For replicating specific figures from the paper, please see scripts in OverallAnalysis. Details on which script is needed for which figure are in: Gerlei_et_at_2020_where_to_find_data_and_code.xlsx (also copied below for convenience)
The grid cell data is available from: https://datashare.is.ed.ac.uk/handle/10283/3674
To use the code for analyzing spatial cells such as head direction cells and grid cells, see scripts in PostSorting. See some examples of using PostSorting here: https://github.com/MattNolanLab/grid_cell_analysis/blob/master/example_spatial_analysis.py
There is more detailed documentation on how the code is organized and what the main data frames contain: https://github.com/MattNolanLab/grid_cell_analysis/wiki/Content-of-data-frame-columns
Please don't hesitate to submit an issue if there's a problem.
| Basic info | Data file / folder name(s) or identifier(s) (add accession number, DOI or web link to data where applicable) | Data file format(s) and file type | Location of data file(s) or repository name | Script(s) used | |
|---|---|---|---|---|---|
| Data supporting figures | |||||
| Data supporting figure 1a | Simulated data to explain hypothesis | /prediction_schematics | pandas (.pkl) data frames | https://datashare.is.ed.ac.uk/handle/10283/777 | model_prediction_schematics_simulated.py |
| Data supporting figure 1b | data from example cells from M12_2018-04-10_14-22-14_of (mouse data) and 11025-01060511 (Sargolini et al) | Spike sorting pipeline output | pandas (.pkl) data frames | https://datashare.is.ed.ac.uk/handle/10283/777 | (control_sorting_analysis.py) |
| Data supporting figure 1c | Watson test results (grid cells only) | /watson_two_test_cells | pandas (.pkl) data frames | https://datashare.is.ed.ac.uk/handle/10283/777 | analyze_hd_from_whole_session.py |
| Data supporting figure 1d | Watson test results (all cells) | /watson_two_test_cells | pandas (.pkl) data frames | https://datashare.is.ed.ac.uk/handle/10283/777 | analyze_hd_from_whole_session.py |
| Data supporting figure 2b | Shuffled analysis example cell | /methods_directional_cell | pandas (.pkl) data frames | https://datashare.is.ed.ac.uk/handle/10283/777 | directional_cell_definition_example_figure.py |
| Data supporting figure 2c | Shuffled analysis for all grid cells | /shuffled_analysis_cell | pandas (.pkl) data frames | https://datashare.is.ed.ac.uk/handle/10283/777 | shuffle_cell_analysis.py |
| Data supporting figure 3a | Firing rate map for M12_2018-04-10_14-22-14_of (mouse data) | Spike sorting pipeline output | pandas (.pkl) data frames | https://datashare.is.ed.ac.uk/handle/10283/777 | (control_sorting_analysis.py) |
| Data supporting figure 3b | Shuffled analysis for fields example | /shuffled_analysis/percentile and in M12_2018-04-10_14-22-14_of folder | pandas (.pkl) data frames | https://datashare.is.ed.ac.uk/handle/10283/777 | shuffle_field_analysis.py and shuffle_field_analysis_all_animals.py |
| Data supporting figure 3c | Shuffled analysis for fields example | /plot_hd_tuning_vs_shuffled_fields/example_mouse_distributive | pandas (.pkl) data frames | https://datashare.is.ed.ac.uk/handle/10283/777 | plot_hd_tuning_vs_shuffled_fields.py |
| Data supporting figure 3d | Shuffled analysis for all grid fields | /shuffled_analysis | pandas (.pkl) data frames | https://datashare.is.ed.ac.uk/handle/10283/777 | shuffle_field_analysis_all_animals.py |
| Data supporting figure 4a | Comparison of classic head direction plots of fields | /field_histogram_shapes | pandas (.pkl) data frames | https://datashare.is.ed.ac.uk/handle/10283/777 | compare_shape_of_fields.py |
| Data supporting figure 4b | Comparison of classic head direction plots of fields | /field_histogram_shapes | pandas (.pkl) data frames, csv files (for the R code) | https://datashare.is.ed.ac.uk/handle/10283/777 | Correlation.Rmd |
| Data supporting figure 4c | Comparison of fields from half sessions | /field_histogram_shapes | csv files | https://datashare.is.ed.ac.uk/handle/10283/777 | RecordingDurations.Rmd |
| Data supporting figure 4d | Comparison of classic head direction plots of fields for centre and border fields | /field_histogram_shapes | csv files | https://datashare.is.ed.ac.uk/handle/10283/777 | Correlation.Rmd |
| Data supporting figure 5a | Firing rate map for M13_2018 05 14 (mouse data) | Spike sorting pipeline output | pandas (.pkl) data frames | https://datashare.is.ed.ac.uk/handle/10283/777 | (control_sorting_analysis.py) |
| Data supporting figure 5b | Head direction plots from first and second half of session from M13 2018 05 14 (mouse data) | /watson_two_test_cells | pandas (.pkl) data frames | https://datashare.is.ed.ac.uk/handle/10283/777 | plot_example_polar_hists_first_and_second_half.py |
| Data supporting figure 5c | Comparison of head direction from first and second half for whole session | /correlation_cell | pandas (.pkl) data frames | https://datashare.is.ed.ac.uk/handle/10283/777 | compare_first_and_second_half_cell.py |
| Data supporting figure 5d | Distributive head direction plots from first and second half of sesssion | /plot_hd_tuning_vs_shuffled | pandas (.pkl) data frames | https://datashare.is.ed.ac.uk/handle/10283/777 | plot_hd_tuning_vs_shuffled.py |
| Data supporting figure 5e | Firing rate map with detected fields for M13_2018 05 14 (mouse data) | Spike sorting pipeline output | pandas (.pkl) data frames | https://datashare.is.ed.ac.uk/handle/10283/777 | (control_sorting_analysis.py) |
| Data supporting figure 5f | Classic head direction plots for half fields | /first_vs_second_fields | pandas (.pkl) data frames | https://datashare.is.ed.ac.uk/handle/10283/777 | compare_shape_of_fields.py |
| Data supporting figure 5g | Comparison of head direction from first and second half for fields | /field_histogram_shapes | pandas (.pkl) data frames | https://datashare.is.ed.ac.uk/handle/10283/777 | compare_shape_of_fields.py |
| Data supporting figure 5h | Distributive head direction plots from first and second half of sesssion for example field | /plot_hd_tuning_vs_shuffled_fields | pandas (.pkl) data frames | https://datashare.is.ed.ac.uk/handle/10283/777 | plot_hd_tuning_vs_shuffled_fields.py |
| Data supporting figure 6a | Grid cell simulation results for Burgess model | /grid_cell_models/pastoll | pandas (.pkl) data frames | https://datashare.is.ed.ac.uk/handle/10283/777 | (control_sorting_analysis.py) |
| Data supporting figure 6b | Grid cell simulation results for Pastoll model | /grid_cell_models/burgess | pandas (.pkl) data frames | https://datashare.is.ed.ac.uk/handle/10283/777 | (control_sorting_analysis.py) |
| Data supporting figure 6c | Comparison of number of significant bins (between models and experimental data) | /simulation_comparisons | csv files | https://datashare.is.ed.ac.uk/handle/10283/777 | 6cd.R |
| Data supporting figure 6d | Comparison of proportion of directional fields (between models and experimental data) | /simulation_comparisons | csv files | https://datashare.is.ed.ac.uk/handle/10283/777 | 6cd.R |
| Data supporting figure 7a | Simulated input conjunctive cells | /grid_cell_models/gerlei_nonuniform | pandas (.pkl) data frames | https://datashare.is.ed.ac.uk/handle/10283/777 | grid_run.py |
| Data supporting figure 7b | Representative ratemap for non-uniform model | /grid_cell_models/gerlei_nonuniform | pandas (.pkl) data frames | https://datashare.is.ed.ac.uk/handle/10283/777 | grid_run.py, analyze_simulated_grid_cells.py, control_sorting_analysis.py |
| Data supporting figure 7c | Representative firing fields for non-uniform model | /grid_cell_models/gerlei_nonuniform | pandas (.pkl) data frames | https://datashare.is.ed.ac.uk/handle/10283/777 | grid_run.py, analyze_simulated_grid_cells.py, control_sorting_analysis.py |
| Data supporting figure 7d | Comparisons of significant bins per field & proportion of direction fields between conjunctive cell input models and experimental data | /simulation_comparisons | csv files | https://datashare.is.ed.ac.uk/handle/10283/777 | 7d.R |
| Data supporting figure 8a | Schematic showing input cells to uniform and non-uniform conjunctive models | ||||
| Data supporting figure 8b | Comparison of classic head direction plots of fields | /field_histogram_shapes | pandas (.pkl) data frames, csv files (for the R code) | https://datashare.is.ed.ac.uk/handle/10283/777 | Correlation.Rmd |
| Data supporting figure 8c | Comparison of fields from half sessions | /field_histogram_shapes | csv files | https://datashare.is.ed.ac.uk/handle/10283/777 | RecordingDurations.Rmd |