Developed Napari plugins
Developed plugins hosted on Napari hub
vollseg-napari
VollSeg is more than just a single segmentation algorithm; it is a meticulously designed modular segmentation tool tailored to diverse model organisms and imaging methods. While a U-Net might suffice for certain image samples, others might benefit from utilizing StarDist, and some could require a blend of both, potentially coupled with denoising or region of interest models. The pivotal decision left to make is how to select the most appropriate VollSeg configuration for your dataset. Click here to find out about different modes of operation of VollSeg.
vollseg-napari-trackmate
Track analysis using TrackMate xml and csv generated tracks using NapaTrackMater as the base library. It can visualize the tracks obtained using TrackMate algorithms in Napari, additionally an autoencoder models can also be used to compute additional shape and dynamic features for cell fate quantification.
vollseg-napari-mtrack
Segment kymographs of microtubules, actin filaments and perform Ransac based fits to compute dynamic instability parameters for individual kymographs and also in batch
vollseg-napari-btrack
Skeletonize tissues and perform tracking of the dynamic end points for quantifying branch morphodynamics of cancerous tissues.
