Allen Institute Mesoscope Hardware

Overview

The Mesoscope is an advanced two-photon calcium imaging system developed by the Allen Institute for Neural Dynamics. This cutting-edge microscopy technology enables simultaneous multi-plane imaging of neural activity across multiple brain regions and depths, significantly increasing data collection throughput compared to conventional single-plane two-photon microscopes.

Dual-Beam Technology

The Allen Institute uses a modified Mesoscope system, also referred to as a "Multiscope," which features innovative dual-beam technology. This design allows researchers to:

  • Image multiple cortical depths simultaneously
  • Record from two different brain areas in a single experiment
  • Acquire data at higher throughput than conventional microscopes

Technical Specifications

The Dual-Beam Mesoscope consists of three key components:

  1. Delay Line: Splits the original laser beam into two separate beams and delays one beam by half a period of the excitation laser
  2. Secondary Z-Scanner: Sends the two beams to different focal planes along the Z-axis
  3. Custom Demultiplexing Unit: Separates fluorescence from the two planes based on the arrival time at the photodetector

Key Features:

  • Laser Source: Ti:Sapphire ultrafast laser (Chameleon Ultra II, Coherent)
  • Control Software: Customized ScanImage software (VidrioTech) with an in-house developed Workflow Sequencing Engine
  • Imaging Rate: 11 Hz per plane
  • Field of View: Full 5mm field of view for targeting, 400-512 μm for recording

Data Analysis

Data from the Mesoscope is processed through standardized pipelines that include:

  • Motion correction
  • ROI extraction
  • Fluorescence trace extraction
  • Deconvolution for estimating neural activity
  • Registration to common coordinate frameworks

References

For more detailed information about the Allen Institute's Mesoscope technology:

Additional Resources

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