You can scan your old diapositive using a scanner provided with special slide attachment or you can use a slide projector project on white wall or a screen projection using a standard digital camera to shoot each slide. If you have the time this is the best way to produce a great work. This need time to adjust parameter if you can link your camera directly to the computer like Canon or Nikon you can produce fantastic result.
PhotoStory is a photo and video editing program. You can scan pbotos, but I would not do this. Your scanner most likely has better scanning software, and I suggest that you use it. Once you have the photos scanned, then use PhotoStory to create a video slideshow using your photos.
As JohnCB says - better to use your scanner software.
However there is an issue that you will have to deal with - because the diapositives are in glass frames - here I presume you mean the film is sandwiched between two thin sheets of glass - you are may get reflection of the scanner light source off the glass reducing the contrast of the image.
If your scanner has a source / document setting for glossy photographs, try this setting first, scan at 300dpi and if necessary use the advanced settings for the scanner to iprove contrast / brightness if required.