The Shear Flow Deformation Cytometer is a method to measure the visco-elastic properties of living cells in suspension. Cells are suspended in a high-viscosity (0.5-5 Pa s) fluid (typically alginate with concentrations 1-2.5%) and exposed to fluid shear during their passage through large (200 µm diameter) microfluidic channels.
The software uses Python, so you need to have a Python installation, e.g. Anaconda.
To install the software package, download the repository from GitHub, open a command line in the downloaded folder (the one containing "setup.py") and execute
pip install .
To record image data, use the script:
recording.py
To evaluate the resulting data (.tif files) use the script:
evaluate.py
To analyse the evaluated data, this script example can serve as a starting point.
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
from shear_flow_deformation_cytometer.evaluation.helper_functions import load_all_data_new, get2Dhist_k_alpha_err
# load all the data in the given folder
# you can also add a list of folders instead
# filenames can also include * for wildcard matches
data, config = load_all_data_new(r"\\path_to_folder_containing_the_data")
# print all the columns, these are the ones from the results.csv and from the meta data files
print(data.columns)
# you can now group by some of the columns
# for example just by the filename to get an evaluation per file
for filename, d in data.groupby("filename"):
# calculate the k and alpha and their bootstrapped errors according to the 2D mode
k, k_err, alpha, alpha_err = get2Dhist_k_alpha_err(d)
print(filename, k, k_err, alpha, alpha_err)
# or directly apply it on the grouped dataframe to get a new dataframe
aggregated_data = data.groupby("filename").apply(get2Dhist_k_alpha_err)
print(aggregated_data)If you use this software for a project that results in a publication we encourage you to cite our publication:
Richard Gerum Elham Mirzahossein Mar Eroles Jennifer Elsterer Astrid Mainka Andreas Bauer Selina Sonntag Alexander Winterl Johannes Bartl Lena Fischer Shada Abuhattum Ruchi Goswami Salvatore Girardo Jochen Guck Stefan Schrüfer Nadine Ströhlein Mojtaba Nosratlo Harald Herrmann Dorothea Schultheis Felix Rico Sebastian Johannes Müller Stephan Gekle Ben Fabry (2022) Viscoelastic properties of suspended cells measured with shear flow deformation cytometry eLife 11:e78823. https://doi.org/10.7554/eLife.78823