Brain-wide 3D imaging of neuronal activity in Caenorhabditis elegans with sculpted light

Schrodel, T., Prevedel, R., Aumayr, K., Zimmer, M., Vaziri, A. (2013). Brain-wide 3D imaging of neuronal activity in C. elegans with sculpted light. Nature Methods.

WF-TeFo (wide-field temporal focusing) imaging of nuclear based calcium indicator can see 70% of c. elegans neurons.

Ok, from what it sounds like this technique is that there is a femto-second laser and the beam is broken up spectrally through a grating. This spreads the frequencies of light in time and space, and only at the focus does all of the laser light come back together. This enhances the 2-photon absorption at the focus, and diminishes any outside absorption. This is because the outside is seeing temporally offset waves of light at different frequencies. They acquire volumes at 5Hz.

So then they start looking at some of the activity, and group the neural responses by "agglomerative hierarchical clustering", which is apparently just the matlab function: linkage. The distance matrix is based on the correlation/covariance matrix of the responses over time.