make_strand_mask {synapsis} | R Documentation

## make_strand_mask

### Description

creates strand mask for strand channel crop

### Usage

    make_strand_mask(
      offset_px,
      stage,
      img_orig,
      disc_size,
      brush_size,
      brush_sigma
    )

### Arguments

`offset_px,` | Pixel value offset used in thresholding of synaptonemal complex channel
`stage,` | meiosis stage of interest. Currently count_foci determines this with thresholding/ object properties in the synaptonemal complex channel by previosly calling the get_pachytene function. Note that if using this option, the count_foci function requires that the input directory contains a folder called “pachytene” with the crops in it.
`img_orig` | original strand crop
`disc_size` | size of disc for local background calculation in synaptonemal complex 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.

### Value

strand mask

[Package synapsis version 1.0.0 Index]