Table 1: Glossary.

Here we define some terms that will be used regularly throughout our protocols.

Channel	Denotes fluorescence intensity data collected from a specific wavelength. Most acquisition systems provide data from one to three channels/wavelengths.
Trace	A time series of fluorescence data, which can be plotted as a continuous line with time on the x-axis and fluorescence intensity on the y-axis as in Fig 4–8. Traces can be plotted from any channel in which fluorescence data was collected and can include raw, normalized, or motion corrected data.
Signal	Refers to fluorescent information collected from the excitation wavelength of your sensor of interest. For instance, for GCaMP, this would be the trace collected from the 470 nm (or similar) wavelength. The raw signal trace will include deflections that represent both true sensor-mediated changes in fluorescence and those introduced from motion artifacts.
Reference	Refers to fluorescent information collected at a signal independent excitation wavelength. See Identifying a reference for more information
Linearization	Both signal and reference are linearized to adjust the trace for photobleaching of the fiber optic and fluorescent sensor (Fig 4a/b).
Motion-corrected	Following normalization, the reference signal is used to remove motion artifacts from the raw signal, yielding an adjusted trace that can be most accurately interpreted in relation to behavior or other variables (Fig 4c/d).
Normalization	A flexible process that can combines linearization and motion-correction to produce a ΔF/F trace from your raw signal trace.
Object	A compilation of all the information and variables associated with one recording from one fiber, including all recording wavelengths and matched behavioral or other data. For a list of data and variables that can be included in an object see Table 2.
Card	A component contained in an individual box within the GUI and used to do a specific task or analysis.
Widget	A subcomponent in a card that allows user input. These include the choose file button, drop down menus and text input boxes.