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@@ -36,15 +36,15 @@ Time ranges : --tranges -t
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- 'sit' : behavioral quiescence (no locomotion)
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- 'nosaccade' : periods with no saccadic eye movements
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- 'noopto' : trials without optogenetic stimulation
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-- 'desync' :
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-- 'sizematched'
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+- 'desync' : exclusion of time periods during which the IMF goes through phase combinations with other IMFs that occur more frequently than by chance (as per the analysis in Figure S1D)
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+- 'sizematched' : time periods sub-sampled so as to match the distribution of pupil sizes across IMF phase bins (as per Figure 3A)
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**Note** : the `imf_decoding.py` script will automatically look for `phasetuning` data from the `noopto` time ranges.
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Analysis and plotting parameters are stored in `parameters.py`. Useful, general-purpose functions are stored in the `util.py` module.
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## Nomenclature
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-Experimental units are defined using a MSEU nomenclature: mouse (the strain, year, and ID of a mouse, e.g. 'PVCre_2020_0001'), series (recording session, during which several experimental stimulation protocols are carried out, e.g. 's01'), experiment (a single experiment, e.g. e01), unit (a putative neuron identified by spike sorting, e.g. 'u10').
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+Experimental units are defined using a MSEU nomenclature: mouse (the strain, year, and ID of a mouse, e.g. 'PVCre_2020_0001'), series (recording session, during which several experimental stimulation protocols are carried out, e.g. 's01'), experiment (a single experiment, e.g. e01), unit (a putative neuron identified by spike sorting, e.g. 'u10'). Every row in a dataframe typically has some combination of these dentifiers which can be used as an index, and to group or merge the data.
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The folloing terms are used interchangeably:
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@@ -52,4 +52,7 @@ Intrinsic mode function (IMF) == component of pupil dynamics (CPD) == timescale
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- a component resulting from application of Empirical Mode Decomposition (EMD) to the pupil size timeseries
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Characteristic frequency == frequency == timescale
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-- the value (1/seconds) used to characterise a CPD by taking the mean amplitude-weighted instantaneous frequency
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+- the value (1/seconds) used to characterise a CPD by taking the mean amplitude-weighted instantaneous frequency
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+
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+Phase tuning == phase coupling
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+- the tendency for spikes or bursts to occur more during certain phases of the IMFs derived from the pupil size time series, as per the analysis method introduced in Figure 2
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