SpikeInterface / SpikeInterface/spikeinterface

warning messages during analyzer computations

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Python
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Description

Hello Devs,
i'm getting all kinds of scipy warnings during the analyzer calculations, and was wondering if this is normal, or do i have an issue with scipy / spike data format?

estimate_sparsity
engine=thread - n_jobs=6 - samples_per_chunk=30,000 - chunk_memory=21.97 MiB - total_memory=131.84 MiB - chunk_duration=1.00s (999.99 ms)
estimate_sparsity (workers: 6 threads): 0%| | 0/6999 [00:00<?, ?it/s]
2025-11-07 09:38:39.506 | WARNING | spikeinterface.core.base:save_to_folder:967 - G:\mambaroot\envs\hir_new\Lib\site-packages\spikeinterface\core\base.py:967: UserWarning: The extractor is not serializable to file. The provenance will not be saved.
warnings.warn("The extractor is not serializable to file. The provenance will not be saved.")

2025-11-07 09:38:40.777 | WARNING | spikeinterface.core.sortinganalyzer:create_binary_folder:497 - G:\mambaroot\envs\hir_new\Lib\site-packages\spikeinterface\core\sortinganalyzer.py:497: UserWarning: The sorting provenance is not serializable! The sorting provenance link will be lost for future load
warnings.warn(

new analyzer created at //gpfs.corp.brain.mpg.de/stem/data/project_hierarchy/data/afm16924/240525/trial0/postscript_2025KS/sorting_analyzer_results
noise_level (workers: 6 threads): 0%| | 0/20 [00:00<?, ?it/s]
compute_waveforms (workers: 6 threads): 0%| | 0/6999 [00:00<?, ?it/s]
computing template simliarity and metrics
2025-11-07 10:00:58.659 | WARNING | scipy.stats._stats_py:linregress:10730 - C:\Users\su-weisss\AppData\Roaming\Python\Python311\site-packages\scipy\stats_stats_py.py:10730: RuntimeWarning: invalid value encountered in scalar divide
slope = ssxym / ssxm

2025-11-07 10:00:58.660 | WARNING | scipy.stats._stats_py:linregress:10744 - C:\Users\su-weisss\AppData\Roaming\Python\Python311\site-packages\scipy\stats_stats_py.py:10744: RuntimeWarning: invalid value encountered in sqrt
t = r * np.sqrt(df / ((1.0 - r + TINY)*(1.0 + r + TINY)))

2025-11-07 10:00:58.661 | WARNING | scipy.stats._stats_py:linregress:10750 - C:\Users\su-weisss\AppData\Roaming\Python\Python311\site-packages\scipy\stats_stats_py.py:10750: RuntimeWarning: invalid value encountered in scalar divide
slope_stderr = np.sqrt((1 - r**2) * ssym / ssxm / df)

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First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start by reproducing the analyzer computation with the reported estimate_sparsity, noise_level, and compute_waveforms settings, then inspect the scipy.stats.linregress warnings and the analyzer steps that trigger them. Done means determining whether the warnings indicate invalid spike data or an analyzer-handling issue, and recording or resolving the cause.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
data
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
35/100

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