This pyramidal image stack is stitched and built into a local server database simultaneously with acquisition. A data tree of 14 WSI is regularly obtained, containing two RL and six of each PPL and XPL WSI (at 18° rotation increments). The repurposed biological scanner produces transmitted light plane- and cross-polarised (TL-PPL and XPL) and unpolarised reflected light (RL) WSI from polished thin sections or slim epoxy mounts at various magnifications, yielding pixel dimensions from ca. Here we report on the calibration strategy of one repurposed slide scanner and describe a pilot image analysis pipeline designed to introduce the wider audience to the complexity of performing computer-assisted feature recognition on mineral groups. Slide scanners are now being modified to enable polarised petrographic microscopy by simulating stage rotation with the acquisition of multiple rotation angles of the polariser–analyser pair for observing randomly oriented anisotropic materials. The availability of WSI has motivated the development of instrument-agnostic advanced image analysis software, helping drug development, pathology, and many other areas of research. In biomedical microscopic imaging, they are widely deployed to generate whole-slide images (WSI) of tissue samples in various modes of illumination. ‘Slide scanners’ are rapid optical microscopes equipped with automated and accurate x-y travel stages with virtual z-motion that cannot be rotated.
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