>>3283
>The values of the scanned image are sampled from inside this area, however the maximum and minimum values were already determined through the marquee in the preview (in Epson software at least). See the histogram video for what the value distribution should look like if you scan with a marquee. Note how there's no big gaps of the value distribution, meaning we get more detail in our scan.
I might be misunderstanding what you are trying to say, but you can also always apply color correction after scanning. Same with cropping, although being able to apply a marque in the scanner program might save time while scanning, perhaps? I never do previews, but I do all my cropping and color-correction as a separate step after the scanning.
>No big gaps in the value distribution
The point is not necessarily to avoid gaps, but to use the full range of values (from 0 to 255 or whatever). If you're scanning a two-tone BW print, your histogram is approximately going to just be two peaks, one for the blacks and one for the whites. But these peaks are never going to be pure white or pure black, due to imperfections in paper and ink. The "histogram stretch" corrects for this and makes the white appear as pure white and black as pure black.
Note that we are not only correcting for the color-inaccuracies due to our scanner, but also due to the printing process used to make the doujin. The reason we are able to do this is because we imagine that the author intended for the pure whites to be white and for the darkest colors to be black, and that any deviation from this is due to imperfect printing and/or scanning.
For scanning color prints and covers, things become much more complicated: we can't be certain exactly which shade of blue the author intended for Wakasagihime to have. There are two approaches one can take here: try to find a digital image of the cover on pixiv or somewhere else. You can use this as a ground truth to calibrate the colors of your scan. The second approach is to just make the colors of your scan as true to the colors in the print as possible. For this, you can use Color Calibration Targets. There is a guy in Germany who basically makes scanner calibration targets for everyone in the world:
http://www.targets.coloraid.de/
You can use these targets to generate ICC profiles to correct for color inaccuracies of your scanning. This calibration will not only depend on your scanner, but also light conditions etc, so try to scan with standardized light conditions. This effect should be pretty small, though. Since most manga is black-and-white, it might not be worth your time to worry about these things: readers do not really expect accurate colors for scans of doujin covers.
Finally, I'd also like to stress that all these things are in some sense optional. You'll go insane if you want your scans to be perfect, and almost no one can tell the difference between a good-enough scan and a perfect scan. It's just good to be aware of these things so you can make a conscious decision about the level of quality you think is worth aiming for.
Let me know if you'd like instructions on how to do individual steps, like histogram stretching and cropping of large number of images. My workflow is all open-source (using imagemagick and GIMP with the batch-processing addon 'BIMP'), so there is no need for specialized commercial software. I should add that I've never actually done color-correction properly, so that part I only know in theory.