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Overview

torch-segment-fiducials-2d contains a small pre-trained CNN for segmenting fiducials in cryo-EM images.

Image title

Installation

pip install torch-segment-fiducials-2d

Usage

import tifffile
from torch_segment_fiducials_2d import (
    predict_fiducial_probabilities,  # predicts probability in range [0, 1]
    predict_fiducial_mask            # predicts a binary mask
)

# load image and mask
image = tifffile.imread("image.tif")

# erase masked regions
probabilities = predict_fiducial_probabilities(image=image, pixel_spacing=8)
mask = predict_fiducial_mask(image=image, pixel_spacing=8, probability_threshold=0.8)