natfeedback_code_eLife

Data and code for Spacek et. al., 2021, "Robust effects of corticothalamic feedback during naturalistic visual stimulation", submitted to eLife.

https://www.biorxiv.org/content/10.1101/776237v5

Use main.py to load data for all LGN opto experiments as a function of stimulus type (movies, gratings), run state, and opto state. Data are loaded from pandas DataFrames, which are saved as Python pickles in the pickles folder.

Run main.py at the IPython command line, or in Jupyter; the -i runs scripts in IPython/Jupyter's namespace instead of an empty one:

run -i main.py

pvmvis (default) or ntsrmvis can be provided as an --exptype= argument to this main.py, to load and then plot PV-Cre (most of the paper) or Ntsr1-Cre (Fig S5) data, respectively.

Results can be plotted by executing the desired figx.py file in the same namespace:

run -i fig1.py
run -i fig2.py
run -i fig3.py
run -i fig4.py
run -i fig5.py
run -i fig6.py

Not all supplementary panels/figures have their own script, some are integrated into their parent figure's script for convenience:

run -i fig1S33S1.py
run -i fig1S4.py
run -i fig4S1.py
run -i ipos.py

Here is the mapping between the old and new supplemental figure names under eLife's parent/child naming scheme. This applies to both the names in the code and the paper:

Old	New
S1	1S1
S2	1S2
S3	4S1
S4a-j	1S3
S4k-t	3S1
S5	1S4
negntsr	1S5
S6	5S1

Note that depending on your system, you may have to call plt.show() to actually display figure windows after running one or more of the above scripts. Use cf() to quickly close all figures.