Data from: Large-scale compressive microscopy via diffractive multiplexing across a sensor array

Data files

Jun 26, 2026 version files 121.39 GB

Abstract

Microscopes face a trade-off between spatial resolution, field of view, and frame rate—improving one typically sacrifices the others because of the sensor’s limited spatiotemporal throughput. We propose a microscope that achieves snapshot gigapixel-scale imaging using a sensor array and a diffractive optical element (DOE). We increase spatiotemporal throughput in two ways. First, we capture data with an array of 48 sensors, yielding 48x more pixels than a single sensor. Second, we use point spread function (PSF) engineering and compressive sensing algorithms to fill in the missing information from the gaps surrounding individual sensors in the array, providing an additional >5.4x increase. The sensor array is modeled as a single large-format “super-sensor,” with erasures corresponding to the gaps between sensors. The array is placed at the output of a nearly 4f imaging system, and we design a DOE for the Fourier plane that generates a distributed PSF encoding information from the entire super-sensor area, including the gaps. We then computationally recover the large-scale image, assuming the object is sparse in some domain. Our calibration-free microscope achieves approximately 3 micrometers resolution over >5.2 cm² field of view at up to 120 fps, for a total spatiotemporal throughput of 25.2 billion pixels per second. We demonstrate versatility in two modes: structural imaging via darkfield contrast and functional fluorescence imaging of calcium dynamics across dozens of freely moving C. elegans simultaneously.

Dataset DOI: 10.5061/dryad.tmpg4f5b6

Summary

This dataset contains the raw, multiplexed video measurements used to demonstrate a large-scale compressive microscope that images dozens of freely moving Caenorhabditis elegans in parallel. The microscope captures snapshot gigapixel-scale data by combining two components: (1) a 48-sensor camera array that acts as a single large-format "super-sensor," and (2) a diffractive optical element (DOE) placed in the pupil plane of a (nearly) 4f imaging system.

Two recordings are provided, one for each imaging mode:

Darkfield (structural) imaging of wild-type worms across a ~20.0 × 26.4 mm² field of view (FOV).
Fluorescence (functional) imaging of worms expressing the genetically encoded calcium indicator GCaMP8f in the pharynx, across a ~9.3 × 9.3 mm² FOV.

Both recordings were acquired at 120 fps for 15 s, yielding 1,800 frames each.

Imaging system overview

The microscope is a pupil-coded, nearly-4f system consisting of an objective lens, a tube lens, a DOE in the pupil plane, and a 2D sensor array in the image plane.

MCAM sensor: a 6 × 8 array of 48 monochrome, 8-bit sensors. Each sensor is 3136 × 4096 pixels with a 1.1 µm pixel pitch and 9 mm center-to-center spacing, for a total of 0.617 gigapixels per snapshot at native sampling. The rectangular hull of the array covers 4.95 cm × 6.64 cm.
Frame rate / binning: at full 0.617 GP sampling the frame rate is bandwidth-limited to ~10 fps (6.17 GB/s data-transfer bandwidth). To reach 120 fps (readout-limited), the data in this release were acquired with 4 × 4 on-sensor pixel binning, giving 784 × 1024 pixels per sensor (38.5 MP per snapshot across the array) and an effective binned pixel pitch of 4.4 µm at the sensor.
DOE: a custom 64-level diffractive optical element fabricated by grayscale lithography on a 50.8 mm-diameter, 500 µm-thick glass substrate. The design (6638 × 6638 height map, 6 µm pixels, max height 0.787 µm ≈ 2π at λ = 515 nm, 39.8 mm effective diameter) produces a 15-spot PSF (one zero order plus 14 diffracted orders) with a spatial extent of ~6.8 mm × 6 mm. The same DOE and tube lens (Jupiter-36B, f = 250 mm, f/3.5) are shared by both imaging modes.

Description of the data and file structure

Both files are NetCDF (.nc) containers holding the raw multi-sensor video for one imaging mode. The data are the captured sensor frames (before background subtraction); preprocessing and reconstruction are performed downstream by the provided code.

File: `mcam_dataset_darkfield.nc`

Description: High-speed (120 fps) darkfield video of freely moving wild-type C. elegans (strain N2, Bristol) crawling across a 2 cm × 2 cm microfluidic arena. Used for structural imaging and worm tracking.

Imaging mode: darkfield
Objective: FJW Industries lens, f = 90 mm, f/1.0 (total magnification ~2.78×)
Reconstructed FOV: ~20.0 × 26.4 mm²
Sensors used: full 6 × 8 array (48 sensors)

File: `mcam_dataset_fluorescence.nc`

Description: High-speed (120 fps) fluorescence video of freely moving C. elegans expressing GCaMP8f in the pharynx (strain INF418, nonEx106[myo-2p::GCaMP8f::unc-54 3’UTR]), crawling in an 8 mm × 8 mm microfluidic chip.

Imaging mode: widefield fluorescence
Objective: Rodenstock lens, f = 42 mm, nominal NA = 0.7, design wavelength 532 nm (total magnification ~6×)
Reconstructed FOV: ~9.3 × 9.3 mm²
Sensors used: central 6 × 6 array (36 sensors)

Code/software

This dataset is the raw data underlying the associated publication. The reconstruction/visualization code is hosted separately on GitHub: https://github.com/kevinczhou/diffractive-compressive-array-microscopy

Use reconstruction_without_fft.ipynb to reconstruct selected frames:

Set optimization_config = 0 for calibration (jointly estimating the lens-distortion and DOE-orientation parameters from a single frame).
Set optimization_config = 1 for the final video reconstruction.
Set dataset_to_recon = 'df' for the darkfield video, or 'fluor' for the fluorescence video.

Experimental details / sample preparation

Microfluidic devices. Monolayer devices with arena areas of 2 cm × 2 cm × 70 µm (darkfield/structural) or 8 mm × 8 mm × 70 µm (fluorescence/functional). Each arena contains a hexagonal array of 200 µm-diameter cylindrical pillars with 300 µm center-to-center spacing, which induces the worms to crawl (rather than swim) in a soil-mimicking environment.

Loading protocol. Before each experiment, ~150 young adult hermaphrodites were collected from cultivation plates using 2 ml S-basal buffer (100 mM NaCl, 50 mM potassium phosphate, pH 6.0), washed twice in fresh 2 ml S-basal to remove excess bacteria, drawn into loading tubing with a 1 ml syringe, and gently introduced into the device (all within ~10 min). Gravity-fed S-basal then flowed through the arena for an additional 10 min, and the loaded worms were left to crawl freely for 1 hour before recording, allowing them to enter a starved state.

Illumination and filtering

Darkfield: four pseudo-collimated off-axis green LEDs (Thorlabs M530L4, collimated with Thorlabs ACL2520U-A, f = 20 mm) and a 514/2 nm bandpass filter (Alluxa) in the pupil plane, plus a 40 mm-diameter aperture near the DOE. The narrow 2 nm bandwidth limits radial spectral blurring of the off-axis diffraction orders.
Fluorescence: high-power blue LED widefield Köhler illumination (Thorlabs SOLIS-470C), a 480/40 nm excitation filter (Chroma), and a 530/55 nm emission filter (Edmund) above the DOE. The broad emission bandwidth maximizes light collection; the resulting radial spectral blur is mitigated by exploiting the objective's axial chromatic aberration.