crop_single_object_fast {synapsis} | R Documentation |
Creates mask for every individual cell candidate in mask
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 )
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. |
Crops around all candidates in both channels