crop_single_object_fast {synapsis} | R Documentation

## crop_single_object_fast

### Description

Creates mask for every individual cell candidate in mask

### Usage

    crop_single_object_fast(
      retained,
      OOI_final,
      counter_final,
      img_orig,
      img_orig_foci,
      img_orig_DAPI = "blank",
      file_sc,
      file_foci,
      file_DAPI = "blank",
      cell_count,
      mean_pix,
      annotation,
      file_base,
      img_path,
      r_max,
      cx,
      cy,
      channel3_string,
      channel2_string,
      channel1_string,
      file_ext,
      third_channel,
      path_out,
      img_orig_highres,
      resize_l,
      crowded_cells,
      cropping_factor
    )

### Arguments

`retained` | Mask of cell candidates which meet size criteria. After smoothing/smudging and thresholding.
`OOI_final,` | Objects of interest count. Total number of cell candidates in retained.
`counter_final,` | Counter for single cell we are focussing on. Remove all other cells where counter_single not equal to counter_final.
`img_orig,` | description
`img_orig_foci,` | description
`img_orig_DAPI,` | description
`file_sc,` | filename of synaptonemal complex channel image
`file_foci,` | filename of foci channel image
`file_DAPI,` | filename of DAPI channel image
`cell_count,` | counter for successful crops around cells
`mean_pix,` | Mean pixel intensity of cell crop (in SYCP3 channel) for normalisation
`annotation,` | Choice to output pipeline choices (recommended to knit)
`file_base,` | filename base common to all three channels i.e. without -MLH3.jpeg etc.
`img_path,` | path containing image data to analyse
`r_max` | maximum radius of blob for cropping
`cx` | centre of blob x
`cy` | centre of blob y
`channel3_string` | Optional. String appended to the files showing the channel illuminating cell structures. Defaults to DAPI, if third channel == "on".
`channel2_string` | String appended to the files showing the channel illuminating synaptonemal complexes. Defaults to SYCP3
`channel1_string` | String appended to the files showing the channel illuminating foci. Defaults to MLH3
`file_ext` | file extension of your images e.g. tif jpeg or png.
`third_channel` | Optional, defaults to "off". Set to "on" if you would also like crops of the third channel.
`path_out,` | user specified output path. Defaults to img_path
`img_orig_highres` | the original strand image with original resolution
`resize_l` | length of square to resize original image to.
`crowded_cells` | TRUE or FALSE, defaults to FALSE. Set to TRUE if you have many cells in a frame that almost touch
`cropping_factor` | size of cropping window square, as factor of characteristic blob radius. Defaults to 1. May need to increase if using watershed.

### Value

Crops around all candidates in both channels

[Package synapsis version 1.0.0 Index]