Rapid volumetric reconstruction and tracking for Fourier light-field microscopy enables real-time calcium imaging in freely behaving Hydra.
- 1Yale University
Abstract
Fourier light field microscopy (FLFM) enables high-speed volumetric imaging by encoding multiple angular perspectives of a three-dimensional sample onto a single image. For this reason, FLFM is well-suited to sparse and rapidly evolving biological systems. To aid in the adoption of FLFM, we present OpenFLR, an open-source software framework for real-time volumetric reconstruction, three-dimensional particle tracking, and calcium image processing using FLFM. OpenFLR reconstruction is distributed as four interchangeable interfaces: a Python library, a command-line script, an interactive web application, and an ImageJ/micromanager plugin, so that the pipeline is accessible to both developers and bench biologists. Building on established Richardson-Lucy deconvolution, we use a hybrid experimental-computational PSF calibration strategy and a triangulation approach to tracking to extract particle positions in 3D directly from raw light field frames, bypassing reconstruction. We validate the complete pipeline on GCaMP6s recordings of freely behaving Hydra vulgaris, tracking sparse populations of neurons as they undergo large three-dimensional displacements.
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BibTeX
@misc{adkins2026rapid,
title = {{Rapid volumetric reconstruction and tracking for Fourier light-field microscopy enables real-time calcium imaging in freely behaving Hydra.}},
author = {R. Adkins and R. Hausen and J. Noss and G. Lemson and J. Howard},
howpublished = {bioRxiv},
year = {2026},
month = sep,
doi = {10.64898/2026.09.17.752193},
url = {https://www.biorxiv.org/content/10.64898/2026.09.17.752193v1},
note = {CC BY},
}
RIS
TY - UNPB
TI - Rapid volumetric reconstruction and tracking for Fourier light-field microscopy enables real-time calcium imaging in freely behaving Hydra.
AU - R. Adkins
AU - R. Hausen
AU - J. Noss
AU - G. Lemson
AU - J. Howard
PY - 2026
DA - 2026/09/17
PB - bioRxiv
DO - 10.64898/2026.09.17.752193
UR - https://www.biorxiv.org/content/10.64898/2026.09.17.752193v1
AB - Fourier light field microscopy (FLFM) enables high-speed volumetric imaging by encoding multiple angular perspectives of a three-dimensional sample onto a single image. For this reason, FLFM is well-suited to sparse and rapidly evolving biological systems. To aid in the adoption of FLFM, we present OpenFLR, an open-source software framework for real-time volumetric reconstruction, three-dimensional particle tracking, and calcium image processing using FLFM. OpenFLR reconstruction is distributed as four interchangeable interfaces: a Python library, a command-line script, an interactive web application, and an ImageJ/micromanager plugin, so that the pipeline is accessible to both developers and bench biologists. Building on established Richardson-Lucy deconvolution, we use a hybrid experimental-computational PSF calibration strategy and a triangulation approach to tracking to extract particle positions in 3D directly from raw light field frames, bypassing reconstruction. We validate the complete pipeline on GCaMP6s recordings of freely behaving Hydra vulgaris, tracking sparse populations of neurons as they undergo large three-dimensional displacements.
ER -