Synthetic Data for Neutrophil Analysis: Sets one large neutrophil shape and Poisson noise

Synthetic Datasets with  one large irregular shape and Poisson noise.

Part of the PhagoSight neutrophil tracking and analysis package (Henry, et al., PLOS ONE, 2013):

https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0072636

http://www.phagosight.org

https://github.com/phagosight/phagosight

A series of synthetic data sets that reproduce different behaviour characteristics of migrating neutrophils were generated in MATLAB. The data sets consisted of one artificial neutrophil that travelled along a path that presented different conditions of tortuosity, times to activation during 98 time frames.

Numerous data sets of neutrophils in zebrafish were carefully observed before setting the characteristics. One trajectory was manually determined by setting the row, column positions of the centroid at every time point for 98 time frames. The trajectory was designed so that it would represent different neutrophil behaviours: some moments were very oriented and had movements with uniform distance between time frames, whilst others were less uniform and would move at different velocities, some were tortuous whilst others were straight.

Each time frame consisted of 11 slices of z-stack each with 275 x 275 pixels, where the neutrophil was formed by Gaussian distributions of higher intensities than the background and Poisson noise (check the corresponding sets with smaller regular shapes with Gaussian noise and irregular shapes with Poisson noise).

Files corresponding to the sets with irregular shapes and Poisson noise (noise increases from 1 to 5):

    Ground Truth       syntheticData_L_mat_La

    First data set         syntheticData_L1_mat_Re

    Second data set     syntheticData_L2_mat_Re

    Third data set       syntheticData_L3_mat_Re

    Fourth data set     syntheticData_L4_mat_Re

    Fifth data set        syntheticData_L5_mat_Re

Corresponding GIF files are also included as illustrations of the cells in motion.

Main Reference:

PhagoSight: An Open-Source MATLAB® Package for the Analysis of Fluorescent Neutrophil and Macrophage Migration in a Zebrafish Model
Henry KM, Pase L, Ramos-Lopez CF, Lieschke GJ, Renshaw SA, Reyes-Aldasoro CC. (2013) PhagoSight: An Open-Source MATLAB® Package for the Analysis of Fluorescent Neutrophil and Macrophage Migration in a Zebrafish Model. PLOS ONE 8(8): e72636. https://doi.org/10.1371/journal.pone.0072636