scalpelStep1: Perform Step 1 of SCALPEL.
In scalpel: Processes Calcium Imaging Data

Description Usage Arguments Details Value See Also Examples

This step involves constructing a spatial component dictionary. We apply a simple image segmentation procedure to each frame of the video in order to derive a dictionary of preliminary dictionary elements. Ideally, this dictionary is a superset of the true spatial components.

scalpelStep1(
  step0Output,
  minSize = 25,
  maxSize = 500,
  maxWidth = 30,
  maxHeight = 30,
  thresholdVec = NULL
)

`step0Output`	An object of class `scalpel` or `scalpelStep0`, which result from running the `scalpel` or `scalpelStep0` functions, respectively.
`minSize, maxSize`	The minimum and maximum size, respectively, for a preliminary dictionary element with default values of 25 and 500, respectively.
`maxWidth, maxHeight`	The maximum width and height, respectively, for a preliminary dictionary element with default values of 30.
`thresholdVec`	Optional advanced user argument: A vector with the desired thresholds to use for image segmentation. If not specified, the default is to use the negative of the minimum of the processed Y data (i.e., `step0Output$highThreshold`), the negative of the 0.1% quantile of the processed Y data (i.e., `step0Output$lowThreshold`), and the mean of these. These automatically chosen thresholds can also be updated using `updateThreshold`.

Several files containing data from this step and a summary of the step are saved in "outputFolder/Step1_version" where version is a 5-digit unique identifier that is automatically generated.

An object of class scalpelStep1, which can be summarized using summary, used to run SCALPEL Step 2 using scalpelStep2, or can be used with the plotting function plotCandidateFrame.

Azero: A matrix containing the preliminary dictionary elements, where the ith column of Azero is a vector of 1's and 0's, indicating whether each pixel is contained in the ith preliminary dictionary element.
AzeroFrames: A vector whose ith element gives the video frame from which the preliminary dictionary element in the ith column of Azero was derived.
AzeroThreshold: A vector whose ith element gives the threshold used to obtain the preliminary dictionary element in the ith column of Azero.
pixelsUse: A vector with the pixels (i.e., indices of the rows of Azero) that are contained in at least one preliminary dictionary element.
version: A 5-digit unique identifier for the output folder name that is automatically generated in this step.
Other elements: As specified by the user or returned from a previous step.

The entire SCALPEL pipeline can be implemented using the scalpel function. The other steps in the pipeline can be run using the scalpelStep0, scalpelStep2, scalpelStep3 functions. Results from this step can be summarized using summary, loaded at a later time using getScalpelStep1, and plotted using plotCandidateFrame.

## Not run: 
### many of the functions in this package are interconnected so the
### easiest way to learn to use the package is by working through the vignette,
### which is available at ajpete.com/software

#assumes you have run the example for the "scalpelStep0" function

#run Step 1 of SCALPEL
Step1Out = scalpelStep1(step0Output = Step0Out)
summary(Step1Out)

## End(Not run)