3D-spatial-analysis-cell-nuclei

3D spatial analysis of cell/nuclei represented by their centroids

Citing: If you use this code or data, please cite the following article in your publications. :)

Dimitriou, N.M., Flores-Torres, S., Kinsella, J.M. et al. Detection and Spatiotemporal Analysis of In-vitro 3D Migratory Triple-Negative Breast Cancer Cells. Ann Biomed Eng (2022). https://doi.org/10.1007/s10439-022-03022-y

Contact: For any questions or comments feel free to contact me at this email address: [email protected]

Folders

1. Complete Spatial Randomness test

• Ripley's K/L function. The CSR test is performed using Ripley's K/L functions in calcEnv.R script, using the spatstat package.
• Visualization. The visualization is performed using the Kenvplot_all.m script in MATLAB. Supporting files to this script are:
  • Kenvplot.m: Plots the summary K-function for a three-dimensional point pattern.
  • envelope.m: Plots the envelope of the summary K-function for three-dimensional point patterns from all the samples.
  • mtit.m: Creates a major title above all subplots. (link)
  • natsort.m: Natural-Order Filename Sort. (link)
  • plotopt.m: Plot options
  • plotshaded.m: Sahdes the envelope of K-Function. Adopted from Jakob Voigts

2. Nucleic Spatial Distributions

• Inter-Nucleic, and Nearest-Neighbour Distance distributions
• Cosine similarity between two distance distributions of different time-points
• Visualization

These three steps are implemented in the dist_all_s1.m script in MATLAB. Supporting files to this script are:

• calc_ind_knd.m: Computes the Inter-Nucleic and the Nearest Neighbor distance distributions and saves both distances and kernel smoothed distributions.
• calc_dist_var.m: Computes the variations between distributions of two different time-points using the Cosine similarity measure and saves them.
• cosine_sim.m: Function for the Cosine-similarity measure. Invoked by calc_dist_var.m.
• violinplot.m: Plots the cosine-similarity between distributions of two different time-points. (link)
• Violin.m: Invoked by violinplot.m. (link)
• mtit.m: Creates a major title above all subplots. (link)
• plotopt.m: Plot options

3. Points to density

• The points2density.m script imports the coordinates of the centroids of the segmented nuclei and calculates their spatial density profiles using the Adaptive kernel density estimator via diffusion.

Supporting files to this script are:

• akde.m: Script for adaptive kernel density estimation for high dimensions. (link)

4. Coordinates of centroids of segmented nuclei

• This directory contains the 3D coordinates of centroids of segmented nuclei from 6 datasets, for each time-point D#. The nuclei were segmented using the pipeline found in this repository.