spotCoords: spotCoords
In CONFESS: Cell OrderiNg by FluorEScence Signal

It estimates the spot location statistics by fluorescence signal in each channel. Then, it integrates the channel-specific data into a single estimate

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spotCoords(centerR, centerG, origImg, chaImgs, minDiff, despeckle,
  ImgLimits, BFarea, chip.type, separator, image.type,
  show.possible.contamination)

`centerR`	Data matrix. The location statistics of one channel.
`centerG`	Data matrix. The location statistics of the other channel.
`origImg`	Data matrix. The original BF image to be read and processed.
`chaImgs`	List. A list of the red and green channel images (data matrices) of a sample
`minDiff`	Float. the mu_hat of the H0: image-to-noise ratio = log(foreground_signal) - log(background_signal) = mu_hat. Rejection of H0 implies that the identified spot is brighter than background. Default is 0.5.
`despeckle`	Logical. If TRUE, the BF image is descpeckled.
`ImgLimits`	Integer. It instructs the algorithm to find spots in a certain central image area. For example, for a 512 x 512 image with ImgLimits = 50, it will search for spots in the central area [ImgLimits:(512-ImgLimits),ImgLimits:(512-ImgLimits)] of the image matrix.
`BFarea`	Integer. Defines a rectangular pseudo-spot size whose fluorescence will be estimated.
`separator`	Character string. Removes the Bright Field ("BF") and channel indicators from the image file names.
`image.type`	Character string. A triplet of IDs to characterize the type of images under study. They refer to the ImageType part of the original image or txt file names.
`show.possible.contamination`	Logical. If TRUE it reports all identified unmatched spots in both channels.
`type`	Character string. It specifies the type of Fluidigm chip to be analyzed.