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Bunch of code to analyze TIFF data (coming from a BIGTIFF)

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.idea
.idea
 
 
preprocess
preprocess
 
 
.gitignore
.gitignore
 
 
2019-10-20-sfnplot.py
2019-10-20-sfnplot.py
 
 
ExpGTE.py
ExpGTE.py
 
 
GC_mice_scripts.py
GC_mice_scripts.py
 
 
GTE_Setup.md
GTE_Setup.md
 
 
README.md
README.md
 
 
SNR_test.py
SNR_test.py
 
 
analysis_functions.py
analysis_functions.py
 
 
archive.py
archive.py
 
 
benchmark.py
benchmark.py
 
 
bursting.py
bursting.py
 
 
caiman_test.py
caiman_test.py
 
 
clustering_functions.py
clustering_functions.py
 
 
deconv_decay.py
deconv_decay.py
 
 
demo_shuffle.py
demo_shuffle.py
 
 
errlog.txt
errlog.txt
 
 
figures.py
figures.py
 
 
filtering.py
filtering.py
 
 
heatmap_temp.py
heatmap_temp.py
 
 
init_cabmi.py
init_cabmi.py
 
 
learning_stats
learning_stats
 
 
make_toy_data.py
make_toy_data.py
 
 
memmap_.npz
memmap_.npz
 
 
mp_test.py
mp_test.py
 
 
peak_extraction_expr.py
peak_extraction_expr.py
 
 
pipeline.py
pipeline.py
 
 
plot_base_end.py
plot_base_end.py
 
 
plot_generation_script.py
plot_generation_script.py
 
 
plot_rewardend.py
plot_rewardend.py
 
 
plotting_functions.py
plotting_functions.py
 
 
preprocessing.py
preprocessing.py
 
 
run_at_night_cabmi.py
run_at_night_cabmi.py
 
 
script.py
script.py
 
 
sessions.py
sessions.py
 
 
shuffling_functions.py
shuffling_functions.py
 
 
simulation.py
simulation.py
 
 
swap_proc.py
swap_proc.py
 
 
tests.py
tests.py
 
 
utils_bursting.py
utils_bursting.py
 
 
utils_cabmi.py
utils_cabmi.py
 
 
utils_clustering.py
utils_clustering.py
 
 
utils_gte.py
utils_gte.py
 
 
utils_loading.py
utils_loading.py
 
 
xgboost_analysis.py
xgboost_analysis.py
 
 
xgboost_init.py
xgboost_init.py
 
 

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DOI

CaBMI_analysis

Dependencies

To use generalized transfer entropy, follow the setup instructions in GTE_Setup.md. You may also need the newest version of Matplotlib. Other dependencies include pandas, seaborn, scikit-image, scikit-learn, networkx, python-louvain, markov-clustering

Files

  • pipeline.py: Wraps the TIFF data (specifically, coming as BIGTIFF data), uses Caiman to extract ROIs and their activity, and stores the data in HDF5 files.
  • plot_CaBMI: Scripts to plot ROI activity
  • analysis_CaBMI.py: Analysis and plotting functions to run on HDF5 files created by the pipeline.
  • utils_cabmi.py: Utility functions for the analysis scripts.
  • utils_gte.py: Utility functions for running generalized transfer entropy.

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Bunch of code to analyze TIFF data (coming from a BIGTIFF)

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