SpikeInterface/spikeinterface

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A Python-based module for creating flexible and robust spike sorting pipelines.

Stars: 847
Forks: 280
Open beginner issues: 2
Indexed issues: 286
Avg merge: 3d 9h
Merged PRs (30d): 29

Dominant language: Python
License: MIT
Last GitHub push: Sep 18, 2026
Latest indexed: Sep 20, 2026
Contributing guide: No contributing guide
Code of conduct: Code of conduct
Beginner labels: No beginner labels indexed

Beginner friendly Everything

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286 open issues indexed

GatherToNpy/Zarr could pre-allocate stores when number of spike is known Open

performance

Difficulty 4/5 3-5 days Newbie friendliness 55/100

SpikeInterface/spikeinterface#4787 · Opened Sep 16, 2026
Lets keep in mind that changing the spike dtype could break the numba kernel Open

Difficulty 4/5 3-5 days Newbie friendliness 30/100

SpikeInterface/spikeinterface#4781 · 1 comment · Opened Sep 15, 2026
DartSort: optimize strategy to retrieve `main_channel_id` from sorting Open

performance sorters

Difficulty 4/5 3-5 days Newbie friendliness 30/100

SpikeInterface/spikeinterface#4777 · Opened Sep 14, 2026
Kilosort4 is much slower when run from Spikeinterface than from Kilosort 4 GUI Open

performance sorters

SpikeInterface/spikeinterface#4768 · 2 comments · 1 assignee · Opened Sep 8, 2026
Extend postprocessing/metrics extensions tests for `SortingAnalyzer` with no units Open

testing

Difficulty 2/5 1-3 hours Newbie friendliness 68/100

SpikeInterface/spikeinterface#4756 · Opened Sep 3, 2026
Add function to `estimate_templates_from_recording` Open

sorters

SpikeInterface/spikeinterface#4747 · 2 assignees · Opened Aug 31, 2026
bad channel detection `psd_hf_threshold` units documentation Open

Difficulty 2/5 1-3 hours Newbie friendliness 74/100

SpikeInterface/spikeinterface#4745 · Opened Aug 28, 2026
Training a curation model with metrics from older version fail Open

Difficulty 3/5 1-2 days Newbie friendliness 55/100

SpikeInterface/spikeinterface#4742 · 1 comment · Opened Aug 27, 2026
Bad channel detection: widget for manual threshold determination Open

Difficulty 4/5 3-5 days Newbie friendliness 55/100

SpikeInterface/spikeinterface#4738 · Opened Aug 25, 2026
Cleaning up units? Open

curation question

Difficulty 3/5 1-2 days Newbie friendliness 45/100

SpikeInterface/spikeinterface#4726 · 2 comments · Opened Jul 31, 2026
Overview (HD-)MEA's in terms of density Open

Difficulty 5/5 Over a week Newbie friendliness 30/100

SpikeInterface/spikeinterface#4722 · Opened Jul 30, 2026
Tracking: Efficient Lazy/Chronic Computations in SortingAnalyzer Open

chronic performance

Difficulty 5/5 Over a week Newbie friendliness 25/100

SpikeInterface/spikeinterface#4719 · Opened Jul 28, 2026
Add `slidingRP` optional dependency Open

dependencies discussion metrics

Difficulty 3/5 1-2 days Newbie friendliness 45/100

SpikeInterface/spikeinterface#4704 · 1 comment · Opened Jul 21, 2026
Sorting simple queries should not force full data reading Open

Difficulty 5/5 Over a week Newbie friendliness 35/100

SpikeInterface/spikeinterface#4702 · 1 reaction · Opened Jul 20, 2026
`Sortinganalyzer.select_channels()`: update select_channel_extension_data for waveforms/PCA Open

core

Difficulty 3/5 1-2 days Newbie friendliness 58/100

SpikeInterface/spikeinterface#4700 · Opened Jul 20, 2026
NWBSortingExtractor: pre-populate `_cached_lexsorted_spike_vector` when building spike vector Open

extractors performance

SpikeInterface/spikeinterface#4698 · 2 assignees · Opened Jul 17, 2026
Rename `MockRecording` to `SimpleNoiseRecording` and handle : gain + pregenerated/on_the_fly. Open

core

SpikeInterface/spikeinterface#4697 · 1 assignee · Opened Jul 17, 2026
Question: Is possible/reasonable to include "select_peaks" to run_node_pipeline? Open

question

Difficulty 4/5 3-5 days Newbie friendliness 42/100

SpikeInterface/spikeinterface#4694 · 3 comments · Opened Jul 17, 2026
Sorters should set `main_channel_id` property, when available Open

core

SpikeInterface/spikeinterface#4692 · 1 assignee · Opened Jul 14, 2026
What should `to_reordered_spike_vector` do? Open

Difficulty 5/5 Over a week Newbie friendliness 35/100

SpikeInterface/spikeinterface#4683 · 4 comments · Opened Jul 10, 2026
Move `sortingcomponents` out of `spikeinterface` Open

discussion

Difficulty 5/5 Over a week Newbie friendliness 35/100

SpikeInterface/spikeinterface#4669 · 5 comments · Opened Jul 9, 2026
export_to_phy vs using kilosort sorter output params.py directly Open

exporters

Difficulty 4/5 3-5 days Newbie friendliness 45/100

SpikeInterface/spikeinterface#4635 · 2 comments · Opened Jul 1, 2026
Template metrics seems to assume negative polarity, causing incorrect "peak_to_trough_duration" and "halfwidth" for positive units Open

metrics question

Difficulty 4/5 3-5 days Newbie friendliness 48/100

SpikeInterface/spikeinterface#4634 · 6 comments · Opened Jul 1, 2026
Extracting recording from multiwell Open

NEO

Difficulty 4/5 3-5 days Newbie friendliness 38/100

SpikeInterface/spikeinterface#4625 · 6 comments · Opened Jun 24, 2026
Proposal: Add anti-aliasing option to decimate() Open

preprocessing

Difficulty 4/5 3-5 days Newbie friendliness 55/100

SpikeInterface/spikeinterface#4605 · 2 comments · Opened Jun 2, 2026
Iterative Isosplit doesn't work with SpykingCircus2 Open

sorters

Difficulty 3/5 1-2 days Newbie friendliness 68/100

SpikeInterface/spikeinterface#4604 · Opened Jun 2, 2026
Question about LFP scaling and units in export_to_ibl_gui() Open

exporters

Difficulty 3/5 1-2 days Newbie friendliness 42/100

SpikeInterface/spikeinterface#4603 · 1 comment · Opened Jun 2, 2026
Clarify scope of `valid_unit_periods` extension and the `periods` argument in metric extensions Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

SpikeInterface/spikeinterface#4590 · 1 comment · Opened May 20, 2026
Aligning waveforms across spike clusters/templates Open

Difficulty 4/5 3-5 days Newbie friendliness 45/100

SpikeInterface/spikeinterface#4582 · 1 comment · Opened May 15, 2026
correlograms with swapped indices are not mirrored versions of each other Open

Difficulty 4/5 3-5 days Newbie friendliness 45/100

SpikeInterface/spikeinterface#4576 · 1 comment · Opened May 7, 2026
Creating a sparse analyzer with multiprocessing crashes if sorting has a lot of units Open

Difficulty 4/5 3-5 days Newbie friendliness 38/100

SpikeInterface/spikeinterface#4566 · 2 comments · Opened Apr 27, 2026
Feature Request: Making order = np.argsort(device_channel_indices) optional Open

Difficulty 3/5 1-2 days Newbie friendliness 52/100

SpikeInterface/spikeinterface#4565 · 11 comments · Opened Apr 25, 2026
Very large difference in sorting using SC2 vs Lupin with dense recordings Open

Difficulty 4/5 3-5 days Newbie friendliness 38/100

SpikeInterface/spikeinterface#4561 · 3 comments · Opened Apr 23, 2026
`aggregate_channels` does not re-index per-channel identifier columns Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 50/100

SpikeInterface/spikeinterface#4546 · 1 comment · Opened Apr 21, 2026
Remove the strategy argument from the noise generators Open

Difficulty 4/5 3-5 days Newbie friendliness 42/100

SpikeInterface/spikeinterface#4522 · 2 comments · 1 reaction · Opened Apr 16, 2026
Copy recording on `register_recording` to avoid shared mutation Open

Difficulty 4/5 3-5 days Newbie friendliness 48/100

SpikeInterface/spikeinterface#4519 · 2 comments · Opened Apr 16, 2026
Lupin clustering distant spikes Open

question

Difficulty 4/5 3-5 days Newbie friendliness 45/100

SpikeInterface/spikeinterface#4517 · 4 comments · Opened Apr 15, 2026
Make `num_channels` available on `BaseRecordingSegment` Open

enhancement

Difficulty 2/5 1-3 hours Newbie friendliness 72/100

SpikeInterface/spikeinterface#4510 · 2 comments · Opened Apr 14, 2026
Delete a failed SortingAnalyzer extension Open

core postprocessing

Difficulty 3/5 1-2 days Newbie friendliness 48/100

SpikeInterface/spikeinterface#4507 · 1 comment · 1 reaction · Opened Apr 10, 2026
applying curaiton fails if all units were either split or deleted Open

bug curation

SpikeInterface/spikeinterface#4501 · 2 comments · 1 assignee · Opened Apr 9, 2026
Duplicate spikes should be removed before SLAy refractory period penalty calculated Open

curation

SpikeInterface/spikeinterface#4498 · 2 comments · 1 assignee · Opened Apr 7, 2026
Monopolar triangulation for compute('unit_locations') is inconsistent with compute('spike_locations') Open

postprocessing

Difficulty 4/5 3-5 days Newbie friendliness 45/100

SpikeInterface/spikeinterface#4486 · 1 comment · Opened Apr 1, 2026
Temporally correlated noise in simulations Open

discussion enhancement generators

Difficulty 4/5 3-5 days Newbie friendliness 35/100

SpikeInterface/spikeinterface#4482 · 7 comments · 1 reaction · Opened Mar 30, 2026
Letting Lupin pass job kwargs to motion correction. Open

sorters

Difficulty 3/5 1-2 days Newbie friendliness 48/100

SpikeInterface/spikeinterface#4475 · 1 comment · Opened Mar 26, 2026
How to concatenate several neuropixels recording from SpikeGLX, especially the ap.meta, nidq.bin and nidq.meta file? Open

question

Difficulty 4/5 3-5 days Newbie friendliness 35/100

SpikeInterface/spikeinterface#4444 · 4 comments · Opened Mar 15, 2026
Workflow hurdles with SpykingCircus2/Tridesclous2: SNR filtering, Probe loss, and Parameter documentation Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

SpikeInterface/spikeinterface#4441 · 9 comments · Opened Mar 13, 2026
Behaviour of detect bad channels outside channel detection Open

Difficulty 4/5 3-5 days Newbie friendliness 42/100

SpikeInterface/spikeinterface#4434 · 2 comments · 1 reaction · Opened Mar 11, 2026
Adding motion_cleaner into High-level API correct_motion Open

motion correction

Difficulty 5/5 Over a week Newbie friendliness 38/100

SpikeInterface/spikeinterface#4432 · 5 comments · Opened Mar 9, 2026
Roadmap question: deep inter-session unit matching / UnitMatch-style matching Open

question

Difficulty 5/5 Over a week Newbie friendliness 25/100

SpikeInterface/spikeinterface#4427 · 5 comments · 2 reactions · Opened Mar 7, 2026
Pick better default for mp_context Open

io performance

Difficulty 4/5 3-5 days Newbie friendliness 45/100

SpikeInterface/spikeinterface#4422 · 7 comments · Opened Mar 4, 2026

SpikeInterface/spikeinterface

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