Spaces:
Sleeping
Sleeping
File size: 1,486 Bytes
8f72b1f |
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 |
from pathlib import Path
import tifffile
root = Path(__file__).parent / "resources"
def example_data_bacteria():
"""Bacteria images and masks from.
Van Vliet et al. Spatially Correlated Gene Expression in Bacterial Groups: The Role of Lineage History, Spatial Gradients, and Cell-Cell Interactions (2018)
https://doi.org/10.1016/j.cels.2018.03.009
subset of timelapse trpL/150310-11
"""
img = tifffile.imread(root / "trpL_150310-11_img.tif")
mask = tifffile.imread(root / "trpL_150310-11_mask.tif")
return img, mask
def example_data_hela():
"""Hela data from the cell tracking challenge.
Neumann et al. Phenotypic profiling of the human genome by time-lapse microscopy reveals cell division genes (2010)
subset of Fluo-N2DL-HeLa/train/02
"""
img = tifffile.imread(root / "Fluo_Hela_02_img.tif")
mask = tifffile.imread(root / "Fluo_Hela_02_ERR_SEG.tif")
print(img.shape, mask.shape)
return img, mask
def example_data_fluo_3d():
"""Fluo-N3DH-CHO data from the cell tracking challenge.
Dzyubachyk et al. Advanced Level-Set-Based Cell Tracking in Time-Lapse Fluorescence Microscopy (2010)
subset of Fluo-N3DH-CHO/train/02
"""
img = tifffile.imread(root / "Fluo-N3DH-CHO_02_img.tif")
mask = tifffile.imread(root / "Fluo-N3DH-CHO_02_ERR_SEG.tif")
return img, mask
def data_hela():
img = tifffile.imread("02_imgs.tif")
mask = tifffile.imread("02_masks.tif")
return img, mask |