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Code used in the hippocampal noise correlations paper.

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@Calc
@Calc
 
 
@Cloud
@Cloud
 
 
@Org
@Org
 
 
ai_figures
ai_figures
 
 
data_loading
data_loading
 
 
decoding
decoding
 
 
distal_opto_analysis
distal_opto_analysis
 
 
events_figs
events_figs
 
 
exploration
exploration
 
 
external
external
 
 
figure1_pdf
figure1_pdf
 
 
figure1_svg
figure1_svg
 
 
figure2_pdf
figure2_pdf
 
 
figure2_svg
figure2_svg
 
 
figure3_pdf
figure3_pdf
 
 
figures_on_events_HD
figures_on_events_HD
 
 
figures_on_events_HD_gamma
figures_on_events_HD_gamma
 
 
figures_on_events_HD_gamma_1s
figures_on_events_HD_gamma_1s
 
 
figures_scratchpad
figures_scratchpad
 
 
final_figures
final_figures
 
 
nn_test
nn_test
 
 
old_code
old_code
 
 
old_graphs
old_graphs
 
 
pipeline
pipeline
 
 
plotting
plotting
 
 
simulation
simulation
 
 
supfigs_code
supfigs_code
 
 
supplements_pdf
supplements_pdf
 
 
supplements_svg
supplements_svg
 
 
utils
utils
 
 
.gitignore
.gitignore
 
 
15pix_separation_decoding.db
15pix_separation_decoding.db
 
 
2s_pad_decoding.db
2s_pad_decoding.db
 
 
Analyzer.m
Analyzer.m
 
 
Asymp_ratio_new.xlsx
Asymp_ratio_new.xlsx
 
 
Asymp_snr.xlsx
Asymp_snr.xlsx
 
 
Asymp_snr_per_single_snr.xlsx
Asymp_snr_per_single_snr.xlsx
 
 
Asymp_snr_shuf.xlsx
Asymp_snr_shuf.xlsx
 
 
DS_README.md
DS_README.md
 
 
DecodeTensor.m
DecodeTensor.m
 
 
DecodingPlotGenerator.m
DecodingPlotGenerator.m
 
 
EvalSettings.m
EvalSettings.m
 
 
Fitted_N.xlsx
Fitted_N.xlsx
 
 
I0N_ratio.xlsx
I0N_ratio.xlsx
 
 
IMSE_ratio_at_150.xlsx
IMSE_ratio_at_150.xlsx
 
 
MultiSessionVisualizer.m
MultiSessionVisualizer.m
 
 
OpenField.m
OpenField.m
 
 
PanelGenerator.m
PanelGenerator.m
 
 
README.md
README.md
 
 
SVMTrack.m
SVMTrack.m
 
 
SessManager.m
SessManager.m
 
 
adjacent_by_bin.mlx
adjacent_by_bin.mlx
 
 
adjacent_decoder_noise_runner.m
adjacent_decoder_noise_runner.m
 
 
aggregator_linear_track_info_per_neuron.m
aggregator_linear_track_info_per_neuron.m
 
 
batch_event_detection.m
batch_event_detection.m
 
 
bin_integration_time_checker.m
bin_integration_time_checker.m
 
 
checking_muti_importance.m
checking_muti_importance.m
 
 
clean_error_decoding.m
clean_error_decoding.m
 
 
confusion_mat_runner.m
confusion_mat_runner.m
 
 
createFit_exp.m
createFit_exp.m
 
 
createFit_infoSaturation.m
createFit_infoSaturation.m
 
 
decoder_by_bins.mlx
decoder_by_bins.mlx
 
 
decoding.db
decoding.db
 
 
decoding_50_bins_partial.db
decoding_50_bins_partial.db
 
 
decoding_50_bins_partial_take2.db
decoding_50_bins_partial_take2.db
 
 
decoding_50_bins_partial_take3.db
decoding_50_bins_partial_take3.db
 
 
decoding_50_bins_partial_take4.db
decoding_50_bins_partial_take4.db
 
 
decoding_all_sess.db
decoding_all_sess.db
 
 
decoding_all_sess_HD.db
decoding_all_sess_HD.db
 
 
decoding_all_sess_HD_gamma.db
decoding_all_sess_HD_gamma.db
 
 
decoding_all_sess_HD_gamma_1s.db
decoding_all_sess_HD_gamma_1s.db
 
 
decoding_all_sess_IED.db
decoding_all_sess_IED.db
 
 
decoding_all_sess_NEWBACKUP.db
decoding_all_sess_NEWBACKUP.db
 
 
decoding_all_sess_spikeDeconvTrace.db
decoding_all_sess_spikeDeconvTrace.db
 
 
decoding_dataseries.db
decoding_dataseries.db
 
 
decoding_from_events.m
decoding_from_events.m
 
 
decoding_with_mindist.db
decoding_with_mindist.db
 
 
error_trial_counter.m
error_trial_counter.m
 
 
error_trial_counter_OLD.m
error_trial_counter_OLD.m
 
 
estimate_position_jitter.m
estimate_position_jitter.m
 
 
exp_noise.m
exp_noise.m
 
 
figure1.m
figure1.m
 
 
figure2.m
figure2.m
 
 
fraction_valid_trials.pdf
fraction_valid_trials.pdf
 
 
fraction_valid_trials.png
fraction_valid_trials.png
 
 
grouped_ballnstick.m
grouped_ballnstick.m
 
 
int_time_runner.m
int_time_runner.m
 
 
lin_track_muti_test.m
lin_track_muti_test.m
 
 
mean_RMS_by_mouse.xlsx
mean_RMS_by_mouse.xlsx
 
 
med_loadings_compute.m
med_loadings_compute.m
 
 
medload_info_plots.m
medload_info_plots.m
 
 
mindist_correction_plots.m
mindist_correction_plots.m
 
 
model_inspection_example.m
model_inspection_example.m
 
 
multi_figure_format.m
multi_figure_format.m
 
 
multiballnstick.m
multiballnstick.m
 
 
multiple_map_check.m
multiple_map_check.m
 
 
nbins_validation.m
nbins_validation.m
 
 
neuropil_contamination_argument.m
neuropil_contamination_argument.m
 
 
non_avg_decoding.m
non_avg_decoding.m
 
 
note.txt
note.txt
 
 

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Noise correlations in neural ensemble activity limit the accuracy of hippocampal spatial representations

The code used for the paper by Omer Hazon, Victor Minces, David Tomàs, Surya Ganguli, Mark Schnitzer, and Pablo Jercog.

Selected functions implementing our methods

  • Code used for detecting events in calcium traces: utils/hyperdetect.m
  • Code used for computing the position signal and noise along the signal direction: DecodeTensor.m function adjacent_metrics
  • Code used for computing the signal, noise, and SNR along the noise covariance eigenvectors: @Cloud/eigen_snr_crossval.m
  • Code used for computing the loadings (cos angle) between the noise covariance eigenvectors and the signal direction, plus related quantities:@Cloud/Cloud.m function Cloud
  • Code used for computing the normalized signal variance: @Org/load_definitions.m lambda function on line 43

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Code used in the hippocampal noise correlations paper.

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