ibllib.pipes.ephys_tasks

Classes

EphysCellsQc

EphysCompressNP1

EphysCompressNP21

EphysCompressNP24

Compresses NP2.4 data by splitting into N binary files, corresponding to N shanks

EphysPulses

Extract Pulses from raw electrophysiology data into numpy arrays Perform the probes synchronisation with nidq (3B) or main probe (3A) First the job extract the sync pulses from the synchronisation task in all probes, and then perform the synchronisation with the nidq

EphysRegisterRaw

Creates the probe insertions and uploads the probe descriptions file, also compresses the nidq files and uploads

EphysSyncPulses

EphysSyncRegisterRaw

Task to rename, compress and register raw daq data with .bin format collected using NIDAQ

RawEphysQC

SpikeSorting

Pykilosort 2.5 pipeline
class EphysRegisterRaw(session_path, **kwargs)[source]

Bases: DynamicTask

Creates the probe insertions and uploads the probe descriptions file, also compresses the nidq files and uploads

priority = 100
job_size = 'small'
property signature

dict() -> new empty dictionary dict(mapping) -> new dictionary initialized from a mapping object’s

(key, value) pairs

dict(iterable) -> new dictionary initialized as if via:

d = {} for k, v in iterable:

d[k] = v

dict(**kwargs) -> new dictionary initialized with the name=value pairs

in the keyword argument list. For example: dict(one=1, two=2)

class EphysSyncRegisterRaw(session_path, **kwargs)[source]

Bases: DynamicTask

Task to rename, compress and register raw daq data with .bin format collected using NIDAQ

priority = 90
cpu = 2
io_charge = 30
job_size = 'small'
property signature

dict() -> new empty dictionary dict(mapping) -> new dictionary initialized from a mapping object’s

(key, value) pairs

dict(iterable) -> new dictionary initialized as if via:

d = {} for k, v in iterable:

d[k] = v

dict(**kwargs) -> new dictionary initialized with the name=value pairs

in the keyword argument list. For example: dict(one=1, two=2)

class EphysCompressNP1(session_path, **kwargs)[source]

Bases: EphysTask

priority = 90
cpu = 2
io_charge = 100
job_size = 'small'
property signature

dict() -> new empty dictionary dict(mapping) -> new dictionary initialized from a mapping object’s

(key, value) pairs

dict(iterable) -> new dictionary initialized as if via:

d = {} for k, v in iterable:

d[k] = v

dict(**kwargs) -> new dictionary initialized with the name=value pairs

in the keyword argument list. For example: dict(one=1, two=2)

class EphysCompressNP21(session_path, **kwargs)[source]

Bases: EphysTask

priority = 90
cpu = 2
io_charge = 100
job_size = 'large'
property signature

dict() -> new empty dictionary dict(mapping) -> new dictionary initialized from a mapping object’s

(key, value) pairs

dict(iterable) -> new dictionary initialized as if via:

d = {} for k, v in iterable:

d[k] = v

dict(**kwargs) -> new dictionary initialized with the name=value pairs

in the keyword argument list. For example: dict(one=1, two=2)

class EphysCompressNP24(session_path, *args, pname=None, device_collection='raw_ephys_data', nshanks=None, **kwargs)[source]

Bases: EphysTask

Compresses NP2.4 data by splitting into N binary files, corresponding to N shanks

Parameters:

  • pname – a probe name string

  • device_collection – the collection containing the probes (usually ‘raw_ephys_data’)

  • nshanks – number of shanks used (usually 4 but it may be less depending on electrode map), optional

priority = 90
cpu = 2
io_charge = 100
job_size = 'large'
property signature

dict() -> new empty dictionary dict(mapping) -> new dictionary initialized from a mapping object’s

(key, value) pairs

dict(iterable) -> new dictionary initialized as if via:

d = {} for k, v in iterable:

d[k] = v

dict(**kwargs) -> new dictionary initialized with the name=value pairs

in the keyword argument list. For example: dict(one=1, two=2)

class EphysSyncPulses(session_path, **kwargs)[source]

Bases: SyncPulses

priority = 90
cpu = 2
io_charge = 30
job_size = 'small'
property signature

dict() -> new empty dictionary dict(mapping) -> new dictionary initialized from a mapping object’s

(key, value) pairs

dict(iterable) -> new dictionary initialized as if via:

d = {} for k, v in iterable:

d[k] = v

dict(**kwargs) -> new dictionary initialized with the name=value pairs

in the keyword argument list. For example: dict(one=1, two=2)

class EphysPulses(*args, **kwargs)[source]

Bases: EphysTask

Extract Pulses from raw electrophysiology data into numpy arrays Perform the probes synchronisation with nidq (3B) or main probe (3A) First the job extract the sync pulses from the synchronisation task in all probes, and then perform the

synchronisation with the nidq

Parameters:

  • pname – a list of probes names or a single probe name string

  • device_collection – the collection containing the probes (usually ‘raw_ephys_data’)

  • sync_collection – the collection containing the synchronisation device - nidq (usually ‘raw_ephys_data’)

priority = 90
cpu = 2
io_charge = 30
job_size = 'small'
property signature

dict() -> new empty dictionary dict(mapping) -> new dictionary initialized from a mapping object’s

(key, value) pairs

dict(iterable) -> new dictionary initialized as if via:

d = {} for k, v in iterable:

d[k] = v

dict(**kwargs) -> new dictionary initialized with the name=value pairs

in the keyword argument list. For example: dict(one=1, two=2)

class RawEphysQC(session_path, **kwargs)[source]

Bases: EphysTask

cpu = 2
io_charge = 30
priority = 10
job_size = 'small'
property signature

dict() -> new empty dictionary dict(mapping) -> new dictionary initialized from a mapping object’s

(key, value) pairs

dict(iterable) -> new dictionary initialized as if via:

d = {} for k, v in iterable:

d[k] = v

dict(**kwargs) -> new dictionary initialized with the name=value pairs

in the keyword argument list. For example: dict(one=1, two=2)

class SpikeSorting(session_path, **kwargs)[source]

Bases: EphysTask

Pykilosort 2.5 pipeline

gpu = 1
io_charge = 100
priority = 60
job_size = 'large'
force = True
SHELL_SCRIPT = PosixPath('/home/runner/Documents/PYTHON/iblscripts/deploy/serverpc/kilosort2/run_pykilosort.sh')
SPIKE_SORTER_NAME = 'pykilosort'
PYKILOSORT_REPO = PosixPath('/home/runner/Documents/PYTHON/SPIKE_SORTING/pykilosort')
property signature

dict() -> new empty dictionary dict(mapping) -> new dictionary initialized from a mapping object’s

(key, value) pairs

dict(iterable) -> new dictionary initialized as if via:

d = {} for k, v in iterable:

d[k] = v

dict(**kwargs) -> new dictionary initialized with the name=value pairs

in the keyword argument list. For example: dict(one=1, two=2)

class EphysCellsQc(session_path, **kwargs)[source]

Bases: EphysTask

priority = 90
job_size = 'small'
property signature

dict() -> new empty dictionary dict(mapping) -> new dictionary initialized from a mapping object’s

(key, value) pairs

dict(iterable) -> new dictionary initialized as if via:

d = {} for k, v in iterable:

d[k] = v

dict(**kwargs) -> new dictionary initialized with the name=value pairs

in the keyword argument list. For example: dict(one=1, two=2)