http://imagej.273.s1.nabble.com/Is-manual-thresholding-methods-accepted-by-scientific-journals-tp5010814p5010815.html
Very interesting question indeed. From my experience I know, that journals
lika PNAS can get along with manual thresholding. At least if it is not the
trying to find balance between subjectivity and well... more accurate
of "empty view". Maybe this advice can be applied to your work too.
> Dear mailing list,
>
> I have developed a nice macro for identifying colocalized signals for
> z-stack confocal images with multiple channels/colors. However, my
> advisor/professor has now come to question my method for setting a
> threshold for signal/no-signal in the infividual channels.
>
> My manual method has been to simply raise the threshold above what I
> relatively confidently can see is background, like large areas with no
> apparent staining. The reason I did it manually is because when I played
> around with the automatic thresholding methods in ImageJ I decided that
> they were not any better than manual and could be subject to mistakes.
>
> My supervisor now feels that this sounds too subjective and would not look
> good in a paper. He therefore asked me to try to find a way that was more
> guided e.g. by the histogram or something, anything that is less subjective
> (not sure if he is worried about accuracy or how it sounds in a paper).
>
> What is the current standard for this kind of analysis in scientific
> journals, in particular with regards to the acceptability of manual
> thresholding of immunofluorescent brain sections stained with various
> antibodies (and nuclear markers and neuron trancers)? Is there a preference
> for automated, manual or some hybrid methods? Could I "get-away" with
> something like this: "Thresholds were set manually at a level that
> excluded most pixels in assumed background areas. Inspection of the
> assigned threshold level in the ImageJ intensity histogram showed that the
> thresholds were set at where the main peak (background pixels) started to
> or had reached a minimum value."
>
> Image set that Im working on:
>
> I am working with images of brain sections with 4 colors/channels: nuclear
> stain, two immunofluorescence staining for transciption factors (nuclear
> localization), and a retrograde nerve cell staning (nuclear + cytoplasm
> staining).
>
> Greateful for any advice!
>
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