Advanced: Analysis Metrics

𝑓(Cell) provides numerous built-in metrics to analyze the summarized iORG data. These metrics can be extracted from individual query locations, or all query locations (referred to as the "population" summary).

Key	Parent Key	Type	Values	Description
"type"	"metrics"	["string list"]	**null**	A list of metrics that will be extracted. This can be amplitude ("amp"), log amplitude ("logamp"), area under the response ("aur"), amplitude-based implicit time ("amp_imp_time"), and half-amplitude-based implicit time ("halfamp_imp_time"). Each of these are described in detail below.
"measured"	"metrics"	"string"	(**stim-relative**, absolute)	How the metric extraction window is determined. By default, we use stim-relative, which makes all values in the following sections calculated relative to when the stimuli are delivered. Otherwise, absolute determines the window from the beginning of the dataset, in frame indexes.
"prestim"	"metrics"	[float, float]	**[-1, 0]**	The pre-stimulus window used for all metric calculations. The two values must monotonically decrease.
"poststim"	"metrics"	[float, float]	**[0, 1]**	The post-stimulus window used for all metric calculations. The two values must monotonically increase.
"units"	"metrics"	"string"	(**time**, frames)	What units the above start and stop values are in. Defaults to time in seconds.

Metric Derivations

Amplitude is defined as: $A = \overline{I_{post}} - \overline{I_{pre}}$

Where the average intensity of the pre-stimulus summary signal \overline{I_{pre}}$ is:

$$\overline{I_{pre}}=\frac{1}{N_{pre}} \displaystyle\sum_{t=start_{pre}}^{end_{pre}} I(t)$$

$N_{pre}$ is the number of valid pre-stimulus data points, $s_{pre}$ and $e_{pre}$ are the starting and ending timepoints of the pre-stimulus signal, respectively, and $I(t)$ is the summary signal as a function of time $t$.

Similarly, the average intensity of the post-stimulus summary signal $I_{post}$ is:

$$\overline{I_{post}}=\frac{1}{N_{post}} \displaystyle\sum_{t=start_{post}}^{end_{post}} I(t)$$

$N_{post}$ is the number of valid post-stimulus data points, $s_{post}$ and $e_{post}$ are the starting and ending timepoints of the post-stimulus signal.

The area under the response $AUR$ is defined as:

$$\$AUR\$=\int_{t=start_{post}}^{end_{post}} I(t)$$

Where integration is perform via the trapezoid method. Note: If a time point does not exist at the end of the post-stim window, then one is created via linear interpolation.

Log Amplitude is defined simply as: $\log{A}$

Implicit time ($T_{A}$) is defined as the timestamp at which $I_{post}$ reaches 99% of $A$.
Note: This value is determined precisely via interpolation of the two neighboring points.

Half-Amplitude Implicit time ($T_{\frac{A}{2}}$) is defined as the timestamp at which $I_{post}$ reaches 50% of $A$.
Note: This value is determined precisely via interpolation of thetwo neighboring points.

Example of Metric extraction