Neural circuit reconstruction

Neural circuit reconstruction is the reconstruction of the detailed circuitry of the nervous system (or a portion of the nervous system) of an animal. It is sometimes called EM reconstruction since the main method used is the electron microscope (EM). 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.

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

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

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.

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.

Understanding the detailed operation of the reconstructed networks also requires knowledge of gap junctions (hard to see with existing techniques), 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.

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