Besides flux density estimate, which, as discussed before, is a non trivial task, analyzing spectral line images may force the astronomer to face some really tricky problems. The two most obvious are moment evaluation and continuum subtraction.
Hence, it is impossible to recommend deconvolving before computing the mean intensity, or summing up the individual cleaned channel maps. In the latter, limited signal to noise can prevent proper deconvolution. In the former, velocity gradients can spread emission over an extended area which is difficult to handle in the deconvolution. Choice can be a matter of trial (and errors).
To avoid introducing noise, a window in velocity is important. While noise on the integrated intensity only increases as the square root of the window width, the effect on the higher order moments is much more dramatic, and results in non-gaussian noise distribution on these variables. A threshold in intensity is useful to prevent spurious noisy features. The window should in principle be pixel dependent to allow for velocity gradients. Smoothing both in the spatial and spectral domains may help in obtaining better results in moment extraction. A line fitting procedure (e.g. a Gaussian line fit at each pixel) may sometimes be the best solution (under construction, check later...).
Moments can be computed using task MOMENTS and displayed using the GO VELOCITY command in GRAPHIC.