DynamicNuclearNet -- Tracking Data
The tracking portion of the DynamicNuclearDataset includes all data used for tracking.
The following files are included:
train.trk- Dimensions: (91, 71, 584, 600, 1) BTYXC
- Tracks: 11,039
- Divisions: 1,608
val.trk- Dimensions: (27, 71, 584, 600, 1) BTYXC
- Tracks: 2,923
- Divisions: 444
test.trk- Dimensions: (12, 71, 584, 600, 1) BTYXC
- Tracks: 1,213
- Divisions: 178
data-source.npz- A record of the source of each batch divided into one array per data split
Each trks file contains three components:
- X: raw fluorescent nuclear data
- y: nuclear segmentation masks
- lineages: lineage records including the cell id, frames present and division links from parents to daughter cells
Change Log
DynamicNuclearNet 1.0 (June 2023): The original dataset used for all experiments in Schwartz et al. 2023
Instructions for use
import os
import numpy as np
import pandas as pd
from deepcell_tracking.trk_io import load_trks
data_dir = 'path_to_data'
data = load_trks(os.path.join(data_dir, 'test.trks'))
X = data['X']
y = data['y']
lineages = data['lineages']
data_source = np.load(os.path.join(data_dir, 'data-source.npz'), allow_pickle=True)
meta = pd.DataFrame(data_source['test'], columns=['filename', 'experiment', 'pixel_size', 'screening_passed', 'time_step', 'specimen'])