This subject is discussed under indexing in MATLAB. Basic script, Img (Img=0) = 1 (All zero intensities changed to one), or can use Img>200, depending on the aforementioned tech. used (one can be replaced by a range of numbers).
You can simply do
img(img==0) = 1
img(img>200) = a % a being a value
img(some condition) take all value where the condition is True.
You can type these commands:
img(img==0) = 1
img(img>200) = a
img(some condition)
If by indexing you mean the coordinates, then the "find " will list the indices of the pixel intensity of a particular value .
Eg: Ids=find(img
This is a very interesting question. In addition to the helpful answers already given, there is a bit more to add.
A good discussion on logical indexing from a Matlab perspective is given in
http://blogs.mathworks.com/loren/2013/02/20/logical-indexing-multiple-conditions/
especially in
http://blogs.mathworks.com/steve/2008/02/25/neighbor-indexing-2/
A detailed example of logical indexing is given in a eye analysis system is given in
https://www.researchgate.net/profile/Edmundas_Zavadskas/publication/257392355_Student_progress_assessment_with_the_help_of_an_intelligent_pupil_analysis_system/links/54b13a800cf28ebe92dff766.pdf
See Algorithm 1.1, starting on page 67.
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