Accessing stack meta-data

Table 1: List of meta-data provided by a FocusStack object. All the parameters listed here are FocusStack class properties, and should be assigned from meta-data stored with the data file, whenever possible.

Meta-data parameter name	Contents
Stack-global meta-data		`.fPixelsPerUM`	Spatial calibration of the stack (X and Y), in pixels per um.
`.tFrameDuration`	Acquisition time per frame, in seconds.
`.fZStep`	Z spacing between subsequent frames, in μm.
`.mfFrameShifts`	Misalignment shifts for each frame, in fractional pixels. Assigned manually, or using alignment method FocusStack/Align.
`.vfBlackTrace`	Black set-point value for each frame, in raw units. Assigned manually, or using utility method FocusStack/DefineBlackRegion.
Stimulus-related meta-data
`.tBlankTime`	Blank time between episodic visual stimuli.
`.vnStimulusIDs`	List of stimuli presented (one stimulus ID per data file). Each stimulus ID can contain a sequence of several individual stimuli.
`.nNumStimuli`	(Read-only)Total number of individual stimulus sequence IDs presented in the entire stack.
`.cvnSequenceIDs`	Cell array, each element containing a vector of stimulus sequence IDs in the order they were presented.
`.vtStimulusDurations`	Vector of stimulus sequence ID durations, in seconds. Each entry specifies the duration of the corresponding stimulus sequence ID.
`.vtStimulusStartTimes`	Vector of onset times for each individual stimulus presentation, as an offset in seconds from the first frame of the stack. Assigned manually, or computed automatically.
`.vtStimulusEndTimes`	Vector of end times for each individual stimulus presentation, as an offset in seconds from the first frame of the stack. Assigned manually, or computed automatically.
`.mtStimulusUseTimes`	Matrix of times indicating which periods of stimulus presentation should be used for analysis. Each row corresponds to a stimulus sequence ID, and is a row vector [tStartTime tStopTime], indicating offsets from the start of the presentation of the corresponding stimulus.

Table 2: List of meta-data provided by a FocusStack object (continued from Table 1). Parameters listed that specify “FSI” for access are obtained using the FocusStack/FrameStimulusInfo class method, and are computed from the parameters given in Table 1.

Meta-data parameter name	Contents
Frame-related meta-data		`vtGlobalTime`	The time in seconds since the first frame in the stack. (FSI)
`vnBlockIndex`	The index of the block (data file) the associated frame falls within. (FSI)
`vnFrameInBlock`	The index of the associated frame within the block, with the first frame given index 1. (FSI)
`vtTimeInBlock`	The time in seconds since the first frame in the block. (FSI)
`vnStimulusSeqID`	The stimulus sequence ID associated with each frame. (FSI)
`vtTimeInStimPresentation`	The time in seconds of the associated frame since the onset of the stimulus in which the frame falls. (FSI)
`vnPresentationIndex`	The index of the current stimulus presentation in the entire stack. The first stimulus is given index 1. (FSI)
`vbUseFrame`	A boolean value associated with each frame, indicating whether that frame should be used for analysis. (FSI)
`tfBlankMean`, `tfBlankStd`	Mean and standard deviation distribution of the baseline distribution assigned to a stack. Obtained by referencing a stack using `fs.BlankFrames(<stack reference>)` or by using the `FocusStack/GetCorrespondingBlankFrames` class method. The baseline distribution is assigned using the `FocusStack/AssignBlankFrame` class method.

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TwoPhotonAnalysis / Metadata

Accessing stack meta-data