A pretty good solution is to use morphological closing to make the brightness uniform and then use a regular (non-adaptive) Otsu threshold:
// Divide the image by its morphologically closed counterpart
Mat kernel = Imgproc.getStructuringElement(Imgproc.MORPH_ELLIPSE, new Size(19,19));
Mat closed = new Mat();
Imgproc.morphologyEx(image, closed, Imgproc.MORPH_CLOSE, kernel);
image.convertTo(image, CvType.CV_32F); // divide requires floating-point
Core.divide(image, closed, image, 1, CvType.CV_32F);
Core.normalize(image, image, 0, 255, Core.NORM_MINMAX);
image.convertTo(image, CvType.CV_8UC1); // convert back to unsigned int
// Threshold each block (3x3 grid) of the image separately to
// correct for minor differences in contrast across the image.
for (int i = 0; i < 3; i++) {
for (int j = 0; j < 3; j++) {
Mat block = image.rowRange(144*i, 144*(i+1)).colRange(144*j, 144*(j+1));
Imgproc.threshold(block, block, -1, 255, Imgproc.THRESH_BINARY_INV+Imgproc.THRESH_OTSU);
}
}
Result:
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