failurecase

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Description

Another helper to re-estimate the spot location or find the capture site location (BF image modelling).

Usage

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failurecase(img, pattern.search, despeckle, ImgLimits, chip.type, separator,
  image.type)

Arguments

pattern.search

Integer. A cutoff to find horizontal and vertical lines on the chip.

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.

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.

origImg

Data matrix. The original BF image to be read and processed.

type

Character string. It specifies the type of Fluidigm chip to be analyzed.

Value

Location statistics and characteristic lines of BF image modelling

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