Various examples are provided related to imaging with augmented stereoscopic microscopes. In one example, an augmented stereoscopic microscope includes an objective lens that can simultaneously receive near infrared (NIR) images and visible bright-field images of an examined object and an augmentation module. The augmentation module can separate the NIR images from the visible bright-field images for processing by an image processing unit to produce synthetic images using the NIR images and combine the synthetic images with the visible bright-field images to form co-registered augmented images that are directed to an eyepiece of the augmented stereoscopic microscope. In another example, a method includes obtaining a NIR image of an examined object; generating a synthetic image using the NIR image; combining the synthetic image with a real-time visual image of the examined object to form an augmented image; and directing the augmented image to an eyepiece of an augmented stereoscopic microscope.