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Examples

This page provides examples on how to run the pipeline for different experimental conditions.

Note: This is still under revision

Spontaneous Activity Recordings
You can leave out any part which need stimulation times for calculation. This usually leaves us with the following functions:
mesc_tiff_extract.analyse_mesc_file()
mesc_data_handling.tiff_merge(stimulation=False)
suite2p_script.run_suite2p()
functions.spontaneous_baseline_val()
cellreg_preprocess.suite2p_to_cellreg_masks()
cellreg_analysis.run_cellreg_matlab()

Bipolar Experiments In bipolar experiments, for one set of parameters we usually have 1 recording. So there is no need to concatenate the tiffs, you can handle them individually. You can use the following functions:
mesc_tiff_extract.analyse_mesc_file()
mesc_data_handling.tiff_merge(stimulation=True)
suite2p_script.run_suite2p()
functions.baseline_val()
functions.plot_stim_traces() - Pay attention to the parameter values. cellreg_preprocess.run_cellreg_matlab() cellreg_preprocess.cellreg_analysis_overlap()

Current steering Experiments
Similarly to bipolar experiments, in current steering experiments we usually have 1 recording for one set of parameters.
In these cases usually you can run the following functions:
mesc_tiff_extract.analyse_mesc_file()
mesc_data_handling.tiff_merge(stimulation=True)
suite2p_script.run_suite2p()
functions.baseline_val()
functions.analyze_merged_activation_and_save()
CoM.plot_weighted_com()- Pay attention to the plot order cellreg_preprocess.run_cellreg_matlab() cellreg_preprocess.cellreg_analysis_overlap()