ΔF/F¶

This tool uses 2.0 compute credits per hour.

The ΔF/F algorithm normalizes each pixel value in the movie, so that it represents a deviation or change from a baseline.

This should be applied to motion corrected microscope movies to remove any remaining spatial variation in the intensity of your signal.

Inputs¶

Parameter	Required?	Default	Description
Input Movie Files	True	N/A	paths to the input movie files
Ref ΔF/F Image	True	mean	The reference image or baseline image used to compute ΔF/F

File Inputs¶

Source Parameter	File Type	File Format
Input Movie Files	miniscope_movie, miniscope_movie	isxd, isxc

Description¶

The ΔF/F algorithm first computes a baseline frame from the input movie that should represent the value of each pixel in the presence of minimal activity. Traditionally, this is the Mean frame of the movie, which is calculated by taking the mean value of each pixel across the entire movie or the Custom frame range. Using the mean as a baseline may seem counterintuitive when we expect large positive deviations due to calcium events, but it is likely that the input movie will mostly contain small, noisy negative/positive deviations from the baseline.

If the input movie exhibits a lot of activity, some mean values will be an overestimate of the baseline activity. In this case, you should consider using the Minimum frame, which is calculated by taking the minimum value of each pixel across the entire movie or the Custom frame range. Using the minimum as a baseline may seem more intuitive than using the Mean frame, but it will almost certainly be an underestimate of the baseline activity.

Each frame of the output movie is calculated as follows

\[ M'(x, y, t) = \frac{ M(x, y, t) - F_\text{baseline}(x, y) }{ F_\text{baseline}(x, y) } \; \forall (x, y, t) \]

where \(M(x, y, t)\) is the value at pixel coordinate \((x, y)\) of frame \(t\) of the movie, \(M'\) is the output movie, and \(F_\text{baseline}(x, y)\) is the value of the baseline frame at pixel coordinate \((x, y)\).

Note that the division in the calculation above means that even if the input movie \(M\) had units, the output movie \(M'\) will not. Instead, values in the output movie are unit-less. Their scale represent the relative change from the baseline image, where a value of 0.5 represents a 50% increase.