get_blobs {synapsis} | R Documentation

## get_blobs

### Description

Makes mask of all objects bright enough to be classified as a cell cadidate

### Usage

    get_blobs(
      img_orig,
      blob_factor,
      bg_blob_factor,
      offset,
      final_blob_amp,
      brush_size_blob,
      sigma_blob,
      watershed_tol,
      watershed_radius,
      crowded_cells,
      annotation
    )

### Arguments

`img_orig` | Original image
`blob_factor,` | Contrast factor to multiply original image by before smoothing/smudging
`bg_blob_factor,` | Contrast factor to multiply original image by to take background. Used prior to thresholding.
`offset,` | Pixel value offset from bg_blob_factor. Used in thresholding to make blob mask.
`final_blob_amp,` | Contrast factor to multiply smoothed/smudged image. Used in thresholding to make blob mask.
`brush_size_blob,` | Brush size for smudging the synaptonemal complex channel to make blobs
`sigma_blob,` | Sigma in Gaussian brush for smudging the synaptonemal complex channel to make blobs
`watershed_tol` | Intensity tolerance for watershed method. Defaults to 0.05.
`watershed_radius` | Radius (ext variable) in watershed method used in strand channel. Defaults to 1 (small)
`crowded_cells` | TRUE or FALSE, defaults to FALSE. Set to TRUE if you have many cells in a frame that almost touch
`annotation,` | Choice to output pipeline choices (recommended to knit) have many cells in a frame that almost touch

### Value

Mask with cell candidates

[Package synapsis version 1.0.0 Index]