Determination of the positions and orientations of concentrated rod-like colloids from 3D microscopy data

摘要: Confocal microscopy in combination with real-space particle tracking has proven to be a powerful tool scientific fields such as soft matter physics, materials science and cell biology. However, 3D of anisotropic particles concentrated phases remains not optimized compared algorithms for spherical particles. To address this problem, we developed new particle-fitting algorithm that can extract the positions orientations fluorescent rod-like from three dimensional confocal data stacks. The is tailored work even when signals overlap considerably threshold method subsequent clusters analysis alone do suffice. We demonstrate our correctly identifies all five coordinates uniaxial both disordered phase liquid-crystalline smectic-B phase. Apart images, also used identify nanorods electron tomography reconstructions. Lastly, determined accuracy using simulated experimental data-stacks diffusing silica rods dilute suspension. This novel allows study structure dynamics dense (such nematic, smectic crystalline phases) well glass transition dimensions on single level.