dinghaoluo/code_mpfi_dinghao

my scripts at mpfi

code_dinghao_mpfi

my scripts at MPFI

caiman_code

includes a working CaImAn analysis pipeline modified to work on Wang Lab data, mostly by Nico Spiller.

imaging_code

includes preliminary analysis scripts for dLight and GRABNE data

• deepvid_grid_roi.py is a working pipeling to extract fluorescence traces and align them to behavioural variables using a grid ROI mask and denoised movies processed by Colin Porter.

HPC_code

includes analysis scripts for behaviour and neural data collected from hippocampus recordings

• HPCLC_all_rasters.py and HPCLCterm_all_rasters.py read spiketime data from behaviour-aligned spiketime files and produce exactly one 1-0 raster array for every recording session
• HPCLC_all_train.py and HPCLCterm_all_train.py read spiketime data similarly to ...rasters.py, but then convolve the spike train with a 100-ms-sigma Gaussian kernel and produce exactly one spike train array for every recording session
• HPCLC_clu_list.py and HPCLCterm_clu_list.py generate a list of clu name for every recording session to accelerate later processing
• HPCLC_place_cell_profiles.py and HPCLCterm_place_cell_profiles.py summarise the place cell indices and number of place cells for each recording session
• HPC_session_PCA_traj.py performs PCA on averaged all trials, averaged stim or control trials, and calculate and plot the distances between points on the trajectories

sequence

• HPC_LC_plot_sequence.py and HPC_LCterm_plot_sequence.py plot temporal cell sequences for single sessions
• HPC_LC_plot_sequence_dist.py and HPC_LCterm_plot_sequence_dist.py plot distance cell sequences for single sessions

stim_stimcont

LC_code

includes analysis scripts for behaviour and neural data collected from locus coeruleus recordings

• all_earlyvlate_rop_population.py compares the population spike rates between early 1st-lick trials and late 1st-lick trials; includes tagged, putative and all LC Dbh+ cells

behaviour

• 1st_lick_profile.py plots a stair histogram of the first-lick distance and time of all the trials in LC-optotagging sessions