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Slide Imaging and Image Analysis for Diatom Morphometrics

Light microscopy analysis of diatom frustules is widely used in basic and applied research [...]. For image acquisition, we use a Metafer slide scanning system [...]. In position list
mode, a list of user-defined positions, spread arbitrarily over the slide, can be imaged. [...] The vertical position of objects can be determined by automatic creation of a focus map, i.e., based on interpolation between reference points, or by autofocusing at each position captured, or using a combination of both. [...] Our two-cycle microscopy and image analysis procedure starts with a low-resolution area scan [...]. The overlapping low-resolution images are stitched together to a virtual slide using the VSlide software [...]. For locating and selecting valves of interest, the low-resolution images [...] are processed by SHERPA. [...] We use the VSViewer software to import the position list provided by SHERPA [...] into the virtual slide [...]. The annotation function of the viewer enables to manually add positions of interest if some objects deemed relevant were missed by SHERPA [...]. This allows for combining (semi-)automated and manual selection of valves of interest. [...] The annotated virtual slide from step 5 contains the (X, Y) position data required for selectively imaging the valves of interest. [...]. Extending the size range reported for F. kerguelensis (quite substantially, by nearly 45% in the case of apical length) nicely illustrates the advantages of a (semi-)automated approach formicroscopic morphometry  of diatom valves, primarily that it makes documenting and measuring large numbers of specimens feasible with moderate effort.

Cited From: Appl. Sci. (2017) Read more...
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