dots_coords_calculations

pysmFISH.dots_coords_calculations.all_dots_removal(combination, all_removed)

Function to remove the overlapping dots.

combination: dict

Dictionary containing hybridization, gene, registation data of the current hybridization and the registerd coords of the selected peaks for the current gene.

all_removed: dict

Dictionary with the coords of the dots that need to be removed or will be kept for all the images

all_coords_cleaned: set

Set containing the coords of the dots after removal of the overlapping ones. No image pos info is kept.

removed_coords: set

Set containing the coords of the dots removed. No image pos info is kept.

all_coords: set

Set containing the coords of all the aligned dots before removal of the overlapping ones. No image pos info is kept.

pysmFISH.dots_coords_calculations.catch_duplicated_dots(combination, image_list, overlapping_percentage, image_size, pxl)

Function used to identify dots that need to be removed or kept in the overlapping region between two images. The overlapping used is calculated according to the stitching information.

combination: dict

Dictionary containing hybridization, gene, registation data of the current hybridization and the registerd coords of the selected peaks for the current gene.

image_list: tuple

Tuple with the index of the the images with ooverlap

overlapping_percentage: float

Percentage of overlap extracted from the Experimental_metadata.yaml.

image_size: int

Size of the image (consider a square image).

pxl: int

Radius of pixel used to create the nhood.

overlapping_result_dict: dict

Dictionary with the coords of the dots that need to be removed or will be kept for the selected pair of images.

pysmFISH.dots_coords_calculations.dots_removing(overlapping_list, pxl)

Function used to identify matching dots that are present in overlapping imaging areas.

overlapping_list: list

List with the coords of the dots located in the overlapping region.

pxl: int

Radius of pixel used to create the nhood.

removed_dots: set

Set with the coords of the removed dots.

single_dots: set

Set with the coords of dots in the overlpping region that do not overlap with any other dot.

pysmFISH.dots_coords_calculations.function_to_run_dots_removal_parallel(combination, overlapping_percentage, image_size, pxl)

Function to run the overlapping dots removal in parallel

combination: dict

Dictionary containing hybridization, gene, registation data of the current hybridization and the registerd coords of the selected peaks for the current gene.

overlapping_percentage: float

Percentage of overlap extracted from the Experimental_metadata.yaml

image_size: int

Size of the image (consider a square image)

plx: int

Radius of pixel used to create the nhood.

all_coords_cleaned_dict: dict

Dictionary with the dots coords of the processed gene before and after removal plus the coords of the removed dots.

pysmFISH.dots_coords_calculations.hood_creation(coords, pxl)

Function that creates the neighborood of coords that are considered same RNA molecule. It is the region used to eliminate overlapping dots.

coords: np.array

Array of the [r,c] of the dots.

pxl: int

Radius of pixel used to create the nhood.

hood: set

Set with the coords of the neighborhood of the selected dot.

pysmFISH.dots_coords_calculations.overlapping_images_grid(micData)

Function used to generate all possible overlapping images (neighborhood).

micData: dict

Dictionary extracted from the reg_data and containing the infomation regarding tiles organization

all_nhood: list

List with all the overlapping tiles combinations

pysmFISH.dots_coords_calculations.processing_combinations(hybridizations, aligned_peaks_dict)

Function used to create a list of tuples containing the pair hybridization and gene (Ex. (Hybridization1, Gfap)) that will be used to process the dots removal in parallel.

hybridizations: list

List of the hybridization to process (ex. [Hybridization1, Hybridization2]).

aligned_peaks_dict: dict

Dictionary containing only the coords of the selected peaks after registration (still with pos information).

combinations: list

List containing the pairs hybridization and gene (Ex. (Hybridization1, Gfap))

pysmFISH.dots_coords_calculations.register_dots_coords(reg_data, hybridization, gene, all_raw_counts)

Function to register the coords of the dots according to the new coords of the corner of the images calculated after registration of the stitched images.

reg_data: dict

Dictionary containing the coords and the joining data calculated after the registration.

hybridization: str

Name of the hybridization processed (Ex. Hybridization2)

gene: str

Processed gene name (Ex. Gfap)

all_raw_counts: dict

Dictionary with all the raw counting from all the hybridizations

all_raw_counts: dict

Dictionary with all the raw counting from all the hybridizations. Added a subgroup containing the aligned coords.