auto_crop_fast {synapsis} | R Documentation |
crop an image around each viable cell candidate.
auto_crop_fast( img_path, max_cell_area = 20000, min_cell_area = 7000, mean_pix = 0.08, annotation = "off", blob_factor = 15, bg_blob_factor = 10, offset = 0.2, final_blob_amp = 10, test_amount = 0, brush_size_blob = 51, sigma_blob = 15, channel3_string = "DAPI", channel2_string = "SYCP3", channel1_string = "MLH3", file_ext = "jpeg", third_channel = "off", cell_aspect_ratio = 2, strand_amp = 2, path_out = img_path, resize_l = 720, crowded_cells = "FALSE", watershed_radius = 50, watershed_tol = 0.2, cropping_factor = 1.3 )
img_path, |
path containing image data to analyse |
max_cell_area, |
Maximum pixel area of a cell candidate |
min_cell_area, |
Minimum pixel area of a cell candidate |
mean_pix, |
Mean pixel intensity of cell crop (in SYCP3 channel) for normalisation |
annotation, |
Choice to output pipeline choices (recommended to knit) |
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. |
test_amount, |
Optional number of first N images you want to run function on. For troubleshooting/testing/variable calibration purposes. |
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 |
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. |
cell_aspect_ratio |
Maximum aspect ratio of blob to be defined as a cell |
strand_amp |
multiplication of strand channel for get_blobs function. |
path_out, |
user specified output path. Defaults to img_path |
resize_l |
length for resized image |
crowded_cells |
TRUE or FALSE, defaults to FALSE. Set to TRUE if you have many cells in a frame that almost touch |
watershed_radius |
Radius (ext variable) in watershed method used in strand channel. Defaults to 1 (small) |
watershed_tol |
Intensity tolerance for watershed method. Defaults to 0.05. |
cropping_factor |
size of cropping window square, as factor of characteristic blob radius. Defaults to 1. May need to increase if using watershed. |
This function takes all images in a directory, and crops around individual cells according to the antibody that stains synaptonemal complexes e.g. SYCP3. First, it increases the brightness and smudges the image with a Gaussian brush, and creates a mask using thresholding (get_blobs). Then it deletes cell candidates in the mask deemed too large, too small, or too long (keep_cells). Using the computeFeatures functions from EBImage to locate centre and radius, the cropping area is determined and the original image cropped. These images are saved in either a user specified directory, or a crops folder at the location of the image files.
cropped synaptonemal complex and foci channels around single cells, regardless of stage
Lucy McNeill
demo_path = paste0(system.file("extdata",package = "synapsis")) auto_crop_fast(demo_path, annotation = "on", max_cell_area = 30000, min_cell_area = 7000, file_ext = "tif",crowded_cells = TRUE)