get_foci_per_cell {synapsis} | R Documentation

## get_foci_per_cell

### Description

creates mask for coincident foci

### Usage

    get_foci_per_cell(
      img_file,
      offset_px,
      stage,
      strands,
      watershed_stop,
      foci_label,
      annotation,
      cell_count,
      img_orig,
      img_orig_foci,
      artificial_amp_factor,
      coincident_foci
    )

### Arguments

`img_file` | cell's file name
`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.
`strands` | black white mask of strand channel
`watershed_stop` | Stop default watershed method with "on"
`foci_label` | black and white mask of foci channel
`annotation,` | Choice to output pipeline choices (recommended to knit)
`cell_count` | unique cell counter
`img_orig` | original strand crop
`img_orig_foci` | cropped foci channel
`artificial_amp_factor` | amplification factor
`coincident_foci` | mask of coincident foci

### Value

number of foci per cell

[Package synapsis version 1.0.0 Index]