Jupyter notebook that repeats the 3D PIV test with visualizations¶

# %load ../../test/3D_test/PIV_3D_test.py
# by Andreas Bauer, 19.06.2020
# This script contains a series of tests for 3D-PIV: The shift of a bar in one direction, the expansion of a 3D block
# and a real data set where we recorded two stacks of collagen fibres at the same field of view with confocal microscopy
#  in reflection mode.  One stack contains a NK cell that deforms the matrix and the other doe not.
# Please download the data at https://github.com/fabrylab/3D_piv_example_data.git (180 MB, unpacked) and provide the
# folder in the code below.
# We tested this on ubuntu 16 and 18, with Anaconda Python installation. The whole script
# takes about 5 minutes on my 4 core-intel i5 @2.5 GHz Laptop. You should have !!! 8 Gb ob Memory !!!! or take care not
# to open  all matplotlib plots as interactive windows at once.
# For questions contact andreas.b.bauer@fau.de


from openpiv.pyprocess3D import *
from openpiv.PIV_3D_plotting import *
from openpiv.validation import sig2noise_val
from openpiv.filters import replace_nans_py, replace_outliers
import time
import glob as glob
import os
from natsort import natsorted
import matplotlib.animation as animation

# Run it only once:
import os
if not os.path.exists('test_3d'):
    import git 
    repo = git.Repo.clone_from("https://github.com/fabrylab/3D_piv_example_data.git", './test_3d', branch='master')

###### real data example ############################
# we recorded stacks of collagen fibres with confocal microscopy in reflection mode
# "alive" stack contains a force generating NK-cell, marked by the red circle in the animation
# "relaxed" stack is the same field of view with out the cell
# download the data at https://github.com/fabrylab/3D_piv_example_data.git
# this calculation takes takes ~ 3-4 minutes on my 4-core Intel i5@2.5 GHz Laptop



### plese enter the path to the dataset provided at
folder = r"test_3d"



if not os.path.exists(folder):
    raise FileNotFoundError("path to 3d piv data '%s' does not exists\n"
                            ". Please download the data from https://github.com/fabrylab/3D_piv_example_data.git" % folder)
# stack properties
# factors for voxel size
du = 0.2407
dv = 0.2407
dw = 1.0071
# total image dimension for x y z
image_dim = (123.02, 123.02, 122.86)

# keep these values for our nk cells stacks
win_um = 12  # window size in µm
fac_overlap = 0.3  # overlap in percent of the window size
signoise_filter = 1.3

# window size for stacks in pixel
window_size = (int(win_um / du), int(win_um / dv), int(win_um / dw))
overlap = (int(fac_overlap * win_um / du), int(fac_overlap * win_um / dv), int(fac_overlap * win_um / dw))
search_area = (int(win_um / du), int(win_um / dv), int(win_um / dw))

# load tense stacks
images = natsorted(glob.glob(os.path.join(folder, "Series001_t22_z*_ch00.tif")))
im_shape = plt.imread(images[0]).shape
alive = np.zeros((im_shape[0], im_shape[1], len(images)))
for i, im in enumerate(images):
    alive[:, :, i] = plt.imread(im)

# load relaxed stack
images = natsorted(glob.glob(os.path.join(folder, "Series003_t05_z*_ch00.tif")))
im_shape = plt.imread(images[0]).shape
relax = np.zeros((im_shape[0], im_shape[1], len(images)))
for i, im in enumerate(images):
    relax[:, :, i] = plt.imread(im)

# 3D PIV
u, v, w, sig2noise = extended_search_area_piv3D(alive, relax, window_size=window_size, overlap=overlap,
                                                search_area_size=search_area, dt=(1 / du, 1 / dv, 1 / dw),
                                                subpixel_method='gaussian',
                                                sig2noise_method='peak2peak',
                                                width=2)

# correcting stage drift between the field of views
u -= np.nanmean(u)
v -= np.nanmean(v)
w -= np.nanmean(w)

# filtering
uf, vf, wf, mask = sig2noise_val(u, v, w=w, sig2noise=sig2noise, threshold=signoise_filter)
uf, vf, wf = replace_outliers(uf, vf, wf, max_iter=1, tol=100, kernel_size=2, method='disk')