AllenNeuralDynamics / AllenNeuralDynamics/aind-ephys-pipeline

Support for recordings with subset of Neuropixels channels saved (e.g., 200 of 384)

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Description

Hello Alessio and team,

First off, great work!

I'm using the aind-ephys-pipeline with Neuropixels 1.0 recordings from Open Ephys where I only saved 200 channels (0-199) to disk, not all 384. The pipeline fails at job_dispatch because the Open Ephys metadata specifies 384 channels but the binary only contains 200:

```
ValueError: The given Probe either has 'device_channel_indices' that does not match channel count
384 vs 200
device_channel_indices are: [0, 1, 2, ... 383]
recording channels are: ['AP0', 'AP1', ... 'AP199']
```

I tried providing a custom 200-channel probe via probe_paths in si_config.json, but the error occurs before the custom probe is applied - the Open Ephys reader attempts to set the 384-channel probe from metadata first.

Would it be possible to add an option to skip automatic probe loading when using openephysbinary reader, similar to how skip_stream_substrings works for filtering streams? Something like:

```
{
"reader_type": "openephysbinary",
"reader_kwargs": {
"folder_path": "/path/to/session",
"stream_name": "Record Node 101#OneBox-100.ProbeA-AP",
"load_probe_info": false
},
"probe_paths": "/path/to/custom_probe.json"
}
```

For now I'm using SpikeInterface directly with BinaryRecordingExtractor, but would prefer the full pipeline for QC outputs.

Thanks!

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