BIDS Extension Proposal for Microelectrode Recordings

[greydon...@gmail.com]

Hello BIDS community!

I have been working on a BIDS specification for microelectrode recordings during deep brain stimulation surgery. Microelectrode recordings are routinely performed during deep brain stimulation surgery for individuals with movement disorders. The proposed document can be found at this link: https://docs.google.com/document/d/14KC1d5-Lx-7ZSMtwS7pVAAvz-2WR_uoo5FvsNirzqJw/edit?usp=sharing. I would appreciate any comments or feedback you can provide.

I am leading this effort, I am a Ph.D. student and clinical intraoperative electrophysiologist at University Hospital in London, Ontario, Canada. I look forward to hearing your thoughts on this proposal.

Cheers,

Greydon Gilmore 

[Chris Gorgolewski]

Thanks for sending this! Would you mind adding this to the list of other proposed extensions by sending a pull request similar to this one: https://github.com/bids-standard/bids-specification/pull/110?

I am not an expert in this field, but I wonder how much MER overlaps with iEEG. Would be nice to get comments from Dora and Chris

I also noticed you are proposing to add support for CT. This has been previously discussed in the context of PET. I wonder if it wouldn't be easier to agree on how to handle CT first and merge that?

Best,

Chris

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[Mastaneh Torkamani]

Dear all,

I am following up with discussions from 2018-2019 on extending BIDS compatibility to microelectrode array (MEA) recordings. Has the community accepted the proposed structure shared by Greydon at https://docs.google.com/document/d/14KC1d5-Lx-7ZSMtwS7pVAAvz-2WR_uoo5FvsNirzqJw/edit?usp=sharing? If not, what are current practices for naming and storing these recordings along with MRI, histology, and other modalities? 

Kind regards,

Mastaneh Torkamani-Azar 

A.I. Virtanen Institute 

University of Eastern Finland  
mastaneh....@uef.fi 

[Stefan Appelhoff]

Dear Mastaneh,

this BIDS Extension Proposal is still in progress. Perhaps the information from these two threads can be of help to you:

• https://github.com/bids-standard/bids-specification/issues/1132
• https://github.com/bids-standard/bids-specification/pull/1352

As for histology, perhaps the microscopy extension to BIDS is relevant: https://bids-specification.readthedocs.io/en/latest/modality-specific-files/microscopy.html

Cheers,

Stefan

[Satrajit Ghosh]

dear mastaneh,

on the microscopy/histology front, this preprint may also be relevant as the community is moving towards ngff, with zarr as the backend format with omero metadata on top of it. bids has support for ngff: https://www.biorxiv.org/content/10.1101/2023.02.17.528834v2 

there are a couple of threads that may be relevant to the abf question:

- BEP032 - https://bep032tools.readthedocs.io/en/latest/ is trying to formalize some of the ephys work bridging the worlds of nwb and bids. we use nwb exclusively in dandi as the standard as it offers significant advantages for long recordings and storing in the cloud. 

- https://neuroconv.readthedocs.io/en/main/ - getting data into nwb

cheers,

satra

On Wed, Apr 5, 2023 at 4:17 AM Mastaneh Torkamani <mastan...@gmail.com> wrote:

Dear Stefan, 

Thank you for pointing me to the right threads and documentations. 

The microscopy extension covers most of our settings for now although we may have to suggest new options for "modality suffixes". I will also follow up with BIDS extension for MEA recordings and inclusion of .msrd, .msrs, and .xml files.  

Finally, is anyone in the community interested in initiating an effort to propose an extension for patch clamp datasets with .abf files recorded by Axon Instruments or other vendors? 

Thanks and kind regards,

Mastaneh 

mastaneh....@uef.fi 

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