GelMetrics: An algorithm for analyzing the dynamics of gel-like phase separated condensates

Cellular compartments and organelles are essential for the spatial organization of biological matter. Recently, membraneless organelles like paraspeckles, stress granules, and Cajal bodies have garnered significant scientific interest due to their lack of membrane boundaries and crucial cellular functions. These organelles self-assemble through phase separation, a process in which a homogeneous solution separates into distinct phases. The phases most commonly encountered in cells are liquids and gels. Various microscopy techniques exist to study these phase-separated compartments. However, these are often inadequate for investigating the dynamics of gel-like condensates, where molecular motion occurs over tens of minutes rather than seconds. Here, we introduce a method to quantitatively measure the dynamics of gel-like phase-separated organelles by tracking their fluorescence signals over extended durations. We demonstrate that our algorithm can identify biological activity amidst measurement noise and estimate biophysical parameters which can provide insights into the dynamic behavior of the condensates. We validated our approach on synthetic RNA-protein granules, demonstrating its applicability both in vitro and in vivo.