get_blobs {synapsis} | R Documentation |
Makes mask of all objects bright enough to be classified as a cell cadidate
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 )
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 |
Mask with cell candidates