Import/export functions

probeinterface has its own format based on JSON. The format can handle several probes in one file. It has a ‘probes’ key that can contain a list of probes.

Each probe field in the json format contains the Probe class attributes.

It also supports reading (and sometimes writing) from these formats:

• PRB (.prb) : used by klusta/spyking-circus/tridesclous

• CSV (.csv): 2 or 3 columns locations in text file

• mearec (.h5) : mearec handles the geometry

• spikeglx (.meta) : spikeglx also handles the geometry

Import

import numpy as np
import matplotlib.pyplot as plt

from probeinterface import Probe, ProbeGroup
from probeinterface.plotting import plot_probe, plot_probe_group
from probeinterface import generate_dummy_probe
from probeinterface import write_probeinterface, read_probeinterface
from probeinterface import write_prb, read_prb

Let’s first generate 2 dummy probes and combine them into a ProbeGroup

probe0 = generate_dummy_probe(elec_shapes='square')
probe1 = generate_dummy_probe(elec_shapes='circle')
probe1.move([250, -90])

probegroup = ProbeGroup()
probegroup.add_probe(probe0)
probegroup.add_probe(probe1)

With the write_probeinterface and read_probeinterface functions we can write to and read from the json-based probeinterface format:

write_probeinterface('my_two_probe_setup.json', probegroup)

probegroup2 = read_probeinterface('my_two_probe_setup.json')
plot_probe_group(probegroup2)

/home/docs/checkouts/readthedocs.org/user_builds/probeinterface/checkouts/main/examples/ex_06_import_export_to_file.py:51: DeprecationWarning: `plot_probe_group` is deprecated and will be removed in 2.23. Use plot_probegroup instead
  plot_probe_group(probegroup2)

The format looks like this:

with open('my_two_probe_setup.json', mode='r') as f:
    txt = f.read()

print(txt[:600], '...')

{
    "specification": "probeinterface",
    "version": "0.2.24",
    "probes": [
        {
            "ndim": 2,
            "si_units": "um",
            "annotations": {
                "manufacturer": "me"
            },
            "contact_annotations": {
                "quality": [
                    1000.0,
                    1000.0,
                    1000.0,
                    1000.0,
                    1000.0,
                    1000.0,
                    1000.0,
                    1000.0,
                    1000.0,
                    1000.0,
                    1000.0,
 ...

PRB is an historical format introduced by the Klusta team and it is also used by SpikeInterface, Spyking-circus, and Tridesclous. The format is in fact a python script that describes a dictionary. This format handles:

• multiple groups (multi-shank or multi-probe)

• contact_positions with ‘geometry’

• device_channel_indices with ‘channels’

Here is an example of a .prb file with 2 channel groups of 4 channels each. It can be easily loaded and plotted with probeinterface

prb_two_tetrodes = """
channel_groups = {
    0: {
            'channels' : [0,1,2,3],
            'geometry': {
                0: [0, 50],
                1: [50, 0],
                2: [0, -50],
                3: [-50, 0],
            }
    },
    1: {
            'channels' : [4,5,6,7],
            'geometry': {
                4: [0, 50],
                5: [50, 0],
                6: [0, -50],
                7: [-50, 0],
            }
    }
}
"""

with open('two_tetrodes.prb', 'w') as f:
    f.write(prb_two_tetrodes)

two_tetrode = read_prb('two_tetrodes.prb')
plot_probe_group(two_tetrode, same_axes=False, with_contact_id=True)

plt.show()

/home/docs/checkouts/readthedocs.org/user_builds/probeinterface/checkouts/main/examples/ex_06_import_export_to_file.py:101: DeprecationWarning: `plot_probe_group` is deprecated and will be removed in 2.23. Use plot_probegroup instead
  plot_probe_group(two_tetrode, same_axes=False, with_contact_id=True)