Getting Started

This tool was created to be an easy-access library for pynwb.

Creating an NWB

To create our NWB object, we’ll use this generic one

 1from simply_nwb import SimpleNWB
 2import pendulum
 3from pynwb.file import Subject
 4
 5
 6def nwb_gen():
 7    return SimpleNWB.create_nwb(
 8        # Required
 9        session_description="Mouse cookie eating session",
10        # Subtract 1 year so we don't run into the 'NWB start time is at a greater date than current' issue
11        session_start_time=pendulum.now().subtract(years=1),
12        experimenter=["Schmoe, Joe"],
13        lab="Felsen Lab",
14        experiment_description="Gave a mouse a cookie",
15
16        # Optional
17        identifier="cookie_0",
18        subject=Subject(**{
19            "subject_id": "1",
20            "age": "P90D",  # ISO-8601 for 90 days duration
21            "strain": "TypeOfMouseGoesHere",  # If no specific used, 'Wild Strain'
22            "description": "Mouse#2 idk",
23            "sex": "M",  # M - Male, F - Female, U - unknown, O - other
24            # NCBI Taxonomy link or Latin Binomial (e.g.'Rattus norvegicus')
25            "species": "http://purl.obolibrary.org/obo/NCBITaxon_10116",
26        }),
27        session_id="session0",
28        institution="CU Anschutz",
29        keywords=["mouse"],
30
31        # related_publications="DOI::LINK GOES HERE FOR RELATED PUBLICATIONS"
32    )

Transform Functions

Transformations take raw data and turn it into a format more easy to manipulate. Some are even required to transform them into usable data, and can take a while to process.

See the Examples for how to use specific transforms.

Also see