[ome-devel] How to use masks for Rois ?

[Thomas Boudier]

Dear OME developers,

I am trying to write some java code to create kinda 3D Rois, but I am not sure how to create MaskData, this is my code :

ImageInt seg = object3D.createSegImage(0, 0, 0);
byte[][] mask = new byte[seg.sizeZ][seg.sizeXY];
int offX = seg.offsetX;
int offY = seg.offsetY;
int offZ = seg.offsetZ;

for (int z = 0; z < seg.sizeZ; z++) {
    byte[] img = mask[z];
    int c = 0;
    for (int y = 0; y < seg.sizeY; y++) {
        for (int x = 0; x < seg.sizeX; x++) {
            if (seg.getPixel(x, y, z) > 0)
                img[c] = (byte) 255;
            else
                img[c] = (byte) 0;
            c++;
        }
    }
}
ROIData data = new ROIData();
data.setImage(image.asImage());
for (int z = 0; z < seg.sizeZ; z++) {
    MaskData maskData = new MaskData(offX, offY, seg.sizeX, seg.sizeY, mask[z]);
    maskData.setZ(z + offZ);
    maskData.setT(T);
    maskData.setText(object3D.getName() + "_" + object3D.getValue());
    data.addShapeData(maskData);
}
// Save ROI
DataManagerFacility dm = gateway.getFacility(DataManagerFacility.class);
ROIFacility roifac = gateway.getFacility(ROIFacility.class);
ROIData roiData = roifac.saveROIs(ctx, image.getId(), Arrays.asList(data)).iterator().next();

Actually I am not sure how such Mask Roi should display inside OMERO, it seems I can only see the bounding box but not the actual mask.

Thanks for any hints.

Best,

Thomas


--
/***************************************************************/
      Thomas Boudier, Senior Research Officer,
      BioImage Analyst, Dynamic Imaging Centre,
      Walter and Eliza Hall Institute (WEHI), Australia.
/**************************************************************/


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