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    e1Coords = autoDetectMarkers(frame1, P1, Q);
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    e1Coords = autoDetectMarkers(frame1, P1, Q);
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    %e0Coords = manuallyDetectMarkers(frame0, P0, Q);
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    %e0Coords = manuallyDetectMarkers(frame0, P0, Q);
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    %e1Coords = manuallyDetectMarkers(frame1, P1, Q);
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    %e1Coords = manuallyDetectMarkers(frame1, P1, Q);
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    e0Coords = undistortPoints(e0Coords, camParams0);
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    %e0Coords = undistortPoints(e0Coords, camParams0);
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    e1Coords = undistortPoints(e1Coords, camParams1);
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    %e1Coords = undistortPoints(e1Coords, camParams1);
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    % match ellipse candidates between cameras based on projection
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    % match ellipse candidates between cameras based on projection
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    E0 = projectOntoPointCloud(e0Coords, P0, Q);
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    E0 = projectOntoPointCloud(e0Coords, P0, Q);
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    E1 = projectOntoPointCloud(e1Coords, P1, Q);
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    E1 = projectOntoPointCloud(e1Coords, P1, Q);
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    end
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    end
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    matchedPairs = matchedPairs(1:nMatchedPairs, :);
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    matchedPairs = matchedPairs(1:nMatchedPairs, :);
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    % triangulate marker centers (lens correction has been performed)
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    % triangulate marker centers (lens correction has been performed)
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    [E{i}, e] = triangulate(e0Coords(matchedPairs(:, 1),:), e1Coords(matchedPairs(:, 2),:), camStereoParams);
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    [E{i}, e] = triangulate(e0Coords(matchedPairs(:, 1),:), e1Coords(matchedPairs(:, 2),:), camStereoParams);
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    E{i} = E{i}(e<1.0, :);
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    E{i} = E{i}(e<3.0, :);
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    display(e);
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    % write point cloud with marker (debugging)
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    % write point cloud with marker (debugging)
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    pcDebug = pointCloud([pc.Location; E{i}], 'Color', [pc.Color; repmat([255, 0, 0], size(E{i}, 1), 1)]);
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    pcDebug = pointCloud([pc.Location; E{i}], 'Color', [pc.Color; repmat([255, 0, 0], size(E{i}, 1), 1)]);
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    pcwrite(pcDebug, 'pcDebug.ply');
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    pcwrite(pcDebug, 'pcDebug.ply');
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% show found markers in optimized alignment
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% show found markers in optimized alignment
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figure;
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figure;
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hold('on');
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hold('on');
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for i=1:nSubScans
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for i=1:nSubScans
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    % fix Ri to be orthogonal
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    Ri = alignment(i).Rotation;
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    [U,~,V] = svd(alignment(i).Rotation);
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    Ri = U*V';
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    Ti = alignment(i).Translation;
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    Ti = alignment(i).Translation;
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    Ea = E{i}*Ri' + repmat(Ti', size(E{i}, 1), 1);
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    Ea = E{i}*Ri' + repmat(Ti', size(E{i}, 1), 1);
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    % bring point cloud into optimized alignment
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    % bring point cloud into optimized alignment
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        %figure; imshowpair(imMarkerSpace, m);
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        %figure; imshowpair(imMarkerSpace, m);
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        % perform image registration
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        % perform image registration
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        % might be better off using subpixel image correlation
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        % might be better off using subpixel image correlation
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        [opt, met] = imregconfig('multimodal');
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        [opt, met] = imregconfig('multimodal');
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        T = imregtform(m, imMarkerSpace, 'translation', opt, met, 'DisplayOptimization', true);
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        T = imregtform(m, imMarkerSpace, 'translation', opt, met, 'DisplayOptimization', false);
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        rege = imwarp(m, T, 'OutputView', imref2d(size(m)));
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        rege = imwarp(m, T, 'OutputView', imref2d(size(m)));
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        %figure; imshowpair(imMarkerSpace, rege);
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        %figure; imshowpair(imMarkerSpace, rege);
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        % measure of correlation
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        % measure of correlation