Automated

neuTube is a collection of neuron reconstruction tools from fluorescence microscope images. It has an interactive system with a 3D viewer, which can be clicked in 3D and perform neuron tracing automatically and semi-automatically. It can automatically recognize branching points as junctions. Traced neurons can be exported to swc format, which could be imported by various software packages. neuTube has Win and Mac OS standalone executable builds and may also be installed by manual compilation. In addition, neuTube can be used as a plugin in Vaa3D.

to be completed

This plugin applies the Hough Transform for Circles to an 8-Bit image, shows the resulting Hough Space in a new window and marks the centers of the found circles.

ABSnake can segment complex structures in 2D images as well as 3D or temporal images. It uses a new active contour model based on a geometrical approach for correctly following invaginated structures.

LocAlization Microscopy Analyzer (LAMA) is a software tool that contains several well-established data post processing algorithms for single-molecule localization microscopy (SMLM) data. LAMA has implemented algorithms for cluster analysis, colocalization analysis, localization precision estimation and image registration. LAMA works with a graphical user interface (GUI), and accepts simple input data formats as supported by various single- molecule localization software tools.