pyElectrode

    Neurophysiogists want to place the tip of an electrode in a specific area of the brain. The coordinates of this area can be obtained from standard stereotaxic atlases. However, individual brains will not align with the atlas exactly. Additionally, for chronic recordings, electrodes are placed relative to a chamber attached to the animal's skull. Thus, the user wants to know where the area of interest is in chamber coordinates, not stereotaxic coordinates. After the chamber has been attached an MRI is often made. This assists in electrode placement, as the location of a target relative to the chamber can be determined based on the atlas. However, doing this in practice requires rough estimation or cumbersome calculations. PyElectrode provides a graphical display that helps the user locate the chamber center, and does the calculations to convert between stereotaxic and chamber coordinates. It can also keep track the electrode tip online, and can mark electrode positions on an oriented slice that is suitable for publication.
    GitHub: https://github.com/pierredaye/pyElectrode
    NEI: http://datashare.nei.nih.gov (click on Laboratory of Sensorimotor Research (LSR) to open a tab containing pyElectrode)