Neural circuit reconstruction


Neural circuit reconstruction is the reconstruction of the detailed circuitry of the nervous system of an animal. It is sometimes called EM reconstruction since the main method used is the electron microscope. This field is a close relative of reverse engineering of human-made devices, and is part of the field of connectomics, which in turn is a sub-field of neuroanatomy.

Model systems

Some of the model systems used for circuit reconstruction are the fruit fly, the mouse, and the nematode C. elegans.

Sample preparation

The sample must be fixed, stained, and embedded in plastic.

Imaging

The sample may be cut into thin slices with a microtome, then imaged using transmission electron microscopy. Alternatively, the sample may be imaged with a scanning electron microscope, then the surface abraded using a focused ion beam, or trimmed using an in-microscope microtome. Then the sample is re-imaged, and the process repeated until the desired volume is processed.

Image processing

The first step is to align the individual images into a coherent three dimensional volume.
The volume is then annotated using one of two main methods. The first manually identifies the skeletons of each neurite. The second techniques uses computer vision software to identify voxels belonging to the same neuron, which are then corrected in the process of proofreading.

Notable examples

Understanding the detailed operation of the reconstructed networks also requires knowledge of gap junctions, the identity of neurotransmitters and the locations and identities of receptors. In addition, neuromodulators can diffuse across large distances and still strongly affect function. Currently these features must be obtained through other techniques. Expansion microscopy may provide an alternative method.