diff --git a/extraction/core/functions/cell.py b/extraction/core/functions/cell.py index f8b48a11088ce5700cfa170adeddea06a311a6a7..c6e7425b07bd2e6af56039fdf22fe0b63f835bd1 100644 --- a/extraction/core/functions/cell.py +++ b/extraction/core/functions/cell.py @@ -84,13 +84,13 @@ def std(cell_mask, trap_image): ## Specialised extraction functions -def foci_area_otsu(cell_mask, trap_image): - # Use otsu threshold to calculate the are of high-expression blobs inside a cell. - cell_pixels = trap_image[cell_mask] - cell_pixels = cell_pixels[~np.isnan(cell_pixels)] - threshold = threshold_otsu(cell_pixels) +# def foci_area_otsu(cell_mask, trap_image): +# # Use otsu threshold to calculate the are of high-expression blobs inside a cell. +# cell_pixels = trap_image[cell_mask] +# cell_pixels = cell_pixels[~np.isnan(cell_pixels)] +# threshold = threshold_otsu(cell_pixels) - return np.sum(cell_pixels > threshold) +# return np.sum(cell_pixels > threshold) def k2_top_median(cell_mask, trap_image):