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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. |
Updated