SpikeInterface / SpikeInterface/spikeinterface

Question: How to insert new data into a recording object. Purpose: "remove_artifacts" by inserting our own cleaned data

Open
#3,585 10 comments 0 reactions 0 assignees View on GitHub

Nobody has claimed this yet.

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

Description

Hello,

Contex:
We have a recording that includes Intracortical Microstimulation (ICMS) multiple times during the session. The data is in NWB format originally.
A collaborator has implemented an artifact removal using ERAASR (https://github.com/djoshea/eraasr) and provided a Matlab file with:

  1. A matrix of [nSnippet X nChans X nStim] which contains snippets (length = nSnippet) of the high-pass filtered & centered cleaned traces for all the channels (nChans) from all the ICMS epochs (nStim)
  2. An array of size [nStim] which contains the start_sample_index of each snippet.

Now, I'm working out how to insert these clean traces into the "filtered & centered" recording object that I got from the same NWB file. Afterward, I will use "neuroconv" to export this recording into a new NWB file (which I have already tested but without the snippet replacement).

Question:
Is there a function to insert these snippets into the recording object?

I hope my question makes sense, if not I can explain anything in further detail.

Thanks for any thoughts and comments on how to approach this.

Best
Pepe

Contributor guide

No contributing guide indexed for this repository

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

The issue names no files or tests. Start by checking the recording object's API and the neuroconv export workflow for support for replacing snippets at the supplied start_sample_index values. Done means determining whether the cleaned traces can be inserted and exported to a new NWB file.

Written by the indexing model from the issue text.

Assessment

Tech stack
matlab, python
Domain
data
Issue type
Feature
Difficulty
5/5
Estimated time
Over a week
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
25/100

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.