zod-ome-ngff

zod schemas for ome-ngff. modules are generated from the NGFF JSON specification and manually refined, providing composable validators for working with NGFF metadata in JavaScript and TypeScript.

install

pnpm install zod zod-ome-ngff

usage

import { z } from "zod";
import * as v04 from "zod-ome-ngff/v04";

let Attrs = z.union([
  v04.StrictImageSchema,
  v04.StrictLabelSchema,
  v04.StrictPlateSchema,
  v04.StrictWellSchema,
]);

let url =
  "https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0048A/9846152.zarr/";

// The following throws a `z.ZodError` if the `.zattrs`
// JSON does not conform to the union schema above.
let attrs = Attrs.parse(
  await fetch(`${url}.zattrs`).then((res) => res.json()),
);

// TypeScript now _knows_ the type of attrs

attrs;
//^? StrictImageSchema | StrictLabelSchema | StrictPlateSchema | StrictWellSchema

if ("multiscales" in attrs) {
  console.log("Multiscales:", attrs.multiscales);
}                           //^? StrictImageSchema

if ("image-label" in attrs) {
  console.log("Label:", attrs["image-label"]);
}                     //^? StrictLabelSchema

if ("well" in attrs) {
  console.log("Well:", attrs.well);
}                    //^? StrictWellSchema

if ("plate" in attrs) {
  console.log("Plate:", attrs.plate);
}                     //^? StrictPlateSchema

sub-packages

Validators are exported for v0.1, v0.2, v0.3, and v0.4 schemas.

import * as v01 from "zod-ome-ngff/0.1";
import * as v02 from "zod-ome-ngff/0.2";
import * as v03 from "zod-ome-ngff/0.3";
import * as v04 from "zod-ome-ngff/0.4";

import * as schemas from "zod-ome-ngff"; // latest

development

The contents of src/ are automatically generated from the NGFF JSON specification via:

node scripts/generate-schemas.mjs latest # or 0.1, 0.2, 0.3, 0.4, latest

changelogs

For changes to be reflected in package changelogs, run pnpm changeset and follow the prompts.

Note not every PR requires a changeset. Since changesets are focused on releases and changelogs, changes to the repository that don't effect these won't need a changeset (e.g., documentation, tests).

release

The Changesets GitHub action will create and update a PR that applies changesets and publishes new versions.

related

• ome/ngff - offcial specification (JSON schemas)
• JaneliaSciComp/pydantic-ome-ngff - pydantic models for ngff (Python)