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buzsakilab / buzcode

Code for internal lab sharing - polishing has started but is by no means complete
http://www.buzsakilab.com/
GNU General Public License v3.0
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NWB integration #153

Open bendichter opened 6 years ago

bendichter commented 6 years ago

Hey all,

What are your thoughts on integrating conversion to NWB as part of buzcode? So far I have been using pynwb for conversion to and from NWB since that repo is under more active development, however all of that code is python-based. There is another repo, matnwb, for converting data to NWB using matlab. The development of matnwb has not been as active an pynwb, however I realize it might be a smoother integration and transition for you all to use matlab to convert to NWB instead of python. Would there be interest in using matnwb to build conversion scripts directly to and from your buzcode format? What would you imagine as the ideal workflow/integration with the current buzcode repo?

dlevenstein commented 6 years ago

Conversion to/from NWB would be very good/useful. IMO

On Mar 4, 2018, at 4:41 PM, Ben Dichter notifications@github.com wrote:

Hey all,

What are your thoughts on integrating conversion to NWB as part of buzcode? So far I have been using pynwb for conversion to and from NWB since this repo is under more active development, however all of that code is python-based. There is another repo, matnwb, for converting data to NWB using matlab. The development of matnwb has not been as active an pynwb, however I realize it might be a smoother integration and transition for you all to use matlab to convert to NWB instead of python. Would there be interest in using matnwb to build conversion scripts directly to and from your buzcode format? What would you imagine as the ideal workflow/integration with the current buzcode repo?

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brendonw1 commented 6 years ago

Seconded, I like the idea. Don't know the details of course

On Sun, Mar 4, 2018 at 3:16 PM, Dan Levenstein notifications@github.com wrote:

Conversion to/from NWB would be very good/useful. IMO

On Mar 4, 2018, at 4:41 PM, Ben Dichter notifications@github.com wrote:

Hey all,

What are your thoughts on integrating conversion to NWB as part of buzcode? So far I have been using pynwb for conversion to and from NWB since this repo is under more active development, however all of that code is python-based. There is another repo, matnwb, for converting data to NWB using matlab. The development of matnwb has not been as active an pynwb, however I realize it might be a smoother integration and transition for you all to use matlab to convert to NWB instead of python. Would there be interest in using matnwb to build conversion scripts directly to and from your buzcode format? What would you imagine as the ideal workflow/integration with the current buzcode repo?

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or mute the thread.

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samamckenzie commented 6 years ago

This is a big priority for Gyuri.

Can we set up a Skype meeting?

Sam

Whatever we can do to help

On Mar 4, 2018 5:24 PM, "Brendon Watson" notifications@github.com wrote:

Seconded, I like the idea. Don't know the details of course

On Sun, Mar 4, 2018 at 3:16 PM, Dan Levenstein notifications@github.com wrote:

Conversion to/from NWB would be very good/useful. IMO

On Mar 4, 2018, at 4:41 PM, Ben Dichter notifications@github.com wrote:

Hey all,

What are your thoughts on integrating conversion to NWB as part of buzcode? So far I have been using pynwb for conversion to and from NWB since this repo is under more active development, however all of that code is python-based. There is another repo, matnwb, for converting data to NWB using matlab. The development of matnwb has not been as active an pynwb, however I realize it might be a smoother integration and transition for you all to use matlab to convert to NWB instead of python. Would there be interest in using matnwb to build conversion scripts directly to and from your buzcode format? What would you imagine as the ideal workflow/integration with the current buzcode repo?

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or mute the thread.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/buzsakilab/buzcode/issues/153#issuecomment-370269409, or mute the thread https://github.com/notifications/unsubscribe-auth/ ADXrTXum3nd2vN_JDEoQFvr8_QvrGCuBks5tbGfNgaJpZM4SbhAe .

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petersenpeter commented 6 years ago

There has been a lot of talk about this and it would be a great addition.

Den 4. mar. 2018 kl. 16.41 skrev Ben Dichter notifications@github.com:

Hey all,

What are your thoughts on integrating conversion to NWB as part of buzcode? So far I have been using pynwb for conversion to and from NWB since this repo is under more active development, however all of that code is python-based. There is another repo, matnwb, for converting data to NWB using matlab. The development of matnwb has not been as active an pynwb, however I realize it might be a smoother integration and transition for you all to use matlab to convert to NWB instead of python. Would there be interest in using matnwb to build conversion scripts directly to and from your buzcode format? What would you imagine as the ideal workflow/integration with the current buzcode repo?

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or mute the thread.

bendichter commented 6 years ago

Thanks for your input, guys. It's helpful to know there is interest in the MATLAB side of NWB. I'm also in touch with with Vijay Iyer, the neuroscience liaison at Mathworks, who is curious about interest in the matnwb project, and I've let him know about your lab's interest in the project.

bendichter commented 6 years ago

Hey all, I just wanted to let you know that I've started to work out data conversion for your format in MATLAB using matnwb. It's not finished yet, but you can track my progress here: https://github.com/bendichter/to_nwb/blob/master/convert_yuta.m

petersenpeter commented 6 years ago

Great Ben

2018-03-29 13:01 GMT-04:00 Ben Dichter notifications@github.com:

Hey all, I just wanted to let you know that I've started to work out data conversion for your format in MATLAB using matnwb. It's not finished yet, but you can track my progress here: https://github.com/bendichter/ to_nwb/blob/master/convert_yuta.m

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DavidTingley commented 6 years ago

In preparation for the coming hackathon, we can upload goals and ideas here: https://github.com/NeurodataWithoutBorders/nwb_hackathons/tree/master/HCK05_2018_Berkeley/projects/Buzsakilab