search

schnitzer-lab / nwbpkg

Repository for NWB standards and converting imaging data to NWB format.
MIT License
0 stars 0 forks source link

Dynamic mask and trace chunk size and dataType #6

Closed bahanonu closed 4 years ago

bendichter commented 4 years ago

Yeah, after noticing that usability issue, we've been doing the same on the matnwb side modeled after h5py's approach to guessing chunk size. It looks like our approaches are similar. It would not be a problem to keep your implementation if you prefer it to matnwb's

bahanonu commented 4 years ago

Sounds good, I'll wait until that is merged to see about incorporating it here.

bahanonu commented 4 years ago

Changed so that it now saves as /processing/ophys/ImageSegmentation/PlaneSegmentation1, etc. as this appears to most closely track the NWB schema (https://nwb-schema.readthedocs.io/en/latest/format.html#planesegmentation). We'll leave the cell-extraction method in the description for now until algorithm field is added to the NWB standard.

bendichter commented 4 years ago

You can technically name the PlaneSegmentation whatever you want, but I think PlaneSegmentation1, etc. is a good idea.

On Sun, Apr 5, 2020 at 6:18 PM Biafra Ahanonu notifications@github.com wrote:

Changed so that it now saves as /processing/ophys/ImageSegmentation/PlaneSegmentation1, etc. as this appears to most closely track the NWB schema ( https://nwb-schema.readthedocs.io/en/latest/format.html#planesegmentation). We'll leave the cell-extraction method in the description for now until algorithm field is added to the NWB standard.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/schnitzer-lab/nwb_schnitzer_lab/pull/6#issuecomment-609493829, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAGOEERJ6NFM7KUESAF7YELRLD7TFANCNFSM4L4RRROQ .

-- Ben Dichter, PhD Data Science Consultant