Public Lab Research note


Using imageJ to adjust threshold using mode Entropy

by damarquis | October 20, 2015 21:26 | 1,599 views | 0 comments | #12322 | 1,599 views | 0 comments | #12322 20 Oct 21:26

Read more: stable.publiclab.org/n/12322


What I want to do document the manual steps to properly adjust the threshold option, the goal is take a full-color microscope image when converting to a high-contrast black and white image through "thresholding". See this note

Steps: Thresholding the image

First, convert the image to greyscale by going to Image > Type > 8 bit

Now we want to threshold the image to a binary image. Go to Image > Adjust > Threshold

Thesholding1.PNG

As you see there are numerous modes to select, options B&W and MaxEntropy seem to produce a decent binary image if the brightness is adjusted correctly.

Comparing Modes

Thesholding_Intermode.PNG Image > Adjust > Threshold > Intermodes

Thesholding_MaxEntropy.PNG Image > Adjust > Threshold > MaxEntropy

You want to select a threshold mode that isolates particles without including noise, MaxEntropy seem to be the best option of the two. This important because it should be the same threshold options used universally during the processing of multiply images.


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