AIBSOPT
<< Virtual sections through a mouse brain show the recording location of Neuropixels probes coated with fluorescent dye.
A low-cost platform for rapid 3D volumetric imaging of cleared specimens 10-50 mm in size.
AIBSOPT is an open-source Optical Projection Tomography instrument optimized for post-hoc tracing of Neuropixels probes, which can be used for a variety of other applications.
Transmission and fluorescence illumination image acquisitions complete in a few minutes. Operating like a visible light analog of a CT scanner, a series of projection images are collected at multiple angles. Reconstruction into an isotropic volume is through freely-available software.
Instrument alignment is straightforward and robust for long-term stability. Configure with efficient LED illumination or a high-powered NicoLase laser launch, depending on your experimental needs.
The GitHub repository includes MicroManager support for image acquisition and Python code for alignment of reconstructed mouse brain volumes into the Allen Institute CCF.
Example data
Example AIBSOPT data. Cleared mouse brain in transmitted light (gray) with fluorescent tracks indicating position of Neuropixels probes (blue).
Reconstructed stack of imaged volume showing Neuropixels probe tracks through cleared mouse brain.
Features
Clear tissue by any protocol
Specimen chamber isolates immersion medium from optics.
Telecentric collection lens
Optimal projection images with plug-and-play assembly.
Transmission and fluorescence illumination
Specific labels captured in tissue context with automated multi-color image acquisition.
LED and laser illumination options
Choose up to two fluorescence LED channels for efficient illumination, or up to five laser lines for high-powered excitation.
Licensing
Licensed from Allen Institute for Brain Science. Redistribution and replication for non-commercial purposes permitted with attribution.