Neo

0.14.4 verified Mon Apr 27 auth: no python

Neo is a Python package for representing electrophysiology data, with support for reading a wide range of neurophysiology file formats. Current version 0.14.4, requires Python >=3.10. Release cadence is irregular.

pip install neo

Common errors

error ImportError: cannot import name 'Block' from 'neo' ↓

cause Block and other core classes moved from neo top-level to neo.core in version 0.10.0.

fix

Use 'from neo.core import Block'.

error ValueError: Must supply units for AnalogSignal ↓

cause AnalogSignal requires units parameter as a quantities object.

fix

Add units='mV' or similar using quantities (import quantities as pq).

error TypeError: unsupported operand type(s) for /: 'Quantity' and 'Quantity' ↓

cause Mixing incompatible units in operations.

fix

Convert units to a common base before arithmetic, e.g., signal.rescale('mV').

Warnings

breaking In version 0.10.0, core classes were moved from neo.core to neo.core, but the top-level imports (e.g., from neo import Block) were removed. Use from neo.core import ... ↓

fix Change 'from neo import Block' to 'from neo.core import Block'.

breaking Units handling changed: quantities become mandatory for signal and spike train objects. Passing plain numbers without units may raise errors or produce unexpected behavior. ↓

fix Always use quantities (e.g., 1.0*pq.s) for time and amplitude values.

deprecated The 'file_io' subpackage is deprecated in favor of 'io'. Importing from neo.file_io will emit a deprecation warning. ↓

fix Use 'from neo.io import ...' instead of 'from neo.file_io import ...'.

gotcha Data arrays for AnalogSignal must be 2D (time x channel) even for single-channel data. If you pass a 1D array, it may automatically reshape but check shape. ↓

fix Ensure signal data is 2D, e.g., np.random.rand(100, 1).

Imports

Block
wrong
```
from neo import Block
```
correct
```
from neo.core import Block
```
Block is now in neo.core, not top-level since 0.10.0.

Segment

wrong

from neo import Segment

correct

from neo.core import Segment

Segment moved to neo.core.

AnalogSignal

wrong

from neo import AnalogSignal

correct

from neo.core import AnalogSignal

AnalogSignal moved to neo.core.

SpikeTrain

wrong

from neo import SpikeTrain

correct

from neo.core import SpikeTrain

SpikeTrain moved to neo.core.

Quickstart

Quickstart: creating a basic hierarchical data structure with Block, Segment, AnalogSignal, and SpikeTrain.

import neo
from neo.core import Block, Segment, AnalogSignal, SpikeTrain
import quantities as pq
import numpy as np

# Create a Block with a Segment
block = Block(name='example')
seg = Segment(name='segment1')
block.segments.append(seg)

# Create an AnalogSignal (1 second of data, 100 Hz)
signal = AnalogSignal(np.random.rand(100), sampling_rate=100*pq.Hz, units='mV', name='test')
seg.analogsignals.append(signal)

# Create a SpikeTrain
st = SpikeTrain([0.1, 0.2, 0.3, 0.5]*pq.s, t_stop=1.0*pq.s, units='s', name='test_spikes')
seg.spiketrains.append(st)

print('Block:', block)
print('Signals:', seg.analogsignals)
print('Spike trains:', seg.spiketrains)