Skip to content

Data Loaders

Annota provides data loaders for importing annotations from various file formats commonly used in digital pathology.

H5 (HDF5) Files

Section titled “H5 (HDF5) Files”

Loading Mask Annotations

Section titled “Loading Mask Annotations”

Load polygon annotations from HDF5 mask files:

import { loadH5Masks } from "annota";


const annotations = await loadH5Masks("/path/to/masks.h5", {
  color: "#FF0000",
  fillOpacity: 0.3,
});

Loading Coordinate Points

Section titled “Loading Coordinate Points”

Load point annotations from HDF5 coordinate files:

import { loadH5Coordinates } from "annota";


const points = await loadH5Coordinates("/path/to/coords.h5", {
  color: "#00FF00",
  fillOpacity: 0.8,
});

JSON Files

Section titled “JSON Files”

Loading

Section titled “Loading”
import { loadJSONFile } from "annota";


const annotations = loadJSONFile(jsonData);

Exporting

Section titled “Exporting”
import { annotationsToJSON } from "annota";


const json = annotationsToJSON(annotations);

PGM Files

Section titled “PGM Files”

Loading Masks

Section titled “Loading Masks”
import { loadPgmFile } from "annota";


const annotations = loadPgmFile(pgmData, {
  threshold: 128,
});

Extracting Polygons

Section titled “Extracting Polygons”
import { loadPgmPolygons } from "annota";


const polygons = loadPgmPolygons(pgmData, {
  threshold: 128,
});

Exporting

Section titled “Exporting”
import { annotationsToPgm } from "annota";


const pgmData = annotationsToPgm(annotations, width, height);

See Also

Section titled “See Also”