neuroinformatics-unit / NeuroBlueprint

Lightweight data specification for systems neuroscience, inspired by BIDS.
http://neuroblueprint.neuroinformatics.dev/
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Add section on identifying datatype modalities with suffixes #48

Closed JoeZiminski closed 3 days ago

JoeZiminski commented 8 months ago

Further to #45, we discussed formalising the modality suffixes for files / folders that go in datatype folders. Here modality is like a sub-datatype, for example ephys is a datatype but patch-clamp electrophysiology and extracellular electrophysiology are modalities, both of which go in the ephys folder.

In general, people are unlikely to collect conflicting datatypes in the same session. However, it is possible (e.g. single-unit + extracellular physiology for validation). In this case we decided to reccomend using modality suffixies, similar to BIDS.

For example an organisation could be:

sub-001/ses-001/ephys/sub-001_ses-001_patchclamp/...
sub-001/ses-001/ephys/sub-001_ses-001_ecephys

In Neuroblueprint, we could have a dropdown that explains this. This is quite an edge case so we can be careful not to distract people with it if they do not need to know. I wonder if we should even, down the line, have an FAQ or Advanced usage section where we put edge cases like this.

An example dropdown menu content:

It is possible that you may collect two different modalities that full under the same datatype within a single session. For example, it is possible that intracellular patch-recordings may be collected at the same time as extracellular probe recordings. Or, [some other imaging example].

In this case, it is recommended to distinguish these two modalities using one of the mandated suffixes below. In this instance, it is permitted to break with key-value pair formatting to add the suffix. 

For example, 
rawdata
  sub-001
    ses-001
        funcimg
              <two example filenames e.g. sub-001_ses_001_run-001_modality.bin with two separate modalities>.

The list of permitted modality suffixes is:
(need to check bids. We would need for:

patch clamp
extracellular ephys
surface recordings (?)
lots of imaging)
JoeZiminski commented 3 days ago

Closed as furthered in #57, we will not go down this route.