TrakEM2 is an open-source software designed for the systematic reconstruction of neuronal circuits from large electron microscopical and optical volume images. It addresses the challenges of image volume composition, reconstruction of neuronal arbors, and annotation of synapses using both manual and semi-automatic methods. The software enables efficient manipulation, visualization, and analysis of neuronal components, and supports hierarchical organization of reconstructions for meaningful analysis. TrakEM2 has been successfully applied in various neuroscience studies, including the reconstruction of neuronal circuits in *Drosophila* and *C. elegans*. The software is optimized for tera-scale serial section EM image data sets and is integrated with Fiji, an open-source image processing application, to facilitate data handling and analysis.TrakEM2 is an open-source software designed for the systematic reconstruction of neuronal circuits from large electron microscopical and optical volume images. It addresses the challenges of image volume composition, reconstruction of neuronal arbors, and annotation of synapses using both manual and semi-automatic methods. The software enables efficient manipulation, visualization, and analysis of neuronal components, and supports hierarchical organization of reconstructions for meaningful analysis. TrakEM2 has been successfully applied in various neuroscience studies, including the reconstruction of neuronal circuits in *Drosophila* and *C. elegans*. The software is optimized for tera-scale serial section EM image data sets and is integrated with Fiji, an open-source image processing application, to facilitate data handling and analysis.