Comment on page
Detecting Collective signalling events in epithelial Cells
This section outlines an example pipeline written in python to get from images of epithelial cells to quantification with ARCOS and visualization with napari.
.gif?alt=media&token=263af571-c85d-495f-9107-1be85c0c1036)
The following describes an example image processing pipeline written in python to analyse collective events in an MDCK epithelium. What we are aiming for can be seen in the gif above. First, the erk measurement is extracted from the images and the individual nuclei are tracked. The second step shows how to analyse the data with ARCOS. Similar results can be achieved with standalone tools such as CellProfiler and Ilastik. And both the R and Python packages can be used after preparing the data.
In the following zip file, you can find both the input data and the generated output from the image segmentation pipeline and ARCOS.
example_data.zip
16MB
Binary
Example Dataset, credit Paolo Gagliardi
The data in this example is from an MDCK cell line that stably expresses a fluorescent FRET biosensor reporting the activity of the ERK kinase.
In the first step, the nuclei are segmented using the stardist python package.
Subsequently, the mean intensity of individual objects in the ratio image is measured and the individual nuclei are tracked over time.
import os
import skimage
import numpy
import errno
from stardist.models import StarDist2D
from csbdeep.utils import normalize
from skimage.measure import regionprops, regionprops_table
from skimage.util import map_array
import pandas as pd
import trackpy
def create_folders(path: str, folder: list):
for i in folder:
folder_to_make = os.path.join(path, i)
try:
os.makedirs(folder_to_make)
print(f'folder "{i}" created')
except OSError as e:
print(f'folder "{i}" alrady exists')
if e.errno != errno.EEXIST:
raise
def remap_segmentation(df: pd.DataFrame, segmentation: list, timepoint_column: str = 'timepoint', label_column: str = 'label', measure_column: str = 'ERK') -> list:
tracked_numpy = df[[timepoint_column, label_column, measure_column]].sort_values(timepoint_column).to_numpy()
grouped_numpy = numpy.split(tracked_numpy,numpy.unique(tracked_numpy[:,0], return_index = True)[1][1:])
ratio_remapped = []
for img, grp in zip(segmentation, grouped_numpy):
img_copy = map_array(img, grp[:,1], grp[:, 2])
ratio_remapped.append(img_copy)
return ratio_remapped
PATH = 'example_data' # where is you data located
FOLDER = 'mdck_ekar' # subfolder of PATH where images are stored
OUT_DATA = 'data' # subfolder of PATH where csv is stored
OUT_LABELS = 'stardist' # subfolder of PATH where stardist segmentation is stored
FILENAME = 'C3-041_Ori.tif'
full_path = os.path.join(PATH, FOLDER)
orig_images_path = os.path.join(PATH, FOLDER)
out_path_csv = os.path.join(PATH, OUT_DATA)
create_folders(PATH, [OUT_DATA, OUT_LABELS])
model = StarDist2D.from_pretrained('2D_versatile_fluo') # standard stardist model for 2d segmentation
image_data = skimage.io.imread(os.path.join(orig_images_path, FILENAME))
out_path_stardist = os.path.join(PATH, OUT_LABELS, 'stardist.tif')
segmentation = []
df = []
for t, tp_data in enumerate(image_data):
print(f'analysing timepoint {t}')
labels, _ = model.predict_instances(normalize(tp_data))
labels = skimage.segmentation.clear_border(labels)
dic = regionprops_table(labels, tp_data, properties=['label', 'centroid', 'intensity_mean', 'area'])
dic['timepoint'] = numpy.repeat(t, len(dic['label']))
df.append(pd.DataFrame(dic))
skimage.segmentation.clear_border(labels)
segmentation.append(labels)
# optionally save segmentation
skimage.io.imsave(out_path_stardist, numpy.stack(segmentation))
Example frame stardist segmentation
df_full = pd.concat(df)
df_full = df_full.rename(columns={"centroid-1": "x", "centroid-0": "y", 'intensity_mean': 'ERK'})
df_full = df_full.sort_values(['timepoint'])
df_tracked = trackpy.link_df(df_full, search_range = 10, memory = 2, t_column = 'timepoint')
df_tracked = df_tracked.reset_index(drop=True).rename(columns={'particle': "track_id"})
df_tracked.to_csv(out_path_csv+'\\tracked_data_fret.csv')
label | y | x | ERK | area | timepoint | track_id |
|---|---|---|---|---|---|---|
1 | 234.0361 | 234.21661 | 24.241877 | 277 | 0 | 0 |
15 | 247.75668 | 17.486647 | 20.970326 | 337 | 0 | 1 |
14 | 201.73333 | 275.54409 | 22.105376 | 465 | 0 | 2 |
13 | 282.29854 | 274.37136 | 23.169903 | 412 | 0 | 3 |
12 | 79.808989 | 26.254682 | 23.794007 | 267 | 0 | 4 |
In this example, the python package arcos4py is used. But the same analysis could be carried out easily with the R package or the napari plugin.
from arcos4py import ARCOS
from arcos4py.tools import filterCollev
from arcos4py.plotting import NoodlePlot
ts = ARCOS(df_tracked, ["x", "y"], 'timepoint','track_id', 'ERK')
ts.interpolate_measurements()
ts.bin_measurements(biasMet='none', binThr=0.28)
df_arcos = ts.trackCollev(eps=40, minClsz=5)
filterer = filterCollev(df_arcos, 'timepoint', 'clTrackID', 'track_id')
ts_filtered = filterer.filter(25, 10)
timepoint | track_id | x | y | clTrackID | label | ERK | area | ERK.resc | ERK.bin |
|---|---|---|---|---|---|---|---|---|---|
41 | 45 | 178.5023 | 159.9447 | 2 | 84 | 24.069124 | 434 | 0.309875 | 1 |
41 | 69 | 133.91586 | 161.19741 | 2 | 66 | 29.385113 | 309 | 0.780246 | 1 |
41 | 80 | 157.38387 | 171.76452 | 2 | 79 | 26.158065 | 310 | 0.575343 | 1 |
41 | 121 | 157.41818 | 112.88182 | 2 | 133 | 22.369697 | 330 | 0.312039 | 1 |
41 | 122 | 118.09012 | 132.79361 | 2 | 92 | 29.494186 | 344 | 0.862141 | 1 |
NoodlePlot(ts_filtered, 'clTrackID', 'track_id', 'timepoint', 'x', 'y').plot('x')
This step is optional and only one way to visualize events but can be usefull to validate correct event detection.
from napari import Viewer
TAB20 = [
"#1f77b4",
"#aec7e8",
"#ff7f0e",
"#ffbb78",
"#2ca02c",
"#98df8a",
"#d62728",
"#ff9896",
"#9467bd",
"#c5b0d5",
"#8c564b",
"#c49c94",
"#e377c2",
"#f7b6d2",
"#7f7f7f",
"#c7c7c7",
"#bcbd22",
"#dbdb8d",
"#17becf",
"#9edae5",
]
np_data = df_tracked[['track_id', 'timepoint', 'y', 'x']].to_numpy()
colors = numpy.take(numpy.array(TAB20), ts_filtered['clTrackID'].unique(), mode="wrap")
df_w_colors = pd.merge(ts_filtered, pd.DataFrame(data={'colors': colors, 'clTrackID': ts_filtered['clTrackID'].unique()}))
points_data = df_w_colors[['timepoint', 'y', 'x']].to_numpy()
colors_data = df_w_colors['colors'].to_numpy('str')
ratio_remapped = remap_segmentation(df_tracked, segmentation)
ratio_remapped = numpy.stack(ratio_remapped)
viewer = Viewer()
viewer.add_image(image_data, name='ERK Ratio image', colormap='inferno')
viewer.add_image(ratio_remapped, colormap='viridis')
viewer.add_labels(numpy.stack(segmentation), name='segmentation', visible=False)
viewer.add_tracks(np_data, name='cell tracks')
viewer.add_points(points_data, face_color=colors_data, name='collective events')
Screenshot of the visualization in napari
arcos_example.ipynb
96KB
Binary
Download the jupyter notebook