annotate_foci_counting {synapsis} | R Documentation

## annotate_foci_counting

### Description

Contains all plotting routines for count foci annotation

### Usage

    annotate_foci_counting(
      img_file,
      cell_count,
      img_orig,
      img_orig_foci,
      artificial_amp_factor,
      strands,
      coincident_foci,
      foci_label,
      alone_foci,
      percent_px,
      foci_per_cell
    )

### Arguments

`img_file` | cell's file name
`cell_count` | unique cell counter
`img_orig` | original strand crop
`img_orig_foci` | cropped foci channel
`artificial_amp_factor` | amplification factor
`strands` | black white mask of strand channel
`coincident_foci` | mask of overlap between strand and foci channel
`foci_label` | black and white mask of foci channel
`alone_foci` | estimated number of foci that are NOT on a strand.
`percent_px` | percentage of foci mask that coincides with strand channel small number indicates potentially problematic image.
`foci_per_cell` | number of foci counted per cell

### Value

displays key steps from raw image to coincident foci count

[Package synapsis version 1.0.0 Index]