High Resolution Lightfield Microscopy

Lightfield Microscopy for Zebrafish Brain Imaging
FPGA Hardware Architecture
ASIC Design
UI & Data Visualization
GUI Development
Lotus

Overview

“Parallel FPGA acquisition unlocked the throughput light-field microscopy needs.” –LeafLabs
“Parallel FPGA acquisition unlocked the throughput light-field microscopy needs.” –LeafLabs
Light-field microscopy can capture rich 3D activity, but traditional systems hit data-rate and synchronization limits long before whole-brain experiments. Lotus removes those bottlenecks. LeafLabs designed a parallel acquisition architecture that ingests and synchronizes streams from high-speed sCMOS sensors, built on a bank of custom FPGA hardware (Willow-based), tightly coupled firmware, and a host acquisition stack. Researchers get deterministic timing, real-time health monitoring, and a UI built for experiments—not demos. The result is a practical platform that delivers a ~100× combined improvement in spatial and temporal resolution, enabling whole-brain imaging at cellular precision and turning previously theoretical experiments into repeatable protocols.
microscope image of probes
microscope image of probes
Lotus

The Challenge

Imaging every neuron in a zebrafish brain meant sustaining data rates on the order of 125 Gbps — comparable to CERN’s ALICE particle detector. Traditional light-field microscopes couldn’t keep up: outputs overwhelmed acquisition hardware and no commercial systems could manage the load. As a result, researchers were forced to compromise on speed, resolution, or field of view.
Imaging every neuron in a zebrafish brain meant sustaining data rates on the order of 125 Gbps — comparable to CERN’s ALICE particle detector. Traditional light-field microscopes couldn’t keep up: outputs overwhelmed acquisition hardware and no commercial systems could manage the load. As a result, researchers were forced to compromise on speed, resolution, or field of view.
Lotus zebrafish imaging lenses
Lotus zebrafish imaging lenses
Lotus zebrafish imaging lenses
image of Lotus device optics
image of Lotus device optics
image of Lotus device optics
image of a labratory device named Lotus
image of a labratory device named Lotus
image of a labratory device named Lotus
Meeting this challenge meant engineering across the stack: FPGA hardware to handle raw throughput, ASIC design for scalability, firmware and GUI so researchers could control experiments in real time, and data visualization to interpret results. It also required product development, live experimentation, and integration with vivarium systems to make sure the platform worked end-to-end.
Meeting this challenge meant engineering across the stack: FPGA hardware to handle raw throughput, ASIC design for scalability, firmware and GUI so researchers could control experiments in real time, and data visualization to interpret results. It also required product development, live experimentation, and integration with vivarium systems to make sure the platform worked end-to-end.
Lotus

The Solution

We designed a custom acquisition platform capable of sustaining 125 Gbps of continuous throughput—enough to capture whole-brain activity in real time. Layering silicon to software innovation, we removed traditional bottlenecks and restored speed, resolution, and field of view to light‑field microscopy.
We designed a custom acquisition platform capable of sustaining 125 Gbps of continuous throughput—enough to capture whole-brain activity in real time. Layering silicon to software innovation, we removed traditional bottlenecks and restored speed, resolution, and field of view to light‑field microscopy.

FPGA Hardware Architecture ASIC Design RTL/Firmware High-Speed Acquisition SCMOS Integration UI/Monitoring Data Visualization Opto-Mechanical Integration

Lotus

Performance Results

The Synthetic Neurobiology Group used Lotus to run high-channel count experiments that were previously impossible. What began as a bottleneck in acquisition has become a platform for discovery: Willow and Lotus now anchor routine workflows in Dr. Boyden’s lab and are spreading into pilot studies across leading institutions.
The Synthetic Neurobiology Group used Lotus to run high-channel count experiments that were previously impossible. What began as a bottleneck in acquisition has become a platform for discovery: Willow and Lotus now anchor routine workflows in Dr. Boyden’s lab and are spreading into pilot studies across leading institutions.
Resolution Increase
Resolution Increase

100× boost in combined spatial and temporal resolution.

64X
64X
64X
Massive Throughput
Massive Throughput

Sustained 125 Gbps acquisition bandwidth.

92Gb
92Gb
92Gb
Neurons Tracked
Neurons Tracked

Simultaneous neurons captured in real time across the zebrafish brain.

82K
82K
82K

Together, these advances let researchers observe whole-brain activity at unprecedented speed, scale, and fidelity.

Lotus

Publications & Info

MIT News
Study: Zebrafish are smarter than we thought.

Synthetic Neurobiology Group.
Imaging the voltage of neurons distributed across entire brains of larval zebrafish.

MIT McGovern Institute.
New method visualizes groups of neurons as they compute.

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The teams who trust us with their hardest problems.
The teams who trust us with their hardest problems.
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