Extracting recording from multiwell

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#4,625 opened on Jun 24, 2026 6 comments 0 reactions 0 assignees View on GitHub

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Assessment

Difficulty: 4/5
Estimated time: 3-5 days
Newbie friendliness: 38/100

Issue type: Bug
Clarity: Needs clarification
Activity status: Quiet
Tech stack: python
Domain: data, tooling

Research direction

Start with the read_biocam extractor and the stream_id handling described in the issue, checking how well_A1 is selected and whether another well can be selected. Then trace the BrainWave6 scale-factor conversion and probe geometry passed to the SpikeInterface GUI. Done means multiwell recordings, analog values, and channel positions are represented correctly.

Written by the indexing model from the issue text.

Description

NEO

Hi,
I'm currently working with a 3Brain multiwell and I noticed that biocamraw is not compatible with the multiwell system. Whenever I use the extractor read_biocam, only the well_A1 is selected.
I tried to modify the script and now I can extract multiwell recordings by specifying the well name as the stream_id (stream_id = well_A2).

On the other hand, I'm not sure about the code line responsible for converting the digital value to the analog one, since in the BrainWave6 output file there is no more the possibility to extract the scale factor (to my knowledge).
Together with this, the probe geometry is not correctly represented when represented in spikeInterface GUI. In particular, channels are not correctly located in the virtual representation of the probe.

Since I'm a beginner with coding I would greatly appreciate if some of you could help me in improving the script.

Thank you for your help.

Best regards,

Dominant language: Python
Stars: 847
Forks: 280
Avg merge: 3d 9h
Merged PRs (30d): 29

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