Exchanging Annotations

Bring annotations in from other tools, send them back out, and share them with a link.

Format	File	Made by	Import	Export	Opens on
GeoJSON	.geojson	QuPath, Find Nuclei	Yes	Yes	Any image
OME-XML ROIs	.ome.xml	OME tools, Find Nuclei	Yes	Yes	Any image
Aperio XML	.xml	Aperio ImageScope	Yes	No	Any slide, made for SVS
ASAP XML	.xml	ASAP, CAMELYON16 and CAMELYON17	Yes	No	Any slide
Hamamatsu NDPA	.ndpa	Hamamatsu NDP.view	Yes	No	NDPI slides only

Share a Slide With Its Annotations

1. Put the slide and the annotation file in storage the viewer can read. See Remote URLs.
2. Open the slide by its address.
3. In the Annotations panel, click Import, then From web address, and paste the address of the annotation file.
4. Click Copy link.

For private storage, see Private Images and Slides. Behind a token, an annotation file opens with the slide's token when both sit on the same server.

The link carries both addresses. Whoever opens it sees the slide with the annotations. Nothing is saved for them until they edit.

Import

In the Annotations tab, click Import, then From file or From web address. The viewer reads:

• GeoJSON, including QuPath exports (.geojson).

• OME-XML ROIs (.ome.xml).

• Aperio ImageScope annotations (.xml), for SVS slides.

• ASAP annotations (.xml), as in the CAMELYON16 and CAMELYON17 challenges.

• Hamamatsu NDP.view annotations (.ndpa), for NDPI slides. Open the NDPI first: the file stores positions on the glass, and the slide says where it was scanned.

• Imported shapes show as a contour. Turn on the fill for one shape in the panel.

• Class names and colours come from the file.

• A class with no colour gets one colour for the whole class.

• Each import adds to the shapes on the slide, so several files can sit together. The same file twice adds nothing. Clear empties the slide.

Export

Export GeoJSON and Export OME-XML write the shapes in the slide's own pixels, at full resolution.

The GeoJSON is the layout QuPath writes, which 10X Genomics Xenium Explorer reads too. See Other Tools.

Other Tools

QuPath

Annotations go both ways, tested with QuPath 0.5.

• From QuPath: File › Export objects as GeoJSON, then import the file here.
• Into QuPath: export GeoJSON here, then drag the file onto the slide in QuPath. Shapes, classes and colours come through.

10X Genomics Xenium Explorer

Our GeoJSON has the layout 10X Genomics documents for import into Xenium Explorer 4.1 and later: Selecting multiple regions of interest. It lists GeoJSON from a third-party tool such as QuPath as a use of its Import button. Click Import there and pick the file.

• Regions only. Xenium Explorer takes closed shapes. Lines and points are left out.
• The same image. Draw on the morphology image or the post-Xenium H&E, so the shapes land in the right place.
• Classes show as labels in its Annotations layer.

Aperio ImageScope

Pens, rectangles, ellipses, arrows and rulers open with their names, descriptions and attributes. Import only.

ASAP

The outlines of the CAMELYON16 and CAMELYON17 challenges, and other sets drawn in ASAP, open on their slides. Polygons, splines, rectangles, dots, point sets and measurements come in. Each group becomes a class, in the group's colour. Import only.

Try it on a public CAMELYON16 lymph node slide. This link opens the slide and the pathologists' two tumour outlines, straight from AWS Open Data:

tumor_001.tif with its tumour outlines

ASAP draws splines as smooth curves. The viewer joins the same points with straight lines, so a spline with few points looks a little more angular here.

Hamamatsu NDP.view

Every NDP.view2 tool opens: freehand lines and regions, rectangles, circles, rulers, pointers, pins and flags, with their titles, details and colours. Import only.

Visiopharm

Annotations go both ways, by the formats the Visiopharm manual lists under Layer Data.

• Into Visiopharm: export GeoJSON here, then import it in Visiopharm as QuPath GeoJSON.
• From Visiopharm: export the labels as GeoJSON for Xenium Explorer (File › Export › LayerData), then import the file here. Only label objects travel this way, such as segmented cells (release notes).

A file of many cells opens what the viewer can draw and tells you about the rest. See Cell Detections.

Cell Detections

A file with many detected cells opens its annotations and shows a message about the rest. To see large detection results, use analysis results.

Coordinates

Coordinates are pixels at full resolution. On .mrxs they start at the top-left of the area holding images, as in QuPath.

Image credits

The screenshot uses CMU-1.ndpi from the OpenSlide test data, CC0, with an annotation file drawn for this guide in NDP.view2. The ASAP example uses CAMELYON16 tumor_001, CC0. See Sample Data and Credits.