@article {70316,
	title = {Measuring Amorphous Motion: Application of Optical Flow to Three-Dimensional Fluorescence Microscopy Images},
	journal = {bioRxiv},
	year = {2026},
	month = {2026 Mar 10},
	abstract = {<p>Motion is an essential component of any living system. It is rich with information, but it is often challenging to quantitatively extract biologically informative results from the motion apparent in microscopy images. This challenge is exacerbated by the wide variety in biological movement, which often takes the form of difficult-to-segment amorphous structures undergoing complex motion. An image processing technique known as optical flow can capture motion at each pixel in an image, thus bypassing the need for object segmentation or a priori definition of motion types. This makes it a powerful tool for quantitative assessment of biological systems from the protein to organism scale. However, despite its flexibility and strengths for analyzing fluorescence microscopy images, its adoption in the bioimaging community has been limited by the availability of easy-to-use tools and guidance in results interpretation. Here we describe an optical flow tool, OpticalFlow3D, that can be run in Python or MATLAB and is compatible with three-dimensional microscopy images. Using biological examples across length scales, we illustrate how OpticalFlow3D can enable new biological insight.</p>
},
	doi = {10.64898/2026.03.06.710169},
	url = {https://www.biorxiv.org/content/early/2026/03/10/2026.03.06.710169},
	author = {Lee, Rachel M and Eisenman, Leanna R. and Hobson, Chad and Aaron, Jesse S. and Chew, Teng-Leong}
}
@article {69528,
	title = {Lattice light sheet microscopy reveals 4D force propagation dynamics and leading-edge behaviors in an embryonic epithelium in Drosophila.},
	journal = {Curr Biol},
	year = {2024},
	month = {2024 Jun 27},
	abstract = {<p>How pulsed contractile dynamics drive the remodeling of cell and tissue topologies in epithelial sheets has been a key question in development and disease. Due to constraints in imaging and analysis technologies, studies that have described the in\&nbsp;vivo mechanisms underlying changes in cell and neighbor relationships have largely been confined to analyses of planar apical regions. Thus, how the volumetric nature of epithelial cells affects force propagation and remodeling of the cell surface in three dimensions, including especially the apical-basal axis, is unclear. Here, we perform lattice light sheet microscopy (LLSM)-based analysis to determine how far and fast forces propagate across different apical-basal layers, as well as where topological changes initiate from in a columnar epithelium. These datasets are highly time- and depth-resolved and reveal that topology-changing forces are spatially entangled, with contractile force generation occurring across the observed apical-basal axis in a pulsed fashion, while the conservation of cell volumes constrains instantaneous cell deformations. Leading layer behaviors occur opportunistically in response to favorable phasic conditions, with lagging layers "zippering" to catch up as new contractile pulses propel further changes in cell topologies. These results argue against specific zones of topological initiation and demonstrate the importance of systematic 4D-based analysis in understanding how forces and deformations in cell dimensions propagate in a three-dimensional environment.</p>
},
	issn = {1879-0445},
	doi = {10.1016/j.cub.2024.06.017},
	url = {https://www.doi.org/10.1016/j.cub.2024.06.017},
	author = {Vanderleest, Timothy E and Xie, Yi and Budhathoki, Rashmi and Linvill, Katie and Hobson, Chad and Heddleston, John and Loerke, Dinah and Blankenship, J Todd}
}
