High-Resolution, Parallelized Imaging of Freely Swimming Zebrafish with a Gigapixel Microscope

Period of Performance: 07/15/2017 - 07/14/2018


Phase 1 SBIR

Recipient Firm

Optical Wavefront Laboratories, LLC
Principal Investigator
Principal Investigator


Significance: High-throughput optical microscopy is currently transforming the research fields of genetics, drug discovery and neuroscience. Large-scale optical assays now routinely use thousands of high-resolution images to offer critical insights into the human body, our brain and the diseases that affect us. Today's optical microscopes, however, are still far from ideal. Due to challenges with large lens design, no standard microscope can capture more than 50 megapixels per image snapshot, which makes it impossible to simultaneously image at cellular-resolution over a multi-centimeter viewing area (field of view, FOV). For screening and monitoring zebrafish in vivo, this resolution/FOV tradeoff is a critical bottleneck: each organism must be constrained or paralyzed to image at high resolution, freely swimming organisms can only be viewed at low resolution, and no setups yet can monitor in parallel multiple swimming zebrafish at cellular resolution. Proposal: Optical Wavefront Laboratories, LLC (OWL) will develop and test a new microscope to overcome these limitations. It will capture sub-cellular resolution images over an 80 cm2 area (an entire large petri dish). This unique micro-camera array microscope (MCAM) is designed to form 0.25 gigapixel images, 10X more pixels per image than the top competing microscopes. This architecture can directly scale into the multi-gigapixel regime. The MCAM will significantly improve the efficiency of high-throughput microscope screening, reduce the complexity of current setups, and enable completely new biological experiments (e.g., SA3). SA1: Finalize MCAM hardware: OWL will complete a prototype MCAM device (currently under construction) consisting of 24 micro-camera units and associated electronics for 8 µm resolution imaging across an 80 cm2 FOV at 1 frame per second. Unlike any competing technology, our unique optical design will produce gigapixel-scale snapshot microscope images. Milestone: Completed MCAM hardware to deliver image data to a desktop computer at 0.25 gigapixels/sec. SA2: Develop MCAM software: A software program will transform the data captured by the MCAM system into standard digital images. The software program will also allow the end user to control and adjust basic imaging parameters (exposure time, contrast, and frame rate). Milestone: A standard Windows desktop computer program to directly control the MCAM and produce and save images (.bmp or .jpg format, 0.25 gigapixels/image) from an attached MCAM device. SA3: Test the MCAM's effectiveness in imaging freely swimming zebrafish: Working with the Engert Lab at Harvard University, OWL will demonstrate the MCAM's benefits in a behavioral imaging experiment to measure the visual function of >10 freely swimming zebrafish (larval stage) simultaneously across an 80 cm2 swim arena at 8 µm resolution. Milestones: 1) Confirm the MCAM accurately measures eye position for stationary zebrafish larvae embedded in agar. 2) Demonstrate the MCAM can measure eye position from 10 freely swimming zebrafish across an 80 cm2 swim area continuously (1 measurement/sec. per larvae). Results will be compared to two top-of-the-line single-lens microscopes. After successfully demonstrating the MCAM provides 10X more pixels per image than current microscopes, OWL plans to use the new device for non-invasive and parallelized in vivo fluorescent imaging of neural activity in multiple freely swimming zebrafish at video frame rates. This will be the subject of a Phase II proposal.