C++

"We have developed an automatic graph algorithm, called the all-path pruning (APP), to trace the 3D structure of a neuron. To avoid potential mis-tracing of some parts of a neuron, an APP first produces an initial over-reconstruction, by tracing the optimal geodesic shortest path from the seed location to every possible destination voxel/pixel location in the image. Since the initial reconstruction contains all the possible paths and thus could contain redundant structural components (SC), we simplify the entire reconstruction without compromising its connectedness by pruning the redundant structural elements, using a new maximal- covering minimal-redundant (MCMR) subgraph algorithm. We show that MCMR has a linear computational complexity and will converge. We examined the performance of our method using challenging 3D neuronal image datasets of model organisms (e.g. fruit fly)"

This plugin can be used with default parameters or user-defined parameters.

SOAX is an open source software tool to extract the centerlines, junctions and filament lengths of biopolymer networks in 2D and 3D images. It facilitates quantitative, reproducible and objective analysis of the image data. The underlying method of SOAX uses multiple Stretching Open Active Contours (SOACs) that are automatically initialized at image intensity ridges and then stretch along the centerlines of filaments in the network. SOACs can merge, stop at junctions, and reconfigure with others to allow smooth crossing at junctions of filaments.

SOAX provides 3D visualization for exploring image data and visually checking results against the image. Quantitative analysis functions based on extracted networks are also implemented in SOAX, including spatial distribution, orientation, and curvature of filamentous structures. SOAX also provides interactive manual editing to further improve the extraction results, which can be saved in a file for archiving or further analysis. Useful for microtubules or actin filaments.

Observation: Depending on the operating system, the installation may or may not require Boost C++, ITK and VTK libraries. Windows has a standalone executable application without the need of those. 

BioImageXD is a free open source software package for analyzing, processing and visualizing multi-dimensional microscopy images. It's a collaborative project, designed and developed by microscopists, cell biologists and software engineers from the Universities of Jyväskylä and Turku in Finland, Max Planck Institute CBG in Dresden, Germany and collaborators worldwide. BioImageXD was published in the July 2012 issue of Nature Methods.

A standalone cell tracking software for single cell migration. Tracking of cells in tissue was also done in Drosophila germband.

ASAP is an open source platform for visualizing, annotating and automatically analyzing whole-slide histopathology images. It consists of several key-components (slide input/output, image processing, viewer) which can be used seperately. It is built on top of several well-developed open source packages like OpenSlide, Qt and OpenCV but also tries to extend them in several meaningful ways.