This image correspond to a specimen deformed in the vertical direction. Would you have any suggestion to lift deformed pixels and make a "perfecly horizontal block"

NOTE: A mask can be easily created. Thank you.

Answer 1

[Image Analyst]

Just go along your mask finding the top line, then use circshift or imtranslate or simple indexing to lift the line.

[rows, columns] = size(mask);
for col = 1 : columns
    thisColumn = grayImage(:, col);
    topLine = find(mask(:, col), 1, 'first');
    thisColumn = [thisColumn(topLine:end), zeros(topLine-1, 1)];
    grayImage(:, col) = thisColumn;
end

Answer 2

[Santi]

Thank you for this great approach; worked and very easy to understand.

Best regards