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    $\begingroup$ LocalAdaptiveBinarize gives you a little more control over the binarization and helps a lot if you have a brightness gradient in you images. $\endgroup$ Commented Nov 2, 2014 at 21:11
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    $\begingroup$ Also try BilateralFilter and MorphologicalBinarize $\endgroup$ Commented Nov 2, 2014 at 22:50
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    $\begingroup$ I wonder if adjusting the image histogram would allow you to make images obtained across multiple days a bit more consistent. $\endgroup$ Commented Nov 3, 2014 at 1:22
  • $\begingroup$ Some denoising, using e.g. WienerFilter or TotalVariationFilter, will also help avoid the "shading in some black in the spots where there's nothing". $\endgroup$ Commented Nov 3, 2014 at 6:04