Structural Features
The following table describes the structural features analyzed by SarcAsM, stored in dictionary motion_obj.loi_data:
Feature (dict key) |
Name |
Function |
Description |
Data Type |
|---|---|---|---|---|
cell_mask_area |
Cell area [µm²] |
Area occupied by cells in image. NOT the area of individual cells. np.ndarray with value for each frame. |
ndarray |
|
cell_mask_area_ratio |
Cell area ratio |
Area ratio of total image occupied by cells. np.ndarray with value for each frame. |
list[ndarray] |
|
cell_mask_intensity |
Cell mask intensity |
Average intensity at cell mask. np.ndarray with value for each frame. |
list[ndarray] |
|
domain_area |
Domain area [µm²] |
Areas of individual sarcomere domains in µm^2. List with np.array for each frame. |
list[ndarray] |
|
domain_area_mean |
Mean domain area [µm²] |
Mean domain area in µm^2. np.array with value for each frame. |
ndarray |
|
domain_area_std |
STD domain area [µm²] |
Standard deviation of domain area in µm^2. np.array with value for each frame. |
ndarray |
|
domain_mask |
Sarcomere domain mask |
Masks of sarcomere domains, pixel values reflects domain indices, 0 is background. Stored as list of sparse arrays. For conversion to np.ndarray, use mask.toarray(). |
list[coo_matrix] |
|
domain_oop |
Domain OOP |
Sarcomere orientational order parameter (OOP) of individual sarcomere domains. List with np.array for each frame. |
list[ndarray] |
|
domain_oop_mean |
Mean domain OOP |
Mean sarcomere orientational order parameter (OOP) of all sarcomere domains in image. np.array with value for each frame. |
ndarray |
|
domain_oop_std |
Standard deviation of domain out-of-plane |
Standard deviation of sarcomere orientational order parameter (OOP) of all sarcomere domains in image. np.array with value for each frame. |
ndarray |
|
domain_orientation |
Domain orientation [rad] |
Sarcomere orientation in radians of individual sarcomere domains. |
list[ndarray] |
|
domain_slen |
Domain sarcomere length [µm] |
Mean sarcomere length within each sarcomere domain. List with np.array for each frame. |
list[ndarray] |
|
domain_slen_timeseries |
Domain sarcomere length time-series [µm] |
Time-series of mean sarcomere length within each sarcomere domain. np.ndarray with shape (n_domains, n_frames). |
ndarray |
|
domain_slen_median_timeseries |
Domain sarcomere length median time-series [µm] |
Time-series of median sarcomere length within each sarcomere domain. np.ndarray with shape (n_domains, n_frames). |
ndarray |
|
domain_slen_std_timeseries |
Domain sarcomere length STD time-series [µm] |
Time-series of standard deviation of sarcomere length within each domain. np.ndarray with shape (n_domains, n_frames). |
ndarray |
|
domain_slen_q25_timeseries |
Domain sarcomere length Q25 time-series [µm] |
Time-series of 25th percentile of sarcomere length within each domain. np.ndarray with shape (n_domains, n_frames). |
ndarray |
|
domain_slen_q75_timeseries |
Domain sarcomere length Q75 time-series [µm] |
Time-series of 75th percentile of sarcomere length within each domain. np.ndarray with shape (n_domains, n_frames). |
ndarray |
|
domain_n_vectors_timeseries |
Domain vector count time-series |
Time-series of number of sarcomere vectors within each domain. np.ndarray with shape (n_domains, n_frames). |
ndarray |
|
domain_contr |
Domain contraction state |
Binary contraction state for each domain over time. np.ndarray with shape (n_domains, n_frames). True = contracting, False = quiescent. |
ndarray |
|
domain_n_contr |
Domain number of contractions |
Number of contraction cycles detected for each domain. np.ndarray with shape (n_domains,). |
ndarray |
|
domain_labels_contr |
Domain contraction labels |
Contraction cycle labels for each domain over time. np.ndarray with shape (n_domains, n_frames). Values 1, 2, 3, … label each contraction cycle. |
ndarray |
|
domain_beating_rate |
Domain beating rate [Hz] |
Beating rate in Hz for each domain. np.ndarray with shape (n_domains,). |
ndarray |
|
domain_beating_rate_variability |
Domain beating rate variability [s] |
Standard deviation of inter-beat interval for each domain. np.ndarray with shape (n_domains,). |
ndarray |
|
domain_equ |
Domain equilibrium sarcomere length [µm] |
Equilibrium (resting) sarcomere length for each domain. np.ndarray with shape (n_domains,). |
ndarray |
|
domain_contr_max |
Domain max contraction [µm] |
Maximum contraction (most negative sarcomere length change from equilibrium) for each domain and contraction cycle. np.ndarray with shape (n_domains, max_n_contr). |
ndarray |
|
domain_elong_max |
Domain max elongation [µm] |
Maximum elongation (most positive sarcomere length change from equilibrium) for each domain and contraction cycle. np.ndarray with shape (n_domains, max_n_contr). |
ndarray |
|
domain_vel_contr_max |
Domain max shortening velocity [µm/s] |
Maximum shortening velocity for each domain and contraction cycle. np.ndarray with shape (n_domains, max_n_contr). |
ndarray |
|
domain_vel_elong_max |
Domain max elongation velocity [µm/s] |
Maximum elongation velocity for each domain and contraction cycle. np.ndarray with shape (n_domains, max_n_contr). |
ndarray |
|
domain_time_to_peak |
Domain time to peak [s] |
Time from contraction start to maximum contraction for each domain and cycle. np.ndarray with shape (n_domains, max_n_contr). |
ndarray |
|
domain_time_to_relax |
Domain time to relaxation [s] |
Time from maximum contraction to relaxation for each domain and cycle. np.ndarray with shape (n_domains, max_n_contr). |
ndarray |
|
domain_time_contr |
Domain contraction duration [s] |
Duration of each contraction cycle for each domain. np.ndarray with shape (n_domains, max_n_contr). |
ndarray |
|
domains |
Sarcomere domains |
Set of sarcomere vectors of each sarcomere domain. List with list of np.arrays for each frame, storing the indices of sarcomere vectors for each domain. |
list[list] |
|
midline_id_vectors |
Midline ID sarcomere vectors |
Midline identifier of each sarcomere vector. Value reflects midline label, with unique label for each sarcomere midline. List with np.array for each frame. |
list[ndarray] |
|
midline_length_vectors |
Midline length vectors [µm] |
Length of repsective sarcomere midline of each sarcomere vector. List with np.array for each frame. |
list[ndarray] |
|
myof_length |
Myofibril lengths [µm] |
Length of myofibril lines. List with np.array for each frame. |
list[ndarray] |
|
myof_length_max |
Max. myofibril length [µm] |
Maximum length of myofibril lines in each frame. np.array with value for each frame. |
ndarray |
|
myof_length_mean |
Mean myofibril length [µm] |
Mean length of myofibril lines in each frame. np.array with value for each frame. |
ndarray |
|
myof_length_std |
STD myofibril length [µm] |
Standard deviation of length of myofibril lines in each frame. np.array with value for each frame. |
ndarray |
|
myof_lines |
Myofibril lines |
Sarcomere vector IDs of myofibril lines. List with list of np.arrays for each frame. |
list[list] |
|
myof_bending |
Myofibril bending |
Bending (mean squared curvature) of myofibril lines. List with np.array for each frame. |
list[ndarray] |
|
myof_bending_mean |
Mean myofibril bending |
Mean of bending (mean squared curvature) of myofibril lines in each frame. np.array with value for each frame. |
ndarray |
|
myof_bending_std |
STD myofibril bending |
Standard deviation of bending (mean squared curvature) of myofibril lines in each frame. np.array with value for each frame. |
ndarray |
|
myof_straightness |
Myofibril straightness |
Frechet straightness (max. perpendicular distance to direct end-to-end line) of myofibril lines in each frame. List with np.ndarray for each frame. |
list[list] |
|
myof_straightness_mean |
Mean myofibril straightness |
Mean of Frechet straightness (max. perpendicular distance to direct end-to-end line) of myofibril lines in each frame. np.ndarray with value for each frame. |
ndarray |
|
myof_straightness_std |
STD myofibril straightness |
Standard deviation of Frechet straightness (max. perpendicular distance to direct end-to-end line) of myofibril lines in each frame. np.ndarray with value for each frame. |
ndarray |
|
n_domains |
# Sarcomere domains |
Number of sarcomere domains in each frame. np.array with value for each frame. |
ndarray |
|
n_mbands |
# M-bands |
Number of estimated m-bands in each frame. np.array with value for each frame. |
ndarray |
|
n_vectors |
# Sarcomere vectors |
Number of sarcomere vectors in each frame. np.array with value for each frame. |
ndarray |
|
n_zbands |
# Z-bands |
Number of Z-bands in each frame. np.array with value for each frame. |
ndarray |
|
pos_vectors |
Sarcomere vector positions [px] |
Position of sarcomere vectors in each frame in pixels. List of np.ndarray for each frame |
list[ndarray] |
|
sarcomere_area |
Sarcomere area [µm²] |
Area occupied by sarcomeres. np.ndarray with value for each frame. |
ndarray |
|
sarcomere_area_ratio |
Sarcomere area ratio |
Ratio of cell mask area occupied by sarcomeres. np.ndarray with value for each frame. |
ndarray |
|
sarcomere_length_mean |
Mean sarcomere length [µm] |
Mean sarcomere length of sarcomere vectors in each frame. np.ndarray with value for each frame. |
ndarray |
|
sarcomere_length_vectors |
Sarcomere length vectors [µm] |
Sarcomere length of sarcomere vectors in each frame. List of np.ndarray for each frame. |
list[ndarray] |
|
sarcomere_length_std |
STD sarcomere length [µm] |
Standard deviation of sarcomere length of sarcomere vectors in each frame. np.ndarray with value for each frame. |
ndarray |
|
sarcomere_oop |
Sarcomere OOP |
Sarcomere orientational order parameter (OOP) of all sarcomere vectors in frame. np.ndarray with value for each frame. |
ndarray |
|
sarcomere_orientation_mean |
Mean sarcomere orientation [rad] |
Mean sarcomere orientation of all sarcomere vectors in each frame. np.ndarray with value for each frame. |
ndarray |
|
sarcomere_orientation_vectors |
Sarcomere orientation vectors [rad] |
Sarcomere orientation of sarcomere vectors. List with np.ndarray for each frame. |
list[ndarray] |
|
sarcomere_orientation_std |
STD sarcomere orientation [rad] |
Standard deviation of sarcomere orientation of all sarcomere vectors in each frame. np.ndarray with value for each frame. |
ndarray |
|
z_avg_intensity |
Z-band intensity |
Average intensity of Z-bands, i.e. average pixel values of all Z-bands. np.ndarray with value for each frame. |
ndarray |
|
z_ends |
Z-band ends [px] |
Position of Z-band ends in pixels. |
list[ndarray] |
|
z_intensity |
Z-band intensity |
Intensity of individual Z-band objects. List with np.ndarray for each frame. |
list[ndarray] |
|
z_intensity_mean |
Mean Z-band intensity |
Mean intensity of Z-band objects. np.ndarray with value for each frame. |
ndarray |
|
z_intensity_std |
STD Z-band intensity |
Standard devialtion of intensity of Z-band objects. np.ndarray with value for each frame. |
ndarray |
|
z_labels |
Z-band labels |
Z-band labels. Image with pixel values reflecting object labels. Stored as a sparse matrix, use labels.to_numpy() to convert to np.ndarray. |
csr_matrix |
|
z_lat_alignment |
Z-band lateral alignment |
Lateral alignment A of pairs of adjacent Z-bands. List with np.ndarray for each frame. |
list[ndarray] |
|
z_lat_alignment_groups |
Z-band alignment lat. groups |
Mean alignment of pairs of adjacent Z-bands in lateral groups. List with np.ndarray for each frame. |
list[ndarray] |
|
z_lat_alignment_groups_mean |
Mean alignment in lateral Z-band groups |
Frame-level average of mean alignment of pairs of Z-bands in lateral groups. np.ndarray with value for each frame. |
ndarray |
|
z_lat_alignment_groups_std |
STD alignment in lateral Z-band groups |
Frame-level standard deviation of mean alignment in lateral groups. np.ndarray with value for each frame. |
ndarray |
|
z_lat_alignment_mean |
Mean Z-band lateral alignment |
Mean lateral alignment of adjacent Z-bands. np.ndarray with value for each frame. |
ndarray |
|
z_lat_alignment_std |
STD Z-band lateral alignment |
Standard deviation of lateral alignment of adjacent Z-bands. np.ndarray with value for each frame. |
ndarray |
|
z_lat_dist |
Z-band lateral distances [µm] |
Distance of pairs of laterally adjacent Z-bands. List with np.ndarray for each frame. |
list[ndarray] |
|
z_lat_dist_mean |
Mean Z-band lateral distance |
Mean lateral distance of pairs of laterally adjacent Z-bands. np.ndarray with value for each frame. |
ndarray |
|
z_lat_dist_std |
STD Z-band lateral distance |
Standard deviation of lateral distance of pairs of laterally adjacent Z-bands. np.ndarray with value for each frame. |
ndarray |
|
z_lat_groups |
Z-band lateral groups |
Groups of laterally aligned Z-band objects. List with lists of Z-band indices for each frame. |
list[list] |
|
z_lat_length_groups |
Lengths lat. Z-band groups [µm] |
Lengths of groups of laterally aligned Z-bands. List with np.ndarray for each frame. |
list[ndarray] |
|
z_lat_length_groups_mean |
Mean length lat. Z-band groups [µm] |
Mean length of groups of laterally aligned Z-bands. np.ndarray with value for each frame. |
ndarray |
|
z_lat_length_groups_std |
STD length lat. Z-band groups [µm] |
Standard deviation of lengths of groups of laterally aligned Z-bands. np.ndarray with value for each frame. |
ndarray |
|
z_lat_links |
Z-band lateral links |
Links between laterally aligned Z-band ends. List with np.ndarray for each frame. |
list[ndarray] |
|
z_lat_neighbors |
Z-band lateral neighbors [#] |
Number of lateral neighbors of each Z-band object (0, 1 or 2). List with np.ndarray for each frame. |
list[ndarray] |
|
z_lat_neighbors_mean |
Mean Z-band lateral neighbors [#] |
Mean number of lateral neighbors of each Z-band object for each frame. np.ndarray with value for each frame. |
ndarray |
|
z_lat_neighbors_std |
STD Z-band lateral neighbors [#] |
Standard deviation of number of lateral neighbors of each Z-band object for each frame. np.ndarray with value for each frame. |
ndarray |
|
z_lat_size_groups |
Size of laterally aligned Z-band groups [#] |
Size of groups of laterally aligned Z-band objects. List with np.ndarray for each frame. |
list[ndarray] |
|
z_lat_size_groups_mean |
Mean size groups lat. aligned Z-band [#] |
Mean size of groups of laterally aligned Z-band objects. np.ndarray with value for each frame. |
ndarray |
|
z_lat_size_groups_std |
STD size lat. aligned Z-band [#] |
Standard deviation of size of groups of laterally aligned Z-band objects. np.ndarray with value for each frame. |
ndarray |
|
z_length |
Z-band length [µm] |
Length of Z-band objects. List with np.ndarray of each frame. |
list[ndarray] |
|
z_length_max |
Max Z length [µm] |
here description |
ndarray |
|
z_length_mean |
Mean Z-band length [µm] |
Mean Z-band length in each frame. np.ndarray with value for each frame. |
ndarray |
|
z_length_std |
STD Z-band length [µm] |
Standard deviation of Z-band lengths in each frame. np.ndarray with value for each frame. |
ndarray |
|
z_oop |
Z-band OOP |
Z-band orientation order parameter. np.ndarray with value for each frame. |
ndarray |
|
z_orientation |
Z-band orientation [rad] |
Orientation of individual Z-band objects. List with np.ndarray for each frame. |
list[ndarray] |
|
z_mask_area |
Z-band mask area |
Total area occupied by Z-bands in each frame. np.ndarray with value for each frame. |
ndarray |
|
z_mask_area_ratio |
Z-band mask area ratio |
Ratio of area occupied by Z-bands to total cell area.np.ndarray with value for each frame. |
ndarray |
|
z_mask_intensity |
Z-band mask intensity |
Average intensity of Z-band mask.np.ndarray with value for each frame. |
ndarray |
|
z_straightness |
Z-band straightness |
Straightness of Z-band objects, measured by ratio of end-to-end length to contour length. List with np.ndarray of each frame. |
list[ndarray] |
|
z_straightness_mean |
Mean Z-band straightness |
Mean Z-band straightness for each frame. np.array with value for each frame. |
ndarray |
|
z_straightness_std |
STD Z-band straightness |
Standard deviation of Z-band straightness for each frame. np.array with value for each frame. |
ndarray |