例えば以下のようにすると、 regionprops 関数でそれぞれの円領域に含まれるピクセルの位置情報を取得したうえで、その情報を使って円ごとの輝度の平均値を算出することができます。
% Read image and convert to gray-scale
I = imread('sample_circles.bmp');
Igray = rgb2gray(I);
% Obtain regions of interest
BW = imbinarize(Igray);
BW = imclearborder(BW);
se = strel('disk',1);
BW = imclose(BW,se);
% Obtain information for each region
s = regionprops('table',BW,{'Centroid','BoundingBox','PixelIdxList'});
% Calculate average luminance for each region
avLuminance = zeros(height(s),1);
for kk = 1:height(s)
avLuminance(kk) = mean(Igray(s.PixelIdxList{kk}));
end
% Show the result
figure
imshow(Igray)
hold on
for kk = 1:height(s)
rectangle('Position', s.BoundingBox(kk,:),'EdgeColor', 'c');
text(s.Centroid(kk,1),s.Centroid(kk,2),...
sprintf('%.1f',avLuminance(kk)),...
'FontWeight', 'bold',...
'HorizontalAlignment','center',...
'Color', 'c')
end