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@jmarkow
jmarkow committed Jan 25, 2016
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Expand Up @@ -40,49 +40,49 @@ Fully automated sorting

``spikoclust_sort`` takes care of all the gory details for you, providing a wrapper for many key steps to spike sorting (extracting spikes, aligning, noise-whitening, cluster). If you want to perform each of these steps separately in the MATLAB command window (perhaps to pipe output to another program, eh em), see below. Here are all of the options you can pass to spikoclust_sort. Note that all options after the second option, the first two being the data matrix and the sampling rate, are as passed parameter/value pairs.

+--------------------+----------------------------------------------------------------------------------+--------------------------------+-------------------------+---------------+
| Parameter | Description | Format | Options | Default |
+====================+==================================================================================+================================+=========================+===============+
| ``noise_removal`` | Method of noise rejection (common average) | string | ``car,none`` | ``none`` |
+--------------------+----------------------------------------------------------------------------------+--------------------------------+-------------------------+---------------+
| ``car_trim`` | If using common average, trim N/2 percent of data on each end before taking mean | float | N/A | ``40`` |
+--------------------+----------------------------------------------------------------------------------+--------------------------------+-------------------------+---------------+
| ``freq_range`` | Frequency range for filtering | 1-2 element vector of floats | N/A | [400] |
+--------------------+----------------------------------------------------------------------------------+--------------------------------+-------------------------+---------------+
| ``filt_type`` | Filter class | ``high``,``low``,``bandpass`` | string | ``high`` |
+--------------------+----------------------------------------------------------------------------------+--------------------------------+-------------------------+---------------+
| ``filt_order`` | Filter order | integer | N/A | ``3`` |
+--------------------+----------------------------------------------------------------------------------+--------------------------------+-------------------------+---------------+
| ``filt_name`` | Filter type | string | ``butter,ellip,kaiser`` | ``ellip`` |
+--------------------+----------------------------------------------------------------------------------+--------------------------------+-------------------------+---------------+
| ``sigma_t`` | Detection threshold (multiple of robust standard deviation) | float | N/A | ``4`` |
+--------------------+----------------------------------------------------------------------------------+--------------------------------+-------------------------+---------------+
| ``detect_method`` | Detect negative-going spikes, positive-going spikes, or both | string | ``n,p,b`` | |
+--------------------+----------------------------------------------------------------------------------+--------------------------------+-------------------------+---------------+
| ``spike_window`` | Size of spike window (in s before and after spike) | 2 element vector of floats (s) | N/A | [.0005 .0005] |
+--------------------+----------------------------------------------------------------------------------+--------------------------------+-------------------------+---------------+
| ``interp_f`` | Interpolation factor (interpolate spikes by a factor of N) | integer | N/A | ``8`` |
+--------------------+----------------------------------------------------------------------------------+--------------------------------+-------------------------+---------------+
| ``align_feature`` | Feature used for spike re-alignment | string | ``min,max,com`` | ``min`` |
+--------------------+----------------------------------------------------------------------------------+--------------------------------+-------------------------+---------------+
| ``jitter`` | Limit on number of samples a spike may be moved for re-alignment | integer | N/A | ``10`` |
+--------------------+----------------------------------------------------------------------------------+--------------------------------+-------------------------+---------------+
| ``gui_clust`` | Use the GUI assistant | logic | N/A | ``1`` |
+--------------------+----------------------------------------------------------------------------------+--------------------------------+-------------------------+---------------+
| ``clust_check`` | Number of spikes to check for | vector of integers | N/A | ``[2:8]`` |
+--------------------+----------------------------------------------------------------------------------+--------------------------------+-------------------------+---------------+
| ``pcs`` | Number of principal components to compute/use | integer | N/A | ``2`` |
+--------------------+----------------------------------------------------------------------------------+--------------------------------+-------------------------+---------------+
| ``garbage`` | Use a garbage component in the mixture to exclude outliers? | logic | N/A | ``1`` |
+--------------------+----------------------------------------------------------------------------------+--------------------------------+-------------------------+---------------+
| ``smem`` | Use split-and-merge EM rather than standard EM? | logic | N/A | ``1`` |
+--------------------+----------------------------------------------------------------------------------+--------------------------------+-------------------------+---------------+
| ``modelselection`` | Technique to use for selecting the number of neurons | string | ``icl,bic,aic`` | ``icl`` |
+--------------------+----------------------------------------------------------------------------------+--------------------------------+-------------------------+---------------+
| ``maxnoisetraces`` | Maximum number of traces to use to compute noise covariance | integer | N/A | ``1e6`` |
+--------------------+----------------------------------------------------------------------------------+--------------------------------+-------------------------+---------------+
| ``noisewhiten`` | Enable noise whitening? | logic | N/A | ``1`` |
+--------------------+----------------------------------------------------------------------------------+--------------------------------+-------------------------+---------------+
+--------------------+----------------------------------------------------------------------------------+--------------------------------+-------------------------+-------------------+
| Parameter | Description | Format | Options | Default |
+====================+==================================================================================+================================+=========================+===================+
| ``noise_removal`` | Method of noise rejection (common average) | string | ``car,none`` | ``none`` |
+--------------------+----------------------------------------------------------------------------------+--------------------------------+-------------------------+-------------------+
| ``car_trim`` | If using common average, trim N/2 percent of data on each end before taking mean | float | N/A | ``40`` |
+--------------------+----------------------------------------------------------------------------------+--------------------------------+-------------------------+-------------------+
| ``freq_range`` | Frequency range for filtering | 1-2 element vector of floats | N/A | ``[400]`` |
+--------------------+----------------------------------------------------------------------------------+--------------------------------+-------------------------+-------------------+
| ``filt_type`` | Filter class | ``high,low,bandpass`` | string | ``high`` |
+--------------------+----------------------------------------------------------------------------------+--------------------------------+-------------------------+-------------------+
| ``filt_order`` | Filter order | integer | N/A | ``3`` |
+--------------------+----------------------------------------------------------------------------------+--------------------------------+-------------------------+-------------------+
| ``filt_name`` | Filter type | string | ``butter,ellip,kaiser`` | ``ellip`` |
+--------------------+----------------------------------------------------------------------------------+--------------------------------+-------------------------+-------------------+
| ``sigma_t`` | Detection threshold (multiple of robust standard deviation) | float | N/A | ``4`` |
+--------------------+----------------------------------------------------------------------------------+--------------------------------+-------------------------+-------------------+
| ``detect_method`` | Detect negative-going spikes, positive-going spikes, or both | string | ``n,p,b`` | |
+--------------------+----------------------------------------------------------------------------------+--------------------------------+-------------------------+-------------------+
| ``spike_window`` | Size of spike window (in s before and after spike) | 2 element vector of floats (s) | N/A | ``[.0005 .0005]`` |
+--------------------+----------------------------------------------------------------------------------+--------------------------------+-------------------------+-------------------+
| ``interp_f`` | Interpolation factor (interpolate spikes by a factor of N) | integer | N/A | ``8`` |
+--------------------+----------------------------------------------------------------------------------+--------------------------------+-------------------------+-------------------+
| ``align_feature`` | Feature used for spike re-alignment | string | ``min,max,com`` | ``min`` |
+--------------------+----------------------------------------------------------------------------------+--------------------------------+-------------------------+-------------------+
| ``jitter`` | Limit on number of samples a spike may be moved for re-alignment | integer | N/A | ``10`` |
+--------------------+----------------------------------------------------------------------------------+--------------------------------+-------------------------+-------------------+
| ``gui_clust`` | Use the GUI assistant | logic | N/A | ``1`` |
+--------------------+----------------------------------------------------------------------------------+--------------------------------+-------------------------+-------------------+
| ``clust_check`` | Number of spikes to check for | vector of integers | N/A | ``[2:8]`` |
+--------------------+----------------------------------------------------------------------------------+--------------------------------+-------------------------+-------------------+
| ``pcs`` | Number of principal components to compute/use | integer | N/A | ``2`` |
+--------------------+----------------------------------------------------------------------------------+--------------------------------+-------------------------+-------------------+
| ``garbage`` | Use a garbage component in the mixture to exclude outliers? | logic | N/A | ``1`` |
+--------------------+----------------------------------------------------------------------------------+--------------------------------+-------------------------+-------------------+
| ``smem`` | Use split-and-merge EM rather than standard EM? | logic | N/A | ``1`` |
+--------------------+----------------------------------------------------------------------------------+--------------------------------+-------------------------+-------------------+
| ``modelselection`` | Technique to use for selecting the number of neurons | string | ``icl,bic,aic`` | ``icl`` |
+--------------------+----------------------------------------------------------------------------------+--------------------------------+-------------------------+-------------------+
| ``maxnoisetraces`` | Maximum number of traces to use to compute noise covariance | integer | N/A | ``1e6`` |
+--------------------+----------------------------------------------------------------------------------+--------------------------------+-------------------------+-------------------+
| ``noisewhiten`` | Enable noise whitening? | logic | N/A | ``1`` |
+--------------------+----------------------------------------------------------------------------------+--------------------------------+-------------------------+-------------------+

Stepwise sorting
----------------
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