I think we need to dissect your question a little bit to first figure out, what you really want to do, then, how this can be done and if such an analysis gives you a valid output
On the contrary, it is perfectly possible to automate analyses based on a color threshold, but first to the definition of the problem:
The combination of the last two statement puzzle me (and I guess also @volker).
Is your purpose to:
- to measure intensity values from the image? Then what do you expect that the RGB and/or the mean intensity (which in your case is just a mathematical combination of the RGB values) will tell you. To this end it would be good if you can provide an example image (as PNG or TIF) and a clearly specified definition of what exactly you try to do or measure in that image.
- do you want to measure and count particles by thresholding them based on their color and intensity?
- do you need to threshold the particles based on color and intensity and then in addition to their number also measure intensity and/or color values.
I am asking so detailed, because depending on what kind of sample you have, analysis of a color value of a mean value from combined colors will not be a valid output. So, this depends on your sample, image and research question.
As @volker elaborated already the two methods are different and you should decide finally for one. The Auto Threshold in the Color Threshold plugin is only calculated for the brightness channel and the result is combined with your manual selections from the other 2 channels (e.g. Hue and Saturation in the HSB color space). So, it also matters in which color space (RGB, HSB, Lab, YUV) you do this and at which values you place the manual thresholds in the remaining 2 channels.
The Auto Threshold you choose from the AutoThreshold plugin or the manual Threshold… plugin works directly on the intensities of the input image and therefore needs a single gray scale channel.
That means for the first method your input is a color image and for the second the input is a grayscale image. This and the way the two thresholding methods work are two reasons why the results naturally will be differ in partical number and size.
Another thing to consider is that when you mention…
…please be aware that if you just convert an RGB image to grayscale (e.g. 8-bit) ImageJ has 2 possible ways in converting your image. In both you loose quite a lot of information because the color image can have over 16 million colors, while the 8-bit image can only store 256 intensity values. Therefore, colors will be combined in either weighted or unweighted fashion. This also influences the final intensity measurement. In most cases measuring intensities from converted images is not meaningful.
So, there are many parameters to consider to define the way in which you can do your analysis and not every one will give you results which scientifically make sense.
Best, post an image and the definition of the exact parameters you want to measure (intensity, particle number,…). This will enable people here to help you in a more specific way.