diff --git a/README.md b/README.md index 710f170..9a8e7f4 100644 --- a/README.md +++ b/README.md @@ -1,17 +1,15 @@ -Code for doing analysis and generating figures for Gillespie et al, "Hippocampal replay represents specific past experiences rather than a plan for subsequent choice" +Code for doing analysis and generating figures for Gillespie et al, "Hippocampal replay represents specific past experiences rather than a plan for subsequent choice" Neuron 2021. Please contact Anna Gillespie (anna.gillespie@ucsf.edu) with any questions about this codebase. Franklab repos needed: -for data processing: trodes2ff_shared (franklab public) +for data processing: trodes2ff_shared -for analysis: filterframework_shared (franklab private) +for analysis: filterframework_shared Context: Data acquired 2018-2020 using trodes1.6.3 and 30-tet DKR drive version for 4 rats: Jaq, Roquefort, Despereaux, Montague Data was extracted using D. Liu's python extractor to run Trodes export functions, then processed and analysed in Matlab 2015b -Decoding results used are "ripdecodesv3.mat" pulled from /filterframework/decoding/animal_day_ep_shuffle_0_posterior_acausalv2_full2state.nc (2-state state space model, decoding all times, 2ms bins, 5cm time bins, uniform and stepwise transmats (equal prob back/forward/stay); decoding done mostly at LLNL) - Figures were saved in as pdf or eps and formatted in Adobe Illustrator Data in NWB format is available on the DANDI Archive: https://dandiarchive.org/dandiset/000115/draft @@ -19,7 +17,7 @@ Data in NWB format is available on the DANDI Archive: https://dandiarchive.org/d saved outputs (f) included: - dfs_ripcontent -> ctrl_ripcontent.mat - - dfs_ripcontent_ripspeed -> ctrl_ripcontent_ripspeed.mat + - dfs_ripcontent_ripspeed -> ctrl_ripcontent_ripspeed.mat [EDIT: too big for github, please request if needed] - dfs_ripcontent_movement -> ctrl_movementquant_full2state_all_withtrialwise.mat Code to generate figures: @@ -98,4 +96,4 @@ Control Analyses (not shown in figures): - Likelihoods (decode without state space model, 20ms bins): dfs_likcontent.m - Use MUA as event detection instead of SWRs: dfs_muacontent.m - Use 3-state decoder instead of 2-state to exclude stationary events: dfs_ripcontent_3state.m - - Use more permissive content threshold: dfs_ripcontent_contentthresh \ No newline at end of file + - Use more permissive content threshold: dfs_ripcontent_contentthresh