Scientific Instrumentation & Process Engineering
Platform
The Scientific Instrumentation and Process Engineering (SIPE) team is a shared engineering resource within the Allen Institute, focused on enabling and scaling cutting-edge bioscience through integrated hardware and software systems. SIPE partners closely with scientists to design, build, and deploy experimental platforms, including behavioral platforms, electrophysiology and imaging instrumentation, and data acquisition pipelines. In addition to enabling internal research, SIPE develops and openly shares a broad portfolio of tools spanning hardware, software, and experimental protocols. These tools are designed to promote standardization, reproducibility, and scalability, helping transform experimental setups into robust, deployable platforms that can be adopted across labs and by the broader scientific community.
Take a closer look at tools SIPE has developed here.
This platform builds on turn-key lightsheet microscopes to image mouse brains at high resolution and throughput. Analysis of the resulting volumetric images, including registration to standard brain coordinates and segmentation and counting of individual neurons, is fully automated.
This platform uses a two-photon microscope SLAP2 that records patterns of synaptic input and output in individual neurons at hundreds to thousands of frames per second in mice performing complex behaviors, using a flexible scan system that combines a digital micromirror device (DMD) with a high-speed scanner.
The Scientific Instrumentation and Process Engineering (SIPE) team is a shared engineering resource within the Allen Institute, focused on enabling and scaling cutting-edge bioscience through integrated hardware and software systems.
This team performs a variety of surgical procedures, including stereotaxic injections and implanting chronic cranial windows and Neuropixels probes.
This platform implements pioneering technology for highly reproducible, targeted, brain-wide, cell-type-specific electrophysiology to record neural activity from defined neuron types across the brain. Analysis and quality control of the electrophysiology data are fully automated.
This platform combines innovative histology, ExA-SPIM microscopy, image handling, and machine learning to map the morphology and molecular identity of individual neurons across the whole brain at high throughput.
This platform enables optical measurement of neural activity and neurotransmitter release in populations of neurons to study neural circuit dynamics in behaving animals.
The Behavior platform uses advanced technology to implement a standardized, modular, multi-task virtual reality gymnasium for mice, with the goal to study brain function across different behaviors at scale.
