pulse2percept.implants.prima

PhotovoltaicPixel, PRIMA, PRIMA75, PRIMA55, PRIMA40

Classes

PRIMA([x, y, z, rot, eye, stim, preprocess, ...])	Create a PRIMA-100 array on the retina
PRIMA40([x, y, z, rot, eye, stim, ...])	Create a PRIMA-40 array on the retina
PRIMA55([x, y, z, rot, eye, stim, ...])	Create a PRIMA-55 array on the retina
PRIMA75([x, y, z, rot, eye, stim, ...])	Create a PRIMA-75 array on the retina
PhotovoltaicPixel(x, y, z, r, a[, name, ...])	Photovoltaic pixel

class pulse2percept.implants.prima.PhotovoltaicPixel(x, y, z, r, a, name=None, activated=True)

Photovoltaic pixel

Added in version 0.7.

Parameters:

• x/y/z (double) – 3D location of the electrode. The coordinate system is centered over the fovea. Positive x values move the electrode into the nasal retina. Positive y values move the electrode into the superior retina. Positive z values move the electrode away from the retina into the vitreous humor (sometimes called electrode-retina distance).

• r (double) – Disk radius in the x,y plane

• a (double) – Length of line drawn from the center of the hexagon to the midpoint of one of its sides.

• activated (bool) – To deactivate, set to False. Deactivated electrodes cannot receive stimuli.

plot(autoscale=False, ax=None)

Plot

Parameters:

• autoscale (bool, optional) – Whether to adjust the x,y limits of the plot

• ax (matplotlib.axes._subplots.AxesSubplot, optional) – A Matplotlib axes object. If None given, a new one will be created.

Returns:

ax (matplotlib.axes.Axes) – Returns the axis object of the plot

class pulse2percept.implants.prima.PRIMA(x=0, y=0, z=-100, rot=0, eye='RE', stim=None, preprocess=False, safe_mode=False)

Create a PRIMA-100 array on the retina

This class creates a PRIMA array with 378 photovoltaic pixels (each 100um in diameter) as used in the clinical trial [Palanker2020], and places it in the subretinal space such that the center of the array is located at 3D location (x,y,z), given in microns, and the array is rotated by rotation angle rot, given in degrees.

The device consists of 378 85um-wide pixels separated by 15um trenches, arranged in a 2-mm wide hexagonal pattern.

This corresponds to a 100um pitch, with adjacent rows separated by 87um. The active electrode is a disk with 28um diameter.

Added in version 0.7.

Parameters:

• x/y/z (double) – 3D location of the center of the electrode array. The coordinate system is centered over the fovea. Positive x values move the electrode into the nasal retina. Positive y values move the electrode into the superior retina. Positive z values move the electrode away from the retina into the vitreous humor (sometimes called electrode-retina distance). z can either be a list with 378 entries or a scalar that is applied to all electrodes.

• rot (float, optional) – Rotation angle of the array (deg). Positive values denote counter-clock-wise (CCW) rotations in the retinal coordinate system.

• eye ({'RE', 'LE'}, optional) – Eye in which array is implanted.

• preprocess (bool or callable, optional) – Either True/False to indicate whether to execute the implant’s default preprocessing method whenever a new stimulus is assigned, or a custom function (callable).

• safe_mode (bool, optional) – If safe mode is enabled, only charge-balanced stimuli are allowed.

Notes

• The diameter of the active electrode and the trench width were estimated from Fig.1 in [Palanker2020].

property eye

Implanted eye

A ProsthesisSystem can be implanted either in a left eye (‘LE’) or right eye (‘RE’). Models such as AxonMapModel will treat left and right eyes differently (for example, adjusting the location of the optic disc).

Examples

Implant Argus II in a left eye:

>>> from pulse2percept.implants import ArgusII
>>> implant = ArgusII(eye='LE')

property earray

Electrode array

property stim

Stimulus

A stimulus can be created from many source types, such as scalars, NumPy arrays, and dictionaries (see Stimulus for a complete list).

A stimulus can be assigned either in the ProsthesisSystem constructor or later by assigning a value to stim.

Note

Unless when using dictionary notation, the number of stimuli must equal the number of electrodes in earray.

Examples

Send a biphasic pulse (30uA, 0.45ms phase duration) to an implant made from a single DiskElectrode:

>>> from pulse2percept.implants import DiskElectrode, ProsthesisSystem
>>> from pulse2percept.stimuli import BiphasicPulse
>>> implant = ProsthesisSystem(DiskElectrode(0, 0, 0, 100))
>>> implant.stim = BiphasicPulse(30, 0.45)

Stimulate Electrode B7 in Argus II with 13 uA:

>>> from pulse2percept.implants import ArgusII
>>> implant = ArgusII(stim={'B7': 13})

check_stim(stim)

Quality-check the stimulus

This method is executed every time a new value is assigned to stim.

If safe_mode is set to True, this function will only allow stimuli that are charge-balanced.

The user can define their own checks in implants that inherit from ProsthesisSystem.

Parameters:

stim (Stimulus source type) – A valid source type for the Stimulus object (e.g., scalar, NumPy array, pulse train).

property electrode_names

Return a list of all electrode names in the electrode array

property electrode_objects

Return a list of all electrode objects in the array

property electrodes

Return all electrode names and objects in the electrode array

Internally, electrodes are stored in an ordered dictionary. You can iterate over different electrodes in the array as follows:

for name, electrode in implant.electrodes.items():
    print(name, electrode)

You can access an individual electrode by indexing directly into the prosthesis system object, e.g. implant['A1'] or implant[0].

property n_electrodes

Number of electrodes in the array

This is equivalent to calling earray.n_electrodes.

plot(annotate=False, autoscale=True, ax=None, stim_cmap=False)

Plot

Parameters:

• annotate (bool, optional) – Whether to scale the axes view to the data

• autoscale (bool, optional) – Whether to adjust the x,y limits of the plot to fit the implant

• ax (matplotlib.axes._subplots.AxesSubplot, optional) – A Matplotlib axes object. If None, will either use the current axes (if exists) or create a new Axes object.

• stim_cmap (bool, str, or matplotlib colormap, optional) – If not false, the fill color of the plotted electrodes will vary based on maximum stimulus amplitude on each electrode. The chosen colormap will be used if provided

Returns:

ax (matplotlib.axes.Axes) – Returns the axis object of the plot

preprocess_stim(stim)

Preprocess the stimulus

This methods is executed every time a new value is assigned to stim.

No preprocessing is performed by default, but the user can define their own method in implants that inherit from return stim ProsthesisSystem.

A custom method must return a Stimulus object with the correct number of electrodes for the implant.

Parameters:

stim (Stimulus source type) – A valid source type for the Stimulus object (e.g., scalar, NumPy array, pulse train).

Returns:

stim_out (Stimulus object)

class pulse2percept.implants.prima.PRIMA75(x=0, y=0, z=-100, rot=0, eye='RE', stim=None, preprocess=False, safe_mode=False)

Create a PRIMA-75 array on the retina

This class creates a PRIMA array with 142 photovoltaic pixels (each 75um in diameter) as described in [Lorach2015], and places it in the subretinal space, such that that the center of the array is located at 3D location (x,y,z), given in microns, and the array is rotated by rotation angle rot, given in degrees.

The device consists of 142 70um-wide pixels separated by 5um trenches, arranged in a 1-mm wide hexagonal pattern.

This corresponds to a 75um pitch, with adjacent rows separated by 65um. The active electrode is a disk with 20um diameter.

Added in version 0.7.

Parameters:

• x/y/z (double) – 3D location of the center of the electrode array. The coordinate system is centered over the fovea. Positive x values move the electrode into the nasal retina. Positive y values move the electrode into the superior retina. Positive z values move the electrode away from the retina into the vitreous humor (sometimes called electrode-retina distance). z can either be a list with 142 entries or a scalar that is applied to all electrodes.

• rot (float, optional) – Rotation angle of the array (deg). Positive values denote counter-clock-wise (CCW) rotations in the retinal coordinate system.

• eye ({'RE', 'LE'}, optional) – Eye in which array is implanted.

• preprocess (bool or callable, optional) – Either True/False to indicate whether to execute the implant’s default preprocessing method whenever a new stimulus is assigned, or a custom function (callable).

• safe_mode (bool, optional) – If safe mode is enabled, only charge-balanced stimuli are allowed.

property eye

Implanted eye

A ProsthesisSystem can be implanted either in a left eye (‘LE’) or right eye (‘RE’). Models such as AxonMapModel will treat left and right eyes differently (for example, adjusting the location of the optic disc).

Examples

Implant Argus II in a left eye:

>>> from pulse2percept.implants import ArgusII
>>> implant = ArgusII(eye='LE')

property earray

Electrode array

property stim

Stimulus

A stimulus can be created from many source types, such as scalars, NumPy arrays, and dictionaries (see Stimulus for a complete list).

A stimulus can be assigned either in the ProsthesisSystem constructor or later by assigning a value to stim.

Note

Unless when using dictionary notation, the number of stimuli must equal the number of electrodes in earray.

Examples

Send a biphasic pulse (30uA, 0.45ms phase duration) to an implant made from a single DiskElectrode:

>>> from pulse2percept.implants import DiskElectrode, ProsthesisSystem
>>> from pulse2percept.stimuli import BiphasicPulse
>>> implant = ProsthesisSystem(DiskElectrode(0, 0, 0, 100))
>>> implant.stim = BiphasicPulse(30, 0.45)

Stimulate Electrode B7 in Argus II with 13 uA:

>>> from pulse2percept.implants import ArgusII
>>> implant = ArgusII(stim={'B7': 13})

check_stim(stim)

Quality-check the stimulus

This method is executed every time a new value is assigned to stim.

If safe_mode is set to True, this function will only allow stimuli that are charge-balanced.

The user can define their own checks in implants that inherit from ProsthesisSystem.

Parameters:

stim (Stimulus source type) – A valid source type for the Stimulus object (e.g., scalar, NumPy array, pulse train).

property electrode_names

Return a list of all electrode names in the electrode array

property electrode_objects

Return a list of all electrode objects in the array

property electrodes

Return all electrode names and objects in the electrode array

Internally, electrodes are stored in an ordered dictionary. You can iterate over different electrodes in the array as follows:

for name, electrode in implant.electrodes.items():
    print(name, electrode)

You can access an individual electrode by indexing directly into the prosthesis system object, e.g. implant['A1'] or implant[0].

property n_electrodes

Number of electrodes in the array

This is equivalent to calling earray.n_electrodes.

plot(annotate=False, autoscale=True, ax=None, stim_cmap=False)

Plot

Parameters:

• annotate (bool, optional) – Whether to scale the axes view to the data

• autoscale (bool, optional) – Whether to adjust the x,y limits of the plot to fit the implant

• ax (matplotlib.axes._subplots.AxesSubplot, optional) – A Matplotlib axes object. If None, will either use the current axes (if exists) or create a new Axes object.

• stim_cmap (bool, str, or matplotlib colormap, optional) – If not false, the fill color of the plotted electrodes will vary based on maximum stimulus amplitude on each electrode. The chosen colormap will be used if provided

Returns:

ax (matplotlib.axes.Axes) – Returns the axis object of the plot

preprocess_stim(stim)

Preprocess the stimulus

This methods is executed every time a new value is assigned to stim.

No preprocessing is performed by default, but the user can define their own method in implants that inherit from return stim ProsthesisSystem.

A custom method must return a Stimulus object with the correct number of electrodes for the implant.

Parameters:

stim (Stimulus source type) – A valid source type for the Stimulus object (e.g., scalar, NumPy array, pulse train).

Returns:

stim_out (Stimulus object)

class pulse2percept.implants.prima.PRIMA55(x=0, y=0, z=-100, rot=0, eye='RE', stim=None, preprocess=False, safe_mode=False)

Create a PRIMA-55 array on the retina

This class creates a PRIMA array with 273 photovoltaic pixels (each 55um in diameter), and places it in the subretinal space, such that that the center of the array is located at 3D location (x,y,z), given in microns, and the array is rotated by rotation angle rot, given in degrees.

The device consists of 273 50um-wide pixels separated by 5um trenches, arranged in a 1-mm wide hexagonal pattern.

This corresponds to a 55um pitch, with adjacent rows separated by 48um. The active electrode is a disk with 16um diameter.

Warning

The exact shape of the device has not been published yet. We assume the array fits on a circular 1mm-diameter substrate, which leaves us with 273 electrodes.

Added in version 0.7.

Parameters:

• x/y/z (double) – 3D location of the center of the electrode array. The coordinate system is centered over the fovea. Positive x values move the electrode into the nasal retina. Positive y values move the electrode into the superior retina. Positive z values move the electrode away from the retina into the vitreous humor (sometimes called electrode-retina distance). z can either be a list with 378 entries or a scalar that is applied to all electrodes.

• rot (float, optional) – Rotation angle of the array (deg). Positive values denote counter-clock-wise (CCW) rotations in the retinal coordinate system.

• eye ({'RE', 'LE'}, optional) – Eye in which array is implanted.

• preprocess (bool or callable, optional) – Either True/False to indicate whether to execute the implant’s default preprocessing method whenever a new stimulus is assigned, or a custom function (callable).

• safe_mode (bool, optional) – If safe mode is enabled, only charge-balanced stimuli are allowed.

property eye

Implanted eye

A ProsthesisSystem can be implanted either in a left eye (‘LE’) or right eye (‘RE’). Models such as AxonMapModel will treat left and right eyes differently (for example, adjusting the location of the optic disc).

Examples

Implant Argus II in a left eye:

>>> from pulse2percept.implants import ArgusII
>>> implant = ArgusII(eye='LE')

property earray

Electrode array

property stim

Stimulus

A stimulus can be created from many source types, such as scalars, NumPy arrays, and dictionaries (see Stimulus for a complete list).

A stimulus can be assigned either in the ProsthesisSystem constructor or later by assigning a value to stim.

Note

Unless when using dictionary notation, the number of stimuli must equal the number of electrodes in earray.

Examples

Send a biphasic pulse (30uA, 0.45ms phase duration) to an implant made from a single DiskElectrode:

>>> from pulse2percept.implants import DiskElectrode, ProsthesisSystem
>>> from pulse2percept.stimuli import BiphasicPulse
>>> implant = ProsthesisSystem(DiskElectrode(0, 0, 0, 100))
>>> implant.stim = BiphasicPulse(30, 0.45)

Stimulate Electrode B7 in Argus II with 13 uA:

>>> from pulse2percept.implants import ArgusII
>>> implant = ArgusII(stim={'B7': 13})

check_stim(stim)

Quality-check the stimulus

This method is executed every time a new value is assigned to stim.

If safe_mode is set to True, this function will only allow stimuli that are charge-balanced.

The user can define their own checks in implants that inherit from ProsthesisSystem.

Parameters:

stim (Stimulus source type) – A valid source type for the Stimulus object (e.g., scalar, NumPy array, pulse train).

property electrode_names

Return a list of all electrode names in the electrode array

property electrode_objects

Return a list of all electrode objects in the array

property electrodes

Return all electrode names and objects in the electrode array

Internally, electrodes are stored in an ordered dictionary. You can iterate over different electrodes in the array as follows:

for name, electrode in implant.electrodes.items():
    print(name, electrode)

You can access an individual electrode by indexing directly into the prosthesis system object, e.g. implant['A1'] or implant[0].

property n_electrodes

Number of electrodes in the array

This is equivalent to calling earray.n_electrodes.

plot(annotate=False, autoscale=True, ax=None, stim_cmap=False)

Plot

Parameters:

• annotate (bool, optional) – Whether to scale the axes view to the data

• autoscale (bool, optional) – Whether to adjust the x,y limits of the plot to fit the implant

• ax (matplotlib.axes._subplots.AxesSubplot, optional) – A Matplotlib axes object. If None, will either use the current axes (if exists) or create a new Axes object.

• stim_cmap (bool, str, or matplotlib colormap, optional) – If not false, the fill color of the plotted electrodes will vary based on maximum stimulus amplitude on each electrode. The chosen colormap will be used if provided

Returns:

ax (matplotlib.axes.Axes) – Returns the axis object of the plot

preprocess_stim(stim)

Preprocess the stimulus

This methods is executed every time a new value is assigned to stim.

No preprocessing is performed by default, but the user can define their own method in implants that inherit from return stim ProsthesisSystem.

A custom method must return a Stimulus object with the correct number of electrodes for the implant.

Parameters:

stim (Stimulus source type) – A valid source type for the Stimulus object (e.g., scalar, NumPy array, pulse train).

Returns:

stim_out (Stimulus object)

class pulse2percept.implants.prima.PRIMA40(x=0, y=0, z=-100, rot=0, eye='RE', stim=None, preprocess=False, safe_mode=False)

Create a PRIMA-40 array on the retina

This class creates a PRIMA array with 532 photovoltaic pixels (each 40um in diameter), and places it in the subretinal space, such that that the center of the array is located at 3D location (x,y,z), given in microns, and the array is rotated by rotation angle rot, given in degrees.

The device consists of 532 35um-wide pixels separated by 5um trenches, arranged in a 1-mm wide hexagonal pattern.

This corresponds to a 40um pitch, with adjacent rows separated by 48um. The active electrode is a disk with 16um diameter.

Important

The exact shape of the device has not been published yet. We assume the array fits on a circular 1mm-diameter substrate, which leaves us with 532 electrodes.

Added in version 0.7.

Parameters:

• x/y/z (double) – 3D location of the center of the electrode array. The coordinate system is centered over the fovea. Positive x values move the electrode into the nasal retina. Positive y values move the electrode into the superior retina. Positive z values move the electrode away from the retina into the vitreous humor (sometimes called electrode-retina distance). z can either be a list with 532 entries or a scalar that is applied to all electrodes.

• rot (float, optional) – Rotation angle of the array (deg). Positive values denote counter-clock-wise (CCW) rotations in the retinal coordinate system.

• eye ({'LE', 'RE'}, optional) – Eye in which array is implanted.

• preprocess (bool or callable, optional) – Either True/False to indicate whether to execute the implant’s default preprocessing method whenever a new stimulus is assigned, or a custom function (callable).

• safe_mode (bool, optional) – If safe mode is enabled, only charge-balanced stimuli are allowed.

property eye

Implanted eye

A ProsthesisSystem can be implanted either in a left eye (‘LE’) or right eye (‘RE’). Models such as AxonMapModel will treat left and right eyes differently (for example, adjusting the location of the optic disc).

Examples

Implant Argus II in a left eye:

>>> from pulse2percept.implants import ArgusII
>>> implant = ArgusII(eye='LE')

property earray

Electrode array

property stim

Stimulus

A stimulus can be created from many source types, such as scalars, NumPy arrays, and dictionaries (see Stimulus for a complete list).

A stimulus can be assigned either in the ProsthesisSystem constructor or later by assigning a value to stim.

Note

Unless when using dictionary notation, the number of stimuli must equal the number of electrodes in earray.

Examples

Send a biphasic pulse (30uA, 0.45ms phase duration) to an implant made from a single DiskElectrode:

>>> from pulse2percept.implants import DiskElectrode, ProsthesisSystem
>>> from pulse2percept.stimuli import BiphasicPulse
>>> implant = ProsthesisSystem(DiskElectrode(0, 0, 0, 100))
>>> implant.stim = BiphasicPulse(30, 0.45)

Stimulate Electrode B7 in Argus II with 13 uA:

>>> from pulse2percept.implants import ArgusII
>>> implant = ArgusII(stim={'B7': 13})

check_stim(stim)

Quality-check the stimulus

This method is executed every time a new value is assigned to stim.

If safe_mode is set to True, this function will only allow stimuli that are charge-balanced.

The user can define their own checks in implants that inherit from ProsthesisSystem.

Parameters:

stim (Stimulus source type) – A valid source type for the Stimulus object (e.g., scalar, NumPy array, pulse train).

property electrode_names

Return a list of all electrode names in the electrode array

property electrode_objects

Return a list of all electrode objects in the array

property electrodes

Return all electrode names and objects in the electrode array

Internally, electrodes are stored in an ordered dictionary. You can iterate over different electrodes in the array as follows:

for name, electrode in implant.electrodes.items():
    print(name, electrode)

You can access an individual electrode by indexing directly into the prosthesis system object, e.g. implant['A1'] or implant[0].

property n_electrodes

Number of electrodes in the array

This is equivalent to calling earray.n_electrodes.

plot(annotate=False, autoscale=True, ax=None, stim_cmap=False)

Plot

Parameters:

• annotate (bool, optional) – Whether to scale the axes view to the data

• autoscale (bool, optional) – Whether to adjust the x,y limits of the plot to fit the implant

• ax (matplotlib.axes._subplots.AxesSubplot, optional) – A Matplotlib axes object. If None, will either use the current axes (if exists) or create a new Axes object.

• stim_cmap (bool, str, or matplotlib colormap, optional) – If not false, the fill color of the plotted electrodes will vary based on maximum stimulus amplitude on each electrode. The chosen colormap will be used if provided

Returns:

ax (matplotlib.axes.Axes) – Returns the axis object of the plot

preprocess_stim(stim)

Preprocess the stimulus

This methods is executed every time a new value is assigned to stim.

No preprocessing is performed by default, but the user can define their own method in implants that inherit from return stim ProsthesisSystem.

A custom method must return a Stimulus object with the correct number of electrodes for the implant.

Parameters:

stim (Stimulus source type) – A valid source type for the Stimulus object (e.g., scalar, NumPy array, pulse train).

Returns:

stim_out (Stimulus object)