[BEP032] improve human-readability of the example datasets

[SylvainTakerkart]

cf example given in https://docs.google.com/document/d/1L2Jaboy6hhvp0kdYfqZ4XM8Zs2mbvwEs-OUDd9YqRsk/edit

[Jay-sanjay]

@SylvainTakerkart would you please specify what exactly the issue is, I would be more than happy to contribute

[lzehl]

• example multi-electrode recording: reach2grasp dataset (in NIX format)
  • @lzehl @hlmore @ree-gupta @SylvainTakerkart
  • ebrains; other example than R2G (@lzehl @chrisvdt)
• example neuropixel probes: (in NWB format)
  • dartmouth (@yarikoptic @TheChymera)
  • dandi (@yarikoptic @bendichter)
• example patch-clamp: (in NWB format)
  • dandi (@yarikoptic @bendichter)
  • ebrains (@lzehl @apdavison)
• toy example (patch clamp) demonstrating two way of presenting the data as suggested by the BEB 032 (@SylvainTakerkart)

(more examples are appreciated)

guidelines:

• avoid unnecessary abbreviations
• include maybe source data as well (to demonstrate the whole pipeline)
• include code and pointers to "containers" to show how to convert to BIDS

Examples we can look at:

• https://www.fieldtriptoolbox.org/example/bids/

[chrisvdt]

Hi Lyuba, After I got this mail from you I've started to try to generate a BIDS compliant datasets for our 2Photon imaging datasets. I've included an example. I clearly have difficulty with some of the requirements. I realize this was not what you were asking for but I thought it would be a nice starting point for me since I have not applied BIDS to any dataset until now. I was wondering what could be the next step. I see you associated with me with an ebrains dataset. What do you require me to do? With kind regards, Chris

…

--------------------------------------------------- Dr. C. van der Togt Data manager Netherlands Institute for Neuroscience Meibergdreef 47 1105BA Amsterdam The Netherlands From: Lyuba Zehl ***@***.***> Sent: Thursday, September 21, 2023 4:43 PM To: INCF/neuroscience-data-structure ***@***.***> Cc: Chris van der Togt ***@***.***>; Mention ***@***.***> Subject: Re: [INCF/neuroscience-data-structure] [BEP032] improve human-readability of the example datasets (Issue #17) * example multi-electrode recording: reach2grasp dataset (in NIX format) * @lzehl<https://github.com/lzehl> @hlmore<https://github.com/hlmore> @ree-gupta<https://github.com/ree-gupta> @SylvainTakerkart<https://github.com/SylvainTakerkart> * ebrains; other example than R2G ***@***.***<https://github.com/lzehl> @chrisvdt<https://github.com/chrisvdt>) * example neuropixel probes: (in NWB format) * dartmouth ***@***.***<https://github.com/yarikoptic> @TheChymera<https://github.com/TheChymera>) * dandi ***@***.***<https://github.com/yarikoptic> @bendichter<https://github.com/bendichter>) * example patch-clamp: (in NWB format) * dandi ***@***.***<https://github.com/yarikoptic> @bendichter<https://github.com/bendichter>) * ebrains ***@***.***<https://github.com/lzehl> @apdavison<https://github.com/apdavison>) * toy example (patch clamp) demonstrating two way of presenting the data as suggested by the BEB 032 ***@***.***<https://github.com/SylvainTakerkart>) (more examples are appreciated) guidelines: * avoid unnecessary abbreviations * include maybe source data as well (to demonstrate the whole pipeline) * include code and pointers to "containers" to show how to convert to BIDS Examples we can look at: * https://www.fieldtriptoolbox.org/example/bids/ - Reply to this email directly, view it on GitHub<#17 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ABIQZHCHSYUKOCNB5ZJHHDDX3RG5RANCNFSM6AAAAAAZ4PEG7E>. You are receiving this because you were mentioned.Message ID: ***@***.******@***.***>>

[lzehl]

@chrisvdt it would be great if you know of a electrophysiology dataset from monkeys that was published in EBRAINS that we can use as another example (besides the R2G dataset where I'm an author on).

It does not surprise me that applying BIDS to 2photon datasets will cause issues. Where did you include the example? which requirements caused issues?

[chrisvdt]

@lzehl<https://github.com/lzehl> These might be suitable datasets; Papale, P., Wang, F., Morgan, A. T., Chen, X., Gilhuis, A., Petro, L., Muckli, L., Roelfsema, P. R., & Self, M. W. (2022). Electrophysiological recordings in macaque V1 during passive viewing of full and occluded natural scenes (v1) [Data set]. EBRAINS. https://doi.org/10.25493/KABE-GS0 Chen, X., Morales-Gregorio, A., Sprenger, J., Kleinjohann, A., Sridhar, S., Van Albada, S., Grün, S., & Roelfsema, P. (2021). 1024-channel electrophysiological recordings in macaque V1 and V4 during resting state (Version 1.0) [Data set]. G-Node. https://doi.org/10.12751/G-NODE.I20KYH Roelfsema, P. R., & Van Vugt, B. (2019). Multiunit recordings from visual areas in monkeys performing a detection task [Data set]. Human Brain Project Neuroinformatics Platform. https://doi.org/10.25493/REHY-EEX

[lzehl]

@chrisvdt thanks I think they will fit. I think I will even meet with one of the authors from the second one next week or the week after.

[umadevi0]

please elaborate the issue so that I also can try to contribute .