I have a 4-axis motorized microscope that takes images of an insect in a 2D raster pattern, and repeats this multiple times while rotating it. Through software like Microsoft ICE, I stitch the images taken in the raster pattern into a single image, with the idea of then using 50+ of these stitched images to create a 3D model of the insect. For instance, here are 20 stitched images of a stink bug. Each image was created using 35 individual images.

The problem is that I have to run the 2D stitching for each set of images, and this is just too labor intensive for larger datasets. Ideally, I would be able to just select a list of folders and stitch the images contained in each folder --- something like microsoft ICE but with batch capability. I've looked far and wide... does anything come to mind?

Thank you.

  • Are you saying each of these stinkbug images consist of stacks of 35 individual frames?
    – voices
    Jul 27, 2018 at 19:13

1 Answer 1


Take a look at Hugin which is a very powerful panorama stitching tool suite, (and more). It comes with a GUI but also allows command line use.

In your case I should imagine that the order and field of view values are reasonably predictable so the stitching sequence should be suitable for scripting.


Sorry no screen shot of the command line usage! enter image description here

Hugin Features

  • Price: $0.00 (Free, Gratis)
  • Platform: Windows Vista & Later (64 bit current version, 32 bit old version & XP with 2013 version), OS-X, Unix & Linux.
  • Open Source GPL
  • Multi-lingual (Brazilian Portuguese, Bulgarian, Catalan, Chinese Simplified, Chinese Traditional, Czech, Dutch, Danish, English, French, German, Hungarian, Italian, Japanese, Korean, Polish, Russian, Slovakian, Slovenian, Spanish, Swedish and Ukranian translations).
  • HDR Support (Including stacking exposure bracketed shots to produce HDR)
  • Focus Stacking (very handy in the macro world)
  • Lens Correction
  • Automatic Control Point Generation
  • Lots more
  • I puttered around with Hugin but was a bit put off by the required input fields, involving camera lens type and such, which I don't have information on (I'm using a cheap generic USB camera). But given the abilities of it I should probably suck it up and give it a try... Thank you, still open to suggestions on other software that might fit the bill. Jul 14, 2018 at 17:39

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