dots_calling

pysmFISH.dots_calling.thr_calculator(filtered_img, min_distance, stringency)

Function used to calculate the threshold to use for the dots counting in a 2D image.

filtered_img: np.array float64

preprocessed image used to count the dots.

min_distance: int

minimum distance that two maxima need to have in order to be defined as separete peaks.

stringency: int

integer used to select the stringency of the generated threshold. By adding stringency to the thr_idx we can select a Thr with higher value from the thr_array.

counting_dict : dict

dictionary containing all the counting infos: selected_thr: float64

Thr used for counting after application of the stringency.

calculated_thr: float64

Calculated Thr

selected_peaks: int64

2D coords of the peaks defined using the selected_thr.

thr_array: float64

Thr array of 100 points distributed between (Img.min(),Img.max()).

peaks_coords: float64

list of all the 3D coords calculated using the Thr array.

total_peaks: list of int

List of the peaks counts.

thr_idx: int64

index of the calculated threshold.

stringency: int64

stringency used for the identification of the selected_peaks