Overview

Sections

The amorphys metadata format consists of the following distinct sections:

1. the “organization” section, describing project organization
2. the “subjects” section, describing the subjects of interest used throughout an experiment.
3. the “setups” section, describing spatial organization of each setup
4. the “acquisition” section, describing programs and channels on each setup
5. the “procedures” section, describing experimental procedures for each subject
6. the “tasks” section, describing the task/protocol controls
7. the “variables” section, describing the experimental conditions and variables

In principle, the six sections are independent from each other: you can only implement some of them while leaving the others unimplemented, if you are fine with this way.

A recommended way of annotation

If you start annotating in amorphys from scratch, here is a recommended way. Note that you can modify or expand the descriptions at any time.

If you are unsure about anything along the way, do not hesitate to write only partially and go on to the next step without fully fill in the previous one (a nice version-control system will help in any case).

1. Write the organization section:

   • what is the name of the project?
   • who are involved in the project, with what funding source(s)?

2. Write the subjects section, whilst adding some subject-specific variables in the variables section:

   • what subject is used in the experiments?
   • in particular, which part of the subject is of interest?

3. Write the procedures section, whilst adding some phase-specific variables in the variables section:

   • in what order are manipulations and perturbations made?

4. Write the setups section:

   • on each setup, what components are there in what layout?

5. Write the acquisition section:

   • what type of signals are recorded and generated?
   • how do the programs make use of them?
   • what kind of data files are generated during each acquisition?

6. Write the tasks section, whilst adding further variables in the variables section:

   • how are the setup and the subject modeled to interact with each other?

“section” class

class section

Each section of amorphys has different properties of its own. But it can have an optional property, $description to describe itself.

$description

a human-readable string description of the section. It is recommended to include this property for every section, for increased understandability.

Formatting options

As described below, there are two ways to organize these sections (i.e. Single-file format and Multi-file format formats), and it is completely up to the user which way to choose.

Single-file format

A most simple way of formatting in amorphys is to make a large, single JSON file:

{
    "$schema": "https://.../amorphys.json",

    "organization" {
        ...
    },

    "setups": {
        ...
    },

    "acquisition": {
        ...
    },

    ...
}

In the example above (the content of each section is omitted for simplicity), each of the implemented sections is represented as a value to the corresponding key.

While it may be simple in reading and parsing, it may be difficult to be read by the human beings.

Multi-file format

Another way of formatting in amorphys involves splitting sections into multiple JSON files:

in: “organization.json”

{
    "$schema": "https://.../amorphys.json#properties/organization",

    "dataset": {
        ...
    },

    "people": {
        ...
    },

    ...
}

in: “setups.json”

{
    "$schema": "https://.../amorphys.json#properties/setups",

    "behavioral-rig": {
        ...
    },

    ...
}

In the example above (again, the details are omitted for brevity), each of the implemented sections are represented as a file with the corresponding name.

This may have some difficulty in referring to an entity across multiple sections, but individual JSON files become much smaller, and may be easier to read by a human being.