optimizing images for thresholding

[Uknalis, Joseph]

Is there an 'expert system' of decisions on how to bring out objects for thresholding and particle analysis?
For a series of images that I try various operations on (adjust window/level, gamma, background subtract)
For each set I usually have to try various combinations, usually different from previous sets.

For some reason subtracting a empty image from a sample image does not give good results- virtually black images, with not much range (even at various lamp intensities,  low mag images have a 'hotspot' from the lamp).

Is there a preferred 'order of operations' for optimizing images for thresholding?

Thanks
  Joe





This electronic message contains information generated by the USDA solely for the intended recipients. Any unauthorized interception of this message or the use or disclosure of the information it contains may violate the law and subject the violator to civil or criminal penalties. If you believe you have received this message in error, please notify the sender and delete the email immediately.

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Gabriel Landini]

On Monday 08 Aug 2016 14:00:55 you wrote:
> Is there an 'expert system' of decisions on how to bring out objects for
> thresholding and particle analysis?

Do you mean for any arbitrary image? I do not think there could be.

> For a series of images that I try
> various operations on (adjust window/level, gamma, background subtract) For
> each set I usually have to try various combinations, usually different from
> previous sets.

Window level and gamma are display operations. Unless you then apply those
tranformations to the pixel data, it would not make any difference, for
example to histogram-based segmentation.

> For some reason subtracting a empty image from a sample image does not give
> good results- virtually black images, with not much range (even at various
> lamp intensities,  low mag images have a 'hotspot' from the lamp).

Am I right guessing that you are using bright field microscopy?
If so, you do not literally "subtract" a bright filed image from the original,
but you compute the transmittance through the sample to correct the background
(it actually means to subtract the uneven illumination).
Here are described some methods to do this:
http://imagejdocu.tudor.lu/doku.php?id=howto:working:how_to_correct_background_illumination_in_brightfield_microscopy

Hope it helps.
Gabriel

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html