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add bap and ais check to feature doc
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Jaquier Aurélien Tristan committed Oct 30, 2024
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34 changes: 33 additions & 1 deletion docs/source/eFeatures.rst
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Expand Up @@ -862,6 +862,17 @@ The burst detection can be fine-tuned by changing the setting strict_burst_facto

return time_to_postburst_adp_peaks

check_ais_initiation
~~~~~~~~~~~~~~~~~~~~

`Validation Python efeature`_ : Checks the initiation of action potential in AIS with respect to soma.
Returns True if no spike in the soma starts earlier than in the AIS.

Attention! This cannot be used with the efel.get_feature_values function. You have to use the efel.pyfeatures.validation.check_ais_initiation function,
and pass it both the soma trace and the ais trace.

- **Required features**: AP_begin_time
- **Units**: constant


Spike shape features
Expand Down Expand Up @@ -1612,6 +1623,21 @@ initburst_sahp_vb

numpy.array([initburst_sahp_value[0] - voltage_base[0]])

bpap_attenuation
~~~~~~~~~~~~~~~~

`bAP Python efeature`_ : Attenuation (ratio of the amplitude of the action potential in the soma and the dendrite) of the backpropagating action potential.
The attenuation is computed by first subtracting the resting potential from the voltage traces.

Attention! This cannot be used with the efel.get_feature_values function. You have to use the efel.pyfeatures.multitrace.bpap_attenuation function,
and pass it both the soma trace and the dendrite trace.

- **Required features**: voltage_base
- **Units**: constant
- **Pseudocode**: ::

return (numpy.max(v_soma) - vb_soma) / (numpy.max(v_dend) - vb_dend)

Subthreshold features
---------------------

Expand Down Expand Up @@ -2216,7 +2242,11 @@ These features were written by Alessio Buccino and are described in
`Buccino et al., 2024 <https://doi.org/10.1162/neco_a_01672>`_ .
The feautures can be either absolute, computed for each channel separately, or
relative, computed with respect to the channel with the largest extracellular
signal amplitude:
signal amplitude.

Attention! These features cannot be extracted with the usual get_feature_values function.
They have to be extracted using the efel.pyfeatures.extrafeats module.
To see how to use it, have a look at the `Extracellular Features Extraction for MEA Data <https://efel.readthedocs.io/en/latest/extrafeats_example.html>`_ examples.


peak_to_valley
Expand Down Expand Up @@ -2487,3 +2517,5 @@ positive signal-amplitude value on the largest-amplitude channel.
.. _Python efeature: https://github.com/BlueBrain/eFEL/blob/master/efel/pyfeatures/pyfeatures.py
.. _ISI Python efeature: https://github.com/BlueBrain/eFEL/blob/master/efel/pyfeatures/isi.py
.. _Extracellular: https://github.com/BlueBrain/eFEL/blob/master/efel/pyfeatures/extrafeats.py
.. _bAP Python efeature: https://github.com/BlueBrain/eFEL/blob/master/efel/pyfeatures/multitrace.py
.. _Validation Python efeature: https://github.com/BlueBrain/eFEL/blob/master/efel/pyfeatures/validation.py
4 changes: 3 additions & 1 deletion efel/units/units.json
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Expand Up @@ -159,5 +159,7 @@
"pos_image": "constant",
"activation_time_constant": "ms",
"deactivation_time_constant": "ms",
"inactivation_time_constant": "ms"
"inactivation_time_constant": "ms",
"check_ais_initiation": "constant",
"bpap_attenuation": "constant"
}

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