Twenty-two landmarks were digitally scored on each skull and seventeen on each mandible to encompass overall shape (Fig. 1), and Thin Plate Spline (TPS) Relative Warp analyses [54] were conducted on the digitized specimens (see Procedure for digital shape analysis S2).
We digitized the outline of the dorsal margins of the carapaces using tpsDig [70] of following numbers of specimens: Lake Vänern: ls 22, cor 22; Lake Stora Färgen ced 22, ls 18, lc 8; Lake Ragnerudsjön: ls 18, kes 21, lc 6; Fleesensee: ber 5, cor 7, gibb 5. We then aligned the digitized specimens in Chainman [71], reducing the curve to twenty landmarks.
For example, the Mycology Collections data Portal (MyCoPortal; http://mycoportal.org/) provides direct access to digitized specimens records provided by The Macrofungi Collection Consortium, a collaboration of 35 institutions in 24 states in the USA (http://mycoportal.org/portal/index.php).org/portal/index.php
It's absolutely inexcusable that we're continuing to add to the backlog of un-databased, un-digitized specimens.
Pixels thus labeled as positive for GLUT-1, CA IX and Ki67 were stored in the green, red and blue channels, respectively, of a new RGB ("merge") image, which had the same pixel dimensions as the corresponding original digitized tumor specimens.
For all specimens, digitized images of cellular organelles (n = 20 for each specimen) were recorded at a magnification of 28000x.
The grade of laryngeal lesions had been previously determined by an experienced pathologist by means of H&E stained digitized images of specimens from the same laryngeal lesions.
The specimen was digitized 10 times blindly by the same observer and then by 10 other observers to calculate intra- and interobserver variance.
The specimen was digitized as disarticulated bones using photogrammetry [ 10] and the freely available software 'VisualSFM' (http://ccwu.me/vsfm) and 'Meshlab' (http://meshlab.sourceforge.net) (electronic supplementary material, S2).
For this purpose, a special test setup was established and a computer algorithm was developed to identify volume of the specimens from digitized images.
