlie the method, and considerations related to experimental design and data analysis. Through a combination of research talks, lectures, and small group discussions, the nanocourse will prepare participants to identify applications of the technique to their own research and to begin planning their own light-sheet microscopy experiments. 

Faculty, postdocs, and students may attend individual sessions, though pre-registration is required. Each session is limited to 30 attendees. Students who wish to receive nanocourse credit must attend all three sessions.

**This course is entirely virtual via Zoom**


Session 1: Foundations and Applications of Light-Sheet Microscopy to Neuroscience

Monday, Aug. 3, 10-12 (Zoom)

Instructors: Aurelien Begue, PhD; Jason DeBruyne, PhD; Chenghua Gu, PhD

This session consists of two research talks that describe the applications of light-sheet microscopy to neuroscience research and didactic sessions that introduce foundational principles of light-sheet microscopy and which compare light-sheet to other microscopy methods. 

At the end of this session, participants should be able to:

  • Identify possible applications of light-sheet microscopy to their own research
  • Describe the basis of the technique 
  • Compare and contrast light-sheet microscopy to other microscopy methods

Session 2: Designing Light-Sheet Microscopy Experiments

Wednesday, Aug. 5, 10-12 (Zoom)

Instructors: Aurelien Begue, PhD; Jason DeBruyne, PhD

Through didactic sessions and small-group discussions, this session introduces participants to the logistics and technical considerations of light-sheet microscopy experiments, including experimental timeline, sample preparation and tissue-clearing approaches, and different variations of light-sheet microscopy. Participants will work in small groups to discuss these aspects of experimental design and to begin outlining their own hypothetical light-sheet microscopy experiments. 

At the end of this session, participants should be able to:

  • Discuss practical and technical considerations when designing imaging experiments using light sheet microscopy
  • Apply these principles of experimental design to their own research and begin to sketch out an experimental plan for a previously identified possible application

Session 3: Managing and Analyzing Light-Sheet Microscopy Data

Friday, Aug. 7, 10-12 (Zoom)

Instructors: Aurelien Begue, PhD; Jason DeBruyne, PhD

In this session, the instructors use didactic sessions and instructor-led demonstrations to introduce participants to the “back-end” of experimental design: data management and data analysis. Participants will learn about technical considerations related to the collection, management, and analysis of large light-sheet microscopy datasets and will be introduced to common data analysis software tools and workflows. 

At the end of this session, participants should be able to:

  • Describe common data analysis workflows for light-sheet microscopy datasets 
  • Discuss practical and technical considerations for collecting and working with light-sheet microscopy datasets
  • Identify software tools and resources within their own research programs that they could use to analyze their own datasets, once collected

Register for the class here.