Detection and Tracking (SarcGraph)

Provides tools to detect and track zdiscs and sarcomeres.

Parent Class

SarcGraph([output_dir, file_type])

Zdiscs and sarcomeres segmentation and tracking.

Methods

zdisc_segmentation([file_path, raw_frames, ...])	Finds Z-Discs in a video/image and extracts related information, (frame number, center position, end points).
zdisc_tracking([file_path, raw_frames, ...])	Track detected Z-Discs in a video.
sarcomere_detection([file_path, raw_frames, ...])	Detect sarcomeres in a video/image.

Private Methods

_data_loader(file_path)	Loads a video/image file.
_to_gray(frames)	Convert RGB frames to grayscale.
_save_numpy(data, file_name)	Saves a numpy array.
_save_dataframe(data, file_name)	Saves a pandas dataframe.
_filter_frames(frames[, sigma])	Convolves all frames with laplacian and gaussian filters.
_process_input([file_path, raw_frames, ...])	Loads a video/image and filter all frames.
_detect_contours(filtered_frames[, ...])	Returns contours of detected zdiscs in each frame.
_process_contour(contour)	Computes the center location of a zdisc as well as its two end points given its 2d contour.
_zdiscs_to_pandas(zdiscs_all)	Creates a pandas dataframe from the information of detected zdiscs in all frames.
_merge_tracked_zdiscs(tracked_zdiscs[, ...])	A post processing step to group related partially tracked zdiscs using the OPTICS algorithm.
_zdisc_to_graph(zdiscs[, K])	Creates a graph with zdiscs as nodes.
_score_graph(G[, c_avg_length, c_angle, ...])	Assigns a score to each connection of the input graph.
_prune_graph(G[, score_threshold, ...])	Prunes the input graph to get rid of invalid or less probable connections.