Bioimage informatics

Blood vessels tracing in 3D image from 3D Gaussian blurring (user defined radius), local thresholding (user defined radius and offset) and 3D skeletonization. Dockerized version for BIAFLOWS,

Blood vessels tracing in 3D image from Tubeness filtering (user defined scale), 3D opening (radius set to 2), thresholding (user defined level) and 3D skeletonization.

3D Neuron Tracing using Dockerized version of Vaa3D Minimum Spanning Tree (MST).

Vaa3d All-Path-Pruning 2.0 (APP2) dockerised workflow for BIAFLOWS.

Nuclei tracking in 2D time-lapse with Octave tracker (adapted from Matlab LOBSTER version).