Charon is an automatic astrometry program from Bill Gray's Project Pluto. It works with Project Pluto's Guide6 (and the older Guide5). It took me a bit of fiddling with the parameters to get it to work with my images, but it wasn't difficult and Bill Gray is very helpful by email should any problems arise.
One must tell Charon the name (and location) of an image file and the name of the object expected within that image (something that can be semi-automated by way of batch files). Charon will then identify star images in the image file, search for pattern matches to the Guide Star Catalog (GSC) within a specified radius of the location of the target, and, if sufficient matches are found, will calibrate the image showing how many stars matched and the overall residual errors in the calibration. With my images, there are often 50 or more matches with overall calibration residuals on the order of .35 arcseconds.
Charon displays the image (with adjustable scales) with a big, red cross at the predicted location of the target. If the target is well characterized (as with numbered asteroids, say), the red cross will be right on, or very close to a stellar image and the coordinates and magnitude of that image will be shown along with the deviation in RA and DEC. If you are making the measurement for the Minor Planet Center or IOTA, pressing 'o' or 'i' will record the measurement in an ascii file in the correct format suitable for sending to the MPC or IOTA by email (no transcription errors). Charon is a very neat, useful program! But what if your object is NOT located where it is expected? Or what about new discoveries, which Charon couldn't possibly be told about? This, of course, is the essence of my work in which I am looking for both new discoveries and large errors in predicted positions. The answer is that images still must be aligned and blinked so that any moving objects can be detected. The row-column identifiers from the blinking process can be used to identify the target to be measured in Charon's image because Charon's cursor notes the row and column as well.