multiscope_fn

Codes used for the analysis of the Allen Institute Multiscope data described in this paper: https://www.biorxiv.org/content/10.1101/2020.10.06.328294v2

The codes in this repository use the Visual Behavior dataset collected at the Allen Institute using Multiplane Mesoscopes. Dataset: https://portal.brain-map.org/explore/circuits/visual-behavior-2p

Define directories:

define the following directories in def_paths.py:

dirAna: directory containing analysis files

dir0: directory for saving figures

Files required to run the scripts (please contact me to send you the files):

Mouse training history:

/allen/programs/braintv/workgroups/nc-ophys/Farzaneh/mouse_trainHist_all2_20210216_151651.h5

Neural responses (a single file includes all sessions data):

/allen/programs/braintv/workgroups/nc-ophys/Farzaneh/omit_traces_peaks/all_sess_omit_traces_peaks_np_corr_dff_20210309_152538.h5

Neural correlations (130 files; each belongs to a single session):

this_sess_omit_traces_peaks_corr_m-440631_s-857040020_20210215_214246.pkl this_sess_omit_traces_peaks_corr_m-485152_s-993738515_20210215_214530.pkl this_sess_omit_traces_peaks_corr_m-479839_s-990139534_20210215_214050.pkl this_sess_omit_traces_peaks_corr_m-484627_s-971632311_20210215_214547.pkl this_sess_omit_traces_peaks_corr_m-449653_s-873247524_20210215_213943.pkl this_sess_omit_traces_peaks_corr_m-453911_s-904418381_20210215_214335.pkl this_sess_omit_traces_peaks_corr_m-435431_s-882674040_20210215_213939.pkl this_sess_omit_traces_peaks_corr_m-453911_s-908441202_20210215_214254.pkl this_sess_omit_traces_peaks_corr_m-453989_s-937682841_20210215_213932.pkl this_sess_omit_traces_peaks_corr_m-448366_s-870762788_20210215_213941.pkl this_sess_omit_traces_peaks_corr_m-485152_s-992393325_20210215_214410.pkl this_sess_omit_traces_peaks_corr_m-523922_s-1051107431_20210215_213926.pkl this_sess_omit_traces_peaks_corr_m-485152_s-993420347_20210215_214248.pkl this_sess_omit_traces_peaks_corr_m-528097_s-1052330675_20210215_213925.pkl this_sess_omit_traces_peaks_corr_m-453911_s-914161594_20210215_214357.pkl this_sess_omit_traces_peaks_corr_m-449653_s-875259383_20210215_213946.pkl this_sess_omit_traces_peaks_corr_m-448366_s-866197765_20210215_213943.pkl this_sess_omit_traces_peaks_corr_m-438912_s-848401585_20210215_213938.pkl this_sess_omit_traces_peaks_corr_m-440631_s-855711263_20210215_214247.pkl this_sess_omit_traces_peaks_corr_m-457841_s-954954402_20210215_213932.pkl this_sess_omit_traces_peaks_corr_m-457841_s-957020350_20210215_213934.pkl this_sess_omit_traces_peaks_corr_m-482853_s-986130604_20210215_214247.pkl this_sess_omit_traces_peaks_corr_m-484627_s-973701907_20210215_214752.pkl this_sess_omit_traces_peaks_corr_m-449653_s-870352564_20210215_213947.pkl this_sess_omit_traces_peaks_corr_m-453911_s-903621170_20210215_214345.pkl this_sess_omit_traces_peaks_corr_m-523922_s-1051319542_20210215_213926.pkl this_sess_omit_traces_peaks_corr_m-453988_s-939526443_20210215_213936.pkl this_sess_omit_traces_peaks_corr_m-456915_s-904771513_20210215_214142.pkl this_sess_omit_traces_peaks_corr_m-453990_s-923705570_20210215_214246.pkl this_sess_omit_traces_peaks_corr_m-523922_s-1050231786_20210215_213935.pkl this_sess_omit_traces_peaks_corr_m-479839_s-988768058_20210215_214118.pkl this_sess_omit_traces_peaks_corr_m-457841_s-952430817_20210215_213928.pkl this_sess_omit_traces_peaks_corr_m-453989_s-940145217_20210215_213936.pkl this_sess_omit_traces_peaks_corr_m-456915_s-907991198_20210215_214042.pkl this_sess_omit_traces_peaks_corr_m-438912_s-850894918_20210215_213939.pkl this_sess_omit_traces_peaks_corr_m-453911_s-914639324_20210215_214355.pkl this_sess_omit_traces_peaks_corr_m-435431_s-886130638_20210215_213949.pkl this_sess_omit_traces_peaks_corr_m-453989_s-946015345_20210215_213931.pkl this_sess_omit_traces_peaks_corr_m-451787_s-886367984_20210215_214601.pkl this_sess_omit_traces_peaks_corr_m-453911_s-906299056_20210215_214254.pkl this_sess_omit_traces_peaks_corr_m-482853_s-976167513_20210215_214242.pkl this_sess_omit_traces_peaks_corr_m-485152_s-993253587_20210215_214402.pkl this_sess_omit_traces_peaks_corr_m-453988_s-929686773_20210215_213940.pkl this_sess_omit_traces_peaks_corr_m-449653_s-871526950_20210215_213948.pkl this_sess_omit_traces_peaks_corr_m-523922_s-1048363441_20210215_213934.pkl this_sess_omit_traces_peaks_corr_m-453991_s-947199653_20210215_214001.pkl this_sess_omit_traces_peaks_corr_m-453911_s-906968227_20210215_214303.pkl this_sess_omit_traces_peaks_corr_m-453991_s-948042811_20210215_213955.pkl this_sess_omit_traces_peaks_corr_m-457841_s-955775716_20210215_213927.pkl this_sess_omit_traces_peaks_corr_m-453990_s-927787876_20210215_214242.pkl this_sess_omit_traces_peaks_corr_m-528097_s-1056238781_20210215_213931.pkl this_sess_omit_traces_peaks_corr_m-453990_s-921922878_20210215_214245.pkl this_sess_omit_traces_peaks_corr_m-440631_s-854060305_20210215_214248.pkl this_sess_omit_traces_peaks_corr_m-435431_s-881094781_20210215_213952.pkl this_sess_omit_traces_peaks_corr_m-482853_s-976382032_20210215_214243.pkl this_sess_omit_traces_peaks_corr_m-482853_s-978201478_20210215_214242.pkl this_sess_omit_traces_peaks_corr_m-453988_s-931326814_20210215_213924.pkl this_sess_omit_traces_peaks_corr_m-453990_s-919041767_20210215_214238.pkl this_sess_omit_traces_peaks_corr_m-453991_s-944888114_20210215_213959.pkl this_sess_omit_traces_peaks_corr_m-435431_s-888009781_20210215_213940.pkl this_sess_omit_traces_peaks_corr_m-438912_s-847758278_20210215_213935.pkl this_sess_omit_traces_peaks_corr_m-484627_s-974486549_20210215_214339.pkl this_sess_omit_traces_peaks_corr_m-451787_s-887031077_20210215_214422.pkl this_sess_omit_traces_peaks_corr_m-528097_s-1052512524_20210215_213933.pkl this_sess_omit_traces_peaks_corr_m-451787_s-888171877_20210215_214423.pkl this_sess_omit_traces_peaks_corr_m-448366_s-874616920_20210215_213944.pkl this_sess_omit_traces_peaks_corr_m-482853_s-977760370_20210215_214244.pkl this_sess_omit_traces_peaks_corr_m-528097_s-1056065360_20210215_213929.pkl this_sess_omit_traces_peaks_corr_m-453911_s-913564409_20210215_214406.pkl this_sess_omit_traces_peaks_corr_m-482853_s-983913570_20210215_214242.pkl this_sess_omit_traces_peaks_corr_m-453911_s-915306390_20210215_214552.pkl this_sess_omit_traces_peaks_corr_m-453991_s-949217880_20210215_214002.pkl this_sess_omit_traces_peaks_corr_m-435431_s-889944877_20210215_213943.pkl this_sess_omit_traces_peaks_corr_m-451787_s-880709154_20210215_214146.pkl this_sess_omit_traces_peaks_corr_m-453991_s-941676716_20210215_213954.pkl this_sess_omit_traces_peaks_corr_m-438912_s-853177377_20210215_213940.pkl this_sess_omit_traces_peaks_corr_m-485152_s-991958444_20210215_214438.pkl this_sess_omit_traces_peaks_corr_m-453988_s-937162622_20210215_213943.pkl this_sess_omit_traces_peaks_corr_m-438912_s-848983781_20210215_213943.pkl this_sess_omit_traces_peaks_corr_m-453988_s-935559843_20210215_213941.pkl this_sess_omit_traces_peaks_corr_m-440631_s-850667270_20210215_214246.pkl this_sess_omit_traces_peaks_corr_m-453911_s-907753304_20210215_214310.pkl this_sess_omit_traces_peaks_corr_m-453911_s-911719666_20210215_214350.pkl this_sess_omit_traces_peaks_corr_m-482853_s-980062339_20210215_214253.pkl this_sess_omit_traces_peaks_corr_m-440631_s-853416532_20210215_214249.pkl this_sess_omit_traces_peaks_corr_m-457841_s-959458018_20210215_213928.pkl this_sess_omit_traces_peaks_corr_m-479839_s-985609503_20210215_214147.pkl this_sess_omit_traces_peaks_corr_m-456915_s-907177554_20210215_214124.pkl this_sess_omit_traces_peaks_corr_m-453990_s-925478114_20210215_214241.pkl this_sess_omit_traces_peaks_corr_m-485152_s-993962221_20210215_214506.pkl this_sess_omit_traces_peaks_corr_m-457841_s-958772311_20210215_213934.pkl this_sess_omit_traces_peaks_corr_m-451787_s-882386411_20210215_214354.pkl this_sess_omit_traces_peaks_corr_m-435431_s-886806800_20210215_213942.pkl this_sess_omit_traces_peaks_corr_m-523922_s-1049240847_20210215_213938.pkl this_sess_omit_traces_peaks_corr_m-479839_s-991639544_20210215_214059.pkl this_sess_omit_traces_peaks_corr_m-453990_s-916650386_20210215_214236.pkl this_sess_omit_traces_peaks_corr_m-479839_s-990464099_20210215_214120.pkl this_sess_omit_traces_peaks_corr_m-528097_s-1052096166_20210215_213928.pkl this_sess_omit_traces_peaks_corr_m-479839_s-989267296_20210215_214153.pkl this_sess_omit_traces_peaks_corr_m-440631_s-849304162_20210215_214253.pkl this_sess_omit_traces_peaks_corr_m-435431_s-884451806_20210215_213940.pkl this_sess_omit_traces_peaks_corr_m-435431_s-882060185_20210215_213953.pkl this_sess_omit_traces_peaks_corr_m-453990_s-920695792_20210215_214248.pkl this_sess_omit_traces_peaks_corr_m-484627_s-973384292_20210215_214500.pkl this_sess_omit_traces_peaks_corr_m-453989_s-938898514_20210215_213937.pkl this_sess_omit_traces_peaks_corr_m-456915_s-902884228_20210215_214342.pkl this_sess_omit_traces_peaks_corr_m-453989_s-948252173_20210215_213937.pkl this_sess_omit_traces_peaks_corr_m-453990_s-919888953_20210215_214251.pkl this_sess_omit_traces_peaks_corr_m-438912_s-846871218_20210215_213944.pkl this_sess_omit_traces_peaks_corr_m-451787_s-885557130_20210215_214251.pkl this_sess_omit_traces_peaks_corr_m-448366_s-868688430_20210215_213942.pkl this_sess_omit_traces_peaks_corr_m-484627_s-974167263_20210215_214528.pkl this_sess_omit_traces_peaks_corr_m-484627_s-971922380_20210215_214548.pkl this_sess_omit_traces_peaks_corr_m-453988_s-933439847_20210215_213940.pkl this_sess_omit_traces_peaks_corr_m-482853_s-981845703_20210215_214252.pkl this_sess_omit_traces_peaks_corr_m-451787_s-883619540_20210215_214135.pkl this_sess_omit_traces_peaks_corr_m-453990_s-917498735_20210215_214245.pkl this_sess_omit_traces_peaks_corr_m-453991_s-950031363_20210215_213955.pkl this_sess_omit_traces_peaks_corr_m-440631_s-852794141_20210215_214255.pkl this_sess_omit_traces_peaks_corr_m-453988_s-938140092_20210215_213942.pkl this_sess_omit_traces_peaks_corr_m-457841_s-958105827_20210215_213928.pkl this_sess_omit_traces_peaks_corr_m-482853_s-975452945_20210215_213950.pkl this_sess_omit_traces_peaks_corr_m-449653_s-876303107_20210215_213951.pkl this_sess_omit_traces_peaks_corr_m-435431_s-880498009_20210215_213937.pkl this_sess_omit_traces_peaks_corr_m-453989_s-940775208_20210215_213939.pkl this_sess_omit_traces_peaks_corr_m-456915_s-906521029_20210215_214308.pkl this_sess_omit_traces_peaks_corr_m-451787_s-884613038_20210215_214245.pkl this_sess_omit_traces_peaks_corr_m-449653_s-872592724_20210215_213944.pkl this_sess_omit_traces_peaks_corr_m-456915_s-903813946_20210215_214356.pkl this_sess_omit_traces_peaks_corr_m-448366_s-867027875_20210215_213941.pkl

Make the population average figures

Run the following script after setting doCorrs=0 at the beginning of the script: omissions_traces_peaks_plots_setVars.py

Then run the script: omissions_traces_peaks_plots_setVars_ave.py

Then run the script: omissions_traces_peaks_plots_sumMice.py

Make the correlation figures

Run the following script after setting doCorrs=1 at the beginning of the script: omissions_traces_peaks_plots_setVars.py

Then run the script: omissions_traces_peaks_plots_setVars_corr.py

Then run the script: omissions_traces_peaks_plots_setVars_corr_eachCre.py

Name		Name	Last commit message	Last commit date
Latest commit History 3 Commits
190407_process_and_load_ophys_session_FN.py		190407_process_and_load_ophys_session_FN.py
190407_production_multi_session_dfs.ipynb		190407_production_multi_session_dfs.ipynb
200628_get_change_aligned_traces_and_running.ipynb		200628_get_change_aligned_traces_and_running.ipynb
200630_FN_clustering_attempt_omission_response_df.ipynb		200630_FN_clustering_attempt_omission_response_df.ipynb
200630_FN_clustering_attempt_stim_response_df_engagement_state.ipynb		200630_FN_clustering_attempt_stim_response_df_engagement_state.ipynb
200630_FN_clustering_attempt_trials_response_df.ipynb		200630_FN_clustering_attempt_trials_response_df.ipynb
200702_create_metrics_array_for_clustering.ipynb		200702_create_metrics_array_for_clustering.ipynb
2019-04-23-omitted_flashes_multiscope_metrics_FN.py		2019-04-23-omitted_flashes_multiscope_metrics_FN.py
2019-04-25 - omitted_flashes_raw_movies_FN.py		2019-04-25 - omitted_flashes_raw_movies_FN.py
README.md		README.md
__init__.py		__init__.py
all_sess_dff_stim_load.py		all_sess_dff_stim_load.py
all_sess_dff_stim_set.py		all_sess_dff_stim_set.py
anova_tukey_ttest_resp_amplitude.py		anova_tukey_ttest_resp_amplitude.py
brain_observatory.ipynb		brain_observatory.ipynb
convert_level_1_to_level_2_pbs.py		convert_level_1_to_level_2_pbs.py
copy_crosstalkFolders_analysisPC_to_allen.ipynb		copy_crosstalkFolders_analysisPC_to_allen.ipynb
copy_crosstalkFolders_analysisPC_to_allen.py		copy_crosstalkFolders_analysisPC_to_allen.py
def_funs.py		def_funs.py
def_funs_general.py		def_funs_general.py
def_paths.py		def_paths.py
get_mouse_pkls.py		get_mouse_pkls.py
get_stage.py		get_stage.py
guide_pandas_at_iat_loc_iloc.py		guide_pandas_at_iat_loc_iloc.py
guide_regex		guide_regex
jerome_cluster_gpu.py		jerome_cluster_gpu.py
keras_DNN_planes_model_fit.py		keras_DNN_planes_model_fit.py
keras_DNN_planes_model_post_plots.py		keras_DNN_planes_model_post_plots.py
keras_DNN_planes_model_post_saveVars.py		keras_DNN_planes_model_post_saveVars.py
keras_DNN_planes_model_setVars.py		keras_DNN_planes_model_setVars.py
keras_cluster_gpu.py		keras_cluster_gpu.py
keras_codes_summary_note.py		keras_codes_summary_note.py
keras_funs.py		keras_funs.py
keras_practice.py		keras_practice.py
load_behavior_ophys_dataset.py		load_behavior_ophys_dataset.py
load_behavior_ophys_dataset_fn.py		load_behavior_ophys_dataset_fn.py
mongo_save_call.py		mongo_save_call.py
mouse_seeks_flags.py		mouse_seeks_flags.py
mouse_seeks_flags_FN.py		mouse_seeks_flags_FN.py
neuropil_subtract.py		neuropil_subtract.py
neuropil_subtract_dff.ipynb		neuropil_subtract_dff.ipynb
omissions_traces_peaks.py		omissions_traces_peaks.py
omissions_traces_peaks_init.py		omissions_traces_peaks_init.py
omissions_traces_peaks_init_pbs.py		omissions_traces_peaks_init_pbs.py
omissions_traces_peaks_pbs.py		omissions_traces_peaks_pbs.py
omissions_traces_peaks_plots_eachMouse.py		omissions_traces_peaks_plots_eachMouse.py
omissions_traces_peaks_plots_numNeurons_depths.py		omissions_traces_peaks_plots_numNeurons_depths.py
omissions_traces_peaks_plots_setVars.py		omissions_traces_peaks_plots_setVars.py
omissions_traces_peaks_plots_setVars_ave.py		omissions_traces_peaks_plots_setVars_ave.py
omissions_traces_peaks_plots_setVars_corr.py		omissions_traces_peaks_plots_setVars_corr.py
omissions_traces_peaks_plots_setVars_corr_eachCre.py		omissions_traces_peaks_plots_setVars_corr_eachCre.py
omissions_traces_peaks_plots_setVars_corr_eachMouse.py		omissions_traces_peaks_plots_setVars_corr_eachMouse.py
omissions_traces_peaks_plots_setVars_corr_sumMice.py		omissions_traces_peaks_plots_setVars_corr_sumMice.py
omissions_traces_peaks_plots_setVars_corr_sumMice_summaryCodeNotes.py		omissions_traces_peaks_plots_setVars_corr_sumMice_summaryCodeNotes.py
omissions_traces_peaks_plots_sumMice.py		omissions_traces_peaks_plots_sumMice.py
omissions_traces_peaks_quantify.py		omissions_traces_peaks_quantify.py
omissions_traces_peaks_quantify_flashAl.py		omissions_traces_peaks_quantify_flashAl.py
ophys_session_query_info.py		ophys_session_query_info.py
run_convert_level_1_to_level_2_mesoscope_fn.py		run_convert_level_1_to_level_2_mesoscope_fn.py
run_convert_level_1_to_level_2_pbs.py		run_convert_level_1_to_level_2_pbs.py
run_convert_level_1_to_level_2_pbs_1exp.py		run_convert_level_1_to_level_2_pbs_1exp.py
set_mouse_trainHist_all2.py		set_mouse_trainHist_all2.py
set_mouse_trainHist_init_pbs.py		set_mouse_trainHist_init_pbs.py
set_mousetrainhist_allsess2an_whatsess.py		set_mousetrainhist_allsess2an_whatsess.py
set_traces_active.py		set_traces_active.py
set_valid_sessions.py		set_valid_sessions.py
svm_funs.py		svm_funs.py
svm_init.py		svm_init.py
svm_init_pbs.py		svm_init_pbs.py
svm_main.py		svm_main.py
svm_main_pbs.py		svm_main_pbs.py
svm_main_post.py		svm_main_post.py
svm_plots_eachMouse.py		svm_plots_eachMouse.py
svm_plots_setVars.py		svm_plots_setVars.py
svm_plots_setVars_sumMice.py		svm_plots_setVars_sumMice.py
svm_plots_sumMice.py		svm_plots_sumMice.py
svm_set_vars_pbs.py		svm_set_vars_pbs.py
test1.py		test1.py
test_keras_pbs.py		test_keras_pbs.py
test_sys.py		test_sys.py

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multiscope_fn

Define directories:

Files required to run the scripts (please contact me to send you the files):

Make the population average figures

Make the correlation figures

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multiscope_fn

Define directories:

Files required to run the scripts (please contact me to send you the files):

Make the population average figures

Make the correlation figures

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