make_foci_mask {synapsis} | R Documentation

## make_foci_mask

### Description

creates foci mask for foci channel crop

### Usage

    make_foci_mask(
      offset_factor,
      bg,
      crowded_foci,
      img_orig_foci,
      brush_size,
      brush_sigma,
      disc_size_foci
    )

### Arguments

`offset_factor` | Pixel value offset used in thresholding of foci channel
`bg` | background value- currently just mean pixel value of whole image
`crowded_foci` | TRUE or FALSE, defaults to FALSE. Set to TRUE if you have foci > 100 or so.
`img_orig_foci` | cropped foci channel
`brush_size` | size of brush to smooth the foci channel. Should be small to avoid erasing foci.
`brush_sigma` | sigma for Gaussian smooth of foci channel. Should be small to avoid erasing foci.
`disc_size_foci` | size of disc for local background calculation in foci channel

### Value

foci mask

[Package synapsis version 1.0.0 Index]