id.spots: Spot Identifier

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

Spot Identifier

Description

A function to identify particles of interest from the stacked tiff microscopy image file of a single-molecule biophysics experiment, and to export signal vs time data for those particles.

Usage

id.spots(time.step,path.to.file='./',file.name=NULL,spot.box=6,spot.radius=6,spot.min=NULL,spot.max=Inf,spot.picking='composite')

Arguments

time.step	A single numerical value, representing the exposure time-step between images in the input file.
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	The name of the tiff file that contains the stacked images to be analyzed. DEFAULT = (any tiff file)
spot.box	A single numerical value, representing the box radius used to scan for local maxima during particle identification. DEFAULT = 6.
spot.radius	A single numerical value, representing the radius (number of pixels) around particles' maxima to be numerically integrated. DEFAULT = 6.
spot.min	A single numerical value, representing the minimum integration volume for identification as a particle. DEFAULT = 200 (spot.picking='comopsite') or 0 (spot.picking='all.frames').
spot.max	A single numerical value, representing the maximum integration volume for identification as a particle. DEFAULT = Inf.
spot.picking	A single character string, designating the spot-picking approach to be used; can be 'composite' (spots are identified on a composite image and filtered by integration volume on the composite image) or 'all.frames' (spots are identified on a composite image then filtered by integration volume on the composite image and dynamic integration volume across all image slices). DEFAULT = 'composite'.

Value

Returns a list with the following components: composite image data = a numerical matrix containing data for a composite image of parent microscopy images, initial particle summary = a data frame containing indices and volume information for the identified particles, particle traces = a matrix providing signal vs time traces for all identified particles, & particle images data = an array providing image data for identified particles across time frames.

Files:

initial_particle_summary.txt	Contains indices and volume information for the identified particles.
initial_particle_traces.txt	Contains signal vs time traces for all identified particles.
Initial-Particle_Data.RData	Contains information from the analysis, including composite image data, initial particle summary data, particle image data, exposure time between images, number of frames, pixel dimensions of images, and radius of integration box.

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