Ferroptosis occurs through an osmotic mechanism and propagates independently of cell rupture

This repository includes python source code and one test dataset.

• Input: path to XYT csv file , containing for each cell (row) three columns: xy position and time of death (see sample data).
• Output:

  • mean_time_death - average difference in time of death between neighboring cells.

  • scramble_mean_time_death - average different in time of death between pairs of cells in the randomly sampled permutations.

  • perm_prob - the probability of a randomly sampled permutations to have scramble_mean_time_death < mean_time_death.

  • scramble_signficance - average different in time of death between pairs of cells in the 95 percentile of the randomly sampled permutations. Experimental values faster than scramble_signficance imply a p-value < 0.05.

  • spatial propagation index - (scramble_signficance - mean_time_death)/ scramble_signficance.

    In order to better compare the propagative features of different forms of cell death, we devised a new measure termed the spatial
    propagation index to quantify the contribution of the spatial component to the observed μexpΔt.

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Additional outputs and their descriptions provided here

Input

We have enabled two options for running the analysis code, each requires different output:

1. Single experiment mode:

• Input: path to XYT csv file , containing for each cell (row) three columns: xy position and time of death, output path, parameters.

Required parameters:

• time_frame % Temporal resolution :time between acquired frames (minutes).
• cell_line % Cell line type tested in the experiment
• treatment % Name of the treatment
• signal_analyzed % The signal analyzed in the experiment

Produces output in the provided directory:

• analyze_single_experiment(file_location, output_location, time_frame, cell_line, treatment, signal_analyzed)

2. Batch mode:

• Input: experiments folder path containing XYT csv file, output path, parameters csv file path.

Parameters file should include the following columns:

• File Name % A file name matching to the name of the experiment file
• Time Interval (min) % Temporal resolution: time between acquired frames (minutes).
• Cell Line % Cell line type tested in the experiment
• Treatment % Name of the treatment
• Signal Analyzed % The signal analyzed in the experiment

Produces output in the provided directory:

• analyze_several_experiments(file_location,output_location, parameters_location)

Test data

Download sample data folder via the link: TestData

The folder includes: datacsv folder containing: XTY csv, called *experiment_name*.csv, File details.csv file containing required parameters set to this data

Output folders

Results folder:

Containing the following-

• Experiment name folder: One folder for each input XYT csv file, named after the experiment’s name. Each folder contains the 'Data' folder which includes a csv file with additional analyzed information (described in ‘AdditionalOutput.md’)
• All: A folder which contains output relevant to all the analyzed experiments. The folder contains the following files:
  • data combined.csv : includes the output specified above
  • data_features_combined.csv : includes additional analyzed information from all the experiments together.

Citation

Please cite the following manuscript when using this code: "Ferroptosis occurs through an osmotic mechanism and propagates independently of cell rupture" (link)

Please contact Assaf Zaritsky at [email protected], or Chen Galed at [email protected] for any questions / suggestions / bug reports.