FRET.align: Image Alignment

In whemphil/SMBalyze: A Package of Tools to Analyze Images from TIRF-Microscopy Single-Molecule Experiments

Image Alignment

Description

A function to align reference images for dual camera single-molecule microscopy experiments.

Usage

FRET.align(path.to.file='./',file.name=NULL,alignment=list('r'=0.97,'theta'=7),search.radius=6,integration.radius=6,spot.min=NULL,spot.max=Inf)

Arguments

path.to.file	Path to the directory where the import file(s) are located. Write-out files will also be exported to this directory. DEFAULT = (working directory)
file.name	A character string vector of length two, indicating the names of the tiff files containing the stacked reference images to be aligned – should be in the order Cy3-camera then Cy5-camera images. DEFAULT = (all tiff files in directory, sorted alphabetically)
alignement	Either a list containing numeric values for the variables 'r' and 'theta', which will be used as the starting parameter estimates for regression-based auto alignment, or the character string 'manual', which will default to no alignment adjustment and begin an iterative manual alignment. DEFAULT = (auto-alignment with empirically determined starting estimates)
search.radius	A single numerical value, representing the box radius used to scan for local maxima during spot identification. DEFAULT = 6.
integration.radius	A single numerical value, representing the radius (number of pixels) around spots' maxima to be numerically integrated. DEFAULT = 6.
spot.min	A single numerical value, representing the minimum integration volume for identification as a spot. DEFAULT = (5-fold the scaled image background).
spot.max	A single numerical value, representing the maximum integration volume for identification as a spot. DEFAULT = Inf.

Value

Returns nothing.

Files:

Alignment_Parameters.RData

Contains the alignment parameters 'r' and 'theta' – used to align images in downstream analyses.

whemphil/SMBalyze documentation built on April 16, 2023, 6:26 p.m.