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@@ -2,7 +2,36 @@
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Data and code for Crombie et al. "Spiking activity in the visual thalamus is coupled to pupil dynamics across temporal scales"
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-### How to
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-To generate figures from already processed data, copy the .pkl files out of data/original_cooked/ into data/ and then run the corresponding cells in the figures notebooks. Note that notebook cells should be run in order to avoid variable name conflicts.
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+## How to
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-To re-generate the processed data, run the corresponding .py file with the desired arguments. The primary argument is the experiment name, which can be 'spontaneous', 'sparsenoise', 'dark', 'natmov', and 'natmov_opto'.
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+### Figures
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+To generate figures from already processed data, copy the `*.pkl` data files out of `data/original_cooked/` and `data/original_raw` into `data/` and then run the corresponding cells in the `figures_*.ipynp` Jupyter notebooks. Note that notebook cells should be run in order to avoid variable name conflicts. Figures will by default be stored in the `figures/` folder, which also contains sub-folder
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+
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+**Note** : Because many of the analyses involve randomization (e.g. comparison to random permutations of the data), the original figures may only be *exactly* reproduced by using the data files from the `original_cooked` folder.
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+
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+### Analyses
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+Data for this project is stored as "pickled" Pandas DataFrame objects. The "raw" data, including `pupil_*.pkl`, `spikes_*.pkl`, `ball_*.pkl`, and `trials_*.pkl`, are minimally-processed data to be used in further analyses.
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+
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+To re-generate the processed ("cooked") data, run the corresponding `*.py` file with the desired arguments. The positional argument `e_name` specifies the experiment name, and is required for all scripts. It can be one of
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+
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+- 'spontaneous' : experiments where the monitor displayed a uniform gray screen
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+- 'sparsenoise' : experiments with sparse noise visual stimulation
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+- 'dark' : experiments where the display monitor was switched off and other sources of illumination were covered
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+- 'natmov' : experiments with repeated trial of a naturalistic video clip
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+- 'natmov_opto' : experiments with repeated trials of a naturalistic video clip, trials with optogenetic stimulation of V1 PV neurons are interleaved pseudo-randomly
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+
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+**Note** : Spontaneous and sparse noise experiments are generally analyzed together, but the analysis scripts need to be run separately for each experiment type.
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+
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+Other arguments may include:
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+
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+Spike type : --spk_type -s
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+- 'tonicskp' : tonic spikes, i.e. all spikes that are not part of a burst
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+- 'burst' : burst events, i.e. the first spike in a burst
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+- 'spk' : all spikes, i.e. any spike regardless of whether it is part of a burst or not
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+
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+Time ranges : --tranges -t
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+- 'run'
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+- 'sit'
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+- 'nosaccade'
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+- 'noopto'
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+- 'desync'
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