counting¶

pysmFISH.counting.counting_only(fpath_img_to_count, counting_gene_dirs, min_distance=5, stringency=0)[source]¶

Function used to clean the images and to count the smFISH dots. It is designed to process in parallel all the tmp file images stored as numpy arrays after conversion from the microscope format.

fpath_img_to_count: str: path to the file to process
counting_gene_dirs: list: list of the paths of the directories where the countings of the filtered images are saved.
min_distance: int: minimum distance between dots.
stringency: int: stringency use to select the threshold used for counting.

pysmFISH.counting.filtering_and_counting(fpath_img_to_filter, filtered_png_img_gene_dirs, filtered_img_gene_dirs, counting_gene_dirs, illumination_correction=False, plane_keep=None, min_distance=5, stringency=0, skip_genes_counting=None, skip_tags_counting=None)[source]¶

Function used to clean the images and to count the smFISH dots. It is designed to process in parallel all the tmp file images stored as numpy arrays after conversion from the microscope format.

fpath_img_to_filter: str: path to the file to process
filtered_png_img_gene_dirs: list: list of the paths of the directories where the filtered images as are saved as pngs.
filtered_img_gene_dirs: list: list of the paths of the directories where the filtered images are saved as .npy.
counting_gene_dirs: list: list of the paths of the directories where the countings of the filtered images are saved.
illumination_correction: bool: if True the illumination correction is run on the dataset.
plane_keep: list: start and end point of the z-planes to keep. Default None keep all the planes (ex. [2,-3]).
min_distance: int: minimum distance between dots.
stringency: int: stringency use to select the threshold used for counting.
skip_genes_counting: list: list of the genes to skip for counting count.
skip_tags_counting: list: list of the tags inside the genes/stainings name to avoid to count.

pysmFISH.counting.filtering_and_counting_experiment(fpath_img_to_filter, filtered_dir_path, counting_dir_path, exp_name, add_slash, plane_keep=None, min_distance=5, stringency=0)[source]¶

Function to filter and count dots in the images generated from a small experiment.

fpath_img_to_filter: str: path to the file to process.
filtered_dir_path: list: list of the paths of the directories where the filtered images are saved.
counting_dir_path: list: list of the paths of the directories where the counting of filtered images are stored.
exp_name: str: name of the experiment to process.
plane_keep: list: start and end point of the z-planes to keep. Default None keep all the planes (ex. [2,-3]).
min_distance: int: minimum distance between dots.
stringency: int: stringency use to select the threshold used for counting.

pysmFISH.counting.filtering_and_counting_ill_correction(fpath_img_to_filter, illumination_function, filtered_png_img_gene_dirs, filtered_img_gene_dirs, counting_gene_dirs, illumination_correction=False, plane_keep=None, min_distance=5, stringency=0, skip_genes_counting=None, skip_tags_counting=None)[source]¶

Function used to clean the images and to count the smFISH dots. Designed to work in parallel processing all the tmp file images stored as numpy arrays after conversion from the microscope format.

fpath_img_to_filter: str: path to the file to process.
illumination_function: np.array float64: illumination function.
filtered_png_img_gene_dirs: list: list of the paths of the directories where the filtered images as are saved as pngs.
filtered_img_gene_dirs: list: list of the paths of the directories where the filtered images are saved as .npy.
counting_gene_dirs: list: list of the paths of the directories where the countings of the filtered images are saved.
illumination_correction: bool: if True the illumination correction is run on the dataset.
plane_keep: list: start and end point of the z-planes to keep. Default None keep all the planes (ex. [2,-3]).
min_distance: int: minimum distance between dots.
stringency: int: stringency use to select the threshold used for counting.
skip_genes_counting: list: list of the genes to skip for counting count.
skip_tags_counting: list: list of the tags inside the genes/stainings name to avoid to count.