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Regions of Interest (ROIs)

ROIs and shape labels may encode phenotypes, diagnoses, sample identifiers, or analysis decisions. Export geometry and labels only within an explicit scope.

Model Semantics

The OMERO 5.6 line uses the June 2016 OME schema. The OME ROI model defines eight concrete 2D shape types:

  • Ellipse
  • Label
  • Line
  • Mask
  • Point
  • Polygon
  • Polyline
  • Rectangle

Plane selectors are optional:

  • TheZ: z-section; absent means all z-sections
  • TheT: timepoint; absent means all timepoints
  • TheC: channel; absent means all channels

Do not coerce absent values to zero. A 3D ROI is represented as a union of 2D shapes across planes; it is not a native volumetric mesh.

Display fields include RGBA fill/stroke colors, stroke width, fill rule, dash array, text label, and font properties. Geometry and display metadata are distinct.

Current Service Status

The current Python examples still retrieve ROIs with:

roi_service = conn.getRoiService()
result = roi_service.findByImage(image_id, None)

However, the current OMERO Blitz API marks the IRoi interface deprecated. That means “still available but at removal risk,” not “already removed.” OME does not document a general replacement for every IRoi method in the pages reviewed for this snapshot.

Therefore:

  • isolate IRoi use behind a small function;
  • do not build new broad workflows around legacy measurement-table helpers;
  • verify the target server's generated API before relying on it;
  • record this dependency in long-lived integrations.

The official OMERO.web JSON API also documents paginated ROI listing by image: /api/v0/m/rois/?image=<id>&limit=<n>&offset=<n>. Use it only when the site exposes the documented api app over HTTPS and its authentication model is appropriate.

Bounded ROI Read

findByImage() does not expose page arguments. Apply explicit image, ROI, and shape caps and report truncation:

image_id = 123
max_rois = 100
max_shapes_per_roi = 500

roi_service = conn.getRoiService()
result = roi_service.findByImage(image_id, None)
rois = list(result.rois)

roi_truncated = len(rois) > max_rois
for roi in rois[:max_rois]:
    shapes = list(roi.copyShapes())
    print(
        {
            "roi_id": roi.getId().getValue(),
            "shape_count_returned": min(len(shapes), max_shapes_per_roi),
            "shape_truncated": len(shapes) > max_shapes_per_roi,
        }
    )

The cap limits client processing/output, not necessarily server work: findByImage() may already have assembled all matching ROIs. For a known very large image, do not call it casually; consider the documented paginated JSON API or a site-reviewed query.

The bundled exporter requires explicit image IDs and uses redaction defaults:

python -B scripts/export_image_metadata.py \
  --image-id 123 \
  --max-rois-per-image 100 \
  --max-shapes-per-roi 500 \
  --output ./image-123-metadata.json

Review the dry run, then add --execute. ROI labels remain redacted unless --include-roi-labels is specified.

Reading Shape Fields

Generated model values are usually wrapped in OMERO rtypes. Preserve None:

def unwrap(value):
    if value is None:
        return None
    getter = getattr(value, "getValue", None)
    return getter() if callable(getter) else value


for roi in result.rois[:max_rois]:
    for shape in list(roi.copyShapes())[:max_shapes_per_roi]:
        record = {
            "id": unwrap(shape.getId()),
            "the_z": unwrap(shape.getTheZ()),
            "the_t": unwrap(shape.getTheT()),
            "the_c": unwrap(shape.getTheC()),
            "label_redacted": True,
        }
        print(record)

Use type checks before geometry access:

import omero.model

if isinstance(shape, omero.model.RectangleI):
    geometry = {
        "x": unwrap(shape.getX()),
        "y": unwrap(shape.getY()),
        "width": unwrap(shape.getWidth()),
        "height": unwrap(shape.getHeight()),
    }
elif isinstance(shape, omero.model.EllipseI):
    geometry = {
        "x": unwrap(shape.getX()),
        "y": unwrap(shape.getY()),
        "radius_x": unwrap(shape.getRadiusX()),
        "radius_y": unwrap(shape.getRadiusY()),
    }
elif isinstance(shape, omero.model.LineI):
    geometry = {
        "x1": unwrap(shape.getX1()),
        "y1": unwrap(shape.getY1()),
        "x2": unwrap(shape.getX2()),
        "y2": unwrap(shape.getY2()),
    }
elif isinstance(shape, (omero.model.PolygonI, omero.model.PolylineI)):
    geometry = {"points": unwrap(shape.getPoints())}

Validate coordinates against image dimensions. Preserve floating-point coordinates; do not truncate them to integers merely for JSON.

For masks:

  • export position, dimensions, plane selectors, and byte count only by default;
  • do not serialize mask bytes into broad JSON;
  • treat decoded masks as pixel-derived data;
  • validate width/height and bit packing against the current model before reconstructing.

Creating an ROI Is a Write

Current core-model pattern:

import omero.model
from omero.rtypes import rdouble, rint, rstring

image = conn.getObject("Image", image_id)
if image is None:
    raise LookupError("Image unavailable")

x = 50.0
y = 100.0
width = 200.0
height = 150.0
z = 0
t = 0

if x < 0 or y < 0 or x + width > image.getSizeX() or y + height > image.getSizeY():
    raise ValueError("Rectangle is outside image bounds")
if not 0 <= z < image.getSizeZ() or not 0 <= t < image.getSizeT():
    raise ValueError("Plane index is outside image bounds")

rectangle = omero.model.RectangleI()
rectangle.setX(rdouble(x))
rectangle.setY(rdouble(y))
rectangle.setWidth(rdouble(width))
rectangle.setHeight(rdouble(height))
rectangle.setTheZ(rint(z))
rectangle.setTheT(rint(t))
rectangle.setTextValue(rstring("reviewed-region"))

roi = omero.model.RoiI()
roi.setImage(image._obj)
roi.addShape(rectangle)

saved = conn.getUpdateService().saveAndReturnObject(roi)
print(saved.getId().getValue())

Before execution, confirm:

  • image ID, group, and dimensions;
  • shape count and coordinate system;
  • Z/T/C semantics;
  • label sensitivity;
  • write permission;
  • whether an existing ROI should be updated rather than duplicated.

RGBA Encoding

The official Python example encodes color bytes as a signed 32-bit integer:

def rgba_to_int(red, green, blue, alpha=255):
    channels = (red, green, blue, alpha)
    if any(not 0 <= value <= 255 for value in channels):
        raise ValueError("RGBA channels must be in 0..255")
    return int.from_bytes(channels, byteorder="big", signed=True)

Use rint(rgba_to_int(...)) for generated shape color fields. Do not swap RGBA order or assume an unsigned representation.

Intensity Measurements

The historical Python example uses IRoi.getShapeStatsRestricted(shape_ids, z, t, channel_indices). Since IRoi is deprecated:

  1. verify the method in the target server's generated API;
  2. cap shape and channel counts;
  3. preserve channel indexing (pixel channels are zero-based);
  4. record the exact server/client versions;
  5. do not describe the result as a replacement for a validated analysis pipeline.

For simple rectangular reads, a bounded pixel tile may be clearer:

pixels = image.getPrimaryPixels()
z = 0
c = 0
t = 0
x = 10
y = 20
width = 100
height = 80

tile = next(pixels.getTiles([(z, c, t, (x, y, width, height))]))

Confirm the current API's tile generator behavior and cap tile area. Polygon, polyline, ellipse, and mask measurements require a correctly defined raster mask; a bounding box alone is not the ROI.

Updates and Deletion

Updating a shape and saving an ROI is a write that can affect downstream measurements. Deleting an ROI removes its shapes. Never add delete support to a read-only export script.

Before update/delete:

  • show image, ROI, and shape IDs;
  • retrieve current values;
  • check permissions and group context;
  • obtain approval for the exact IDs;
  • avoid namespace/label-based bulk selection;
  • wait for command completion and verify the result.

ROI Export Checklist

  • Explicit image IDs only
  • One group context
  • Maximum images, ROIs per image, and shapes per ROI
  • Labels redacted by default
  • Mask bytes omitted
  • No pixel values unless separately requested
  • Plane selectors preserve None
  • Geometry strings have a length cap
  • IRoi deprecation recorded
  • Connection closed in finally