Swarming intelligence emergence underlying monocyte communication and activation in cellular immunity

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Introduction

Code for manuscript " Swarming intelligence emergence underlying monocyte communication and activation in cellular immunity ".

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Dataset

To uncover the molecular basis that modulates the pattern of monocyte migration, we collected comprehensive data of the monocyte migration through intravital imaging under different experiments. Here, we only upload the demo dataset with our code for validation and investigation. The complete monocyte migration dataset is available after contacting the corresponding authors on reasonable request.

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Usage

Classification and Simulation

classifier.py provides cell contacting classifiers.
Cell_simulation generates cell motion simulation trajectories.
The data used to train the cell contacting classifier and the classification model are in /data.

Calcium ion analysis

distance_distribution.py provides statistics of cell distances.
generate_contact_data_csv.py generates data on contacting cells.
generate_spike_data_csv.py generates data on calcium spikes.
generate_peak_contact.py generates contacting data for cells with calcium spikes.

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##Requirements numpy >= 1.21.2
pandas >= 1.3.3
xgboost >= 1.6.1
scikit-learn >= 0.24.2