In Fig. 18, a schematic of different convex cell outlines and their designations is given.
Closed curves were drawn using the points of cell outlines on the planes with a height interval of 1 m.
Table 2 summarizes the error estimates for the cell outlines that were identified by the T1 and T2 threshold values.
Using the loft command, a free surface of the cell was constructed from a set of closed curves of cell outlines and an additional very small circle that was 0.5 or 1 m above the top slice.
Single cells were selected by manually tracing cell outlines, the background was subtracted in each channel, and the fraction of Trak1 (or GFP) overlapping with TOM20 was determined by Mander's colocalization coefficient using the NIS-Elements software (Nikon Instruments, Melville, NY).
Open image in new window Fig. 18 A schematic of different convex cell outlines and their aspect ratios (ß = width/height) of the convex cell types and their terminology: convex (ß > 3/1), hemispherical (ß ~ 2/1), cupola (ß < 3/2), conical (ß > 3/2), papilla (ß < 3/2 and > 1/2), hair-papilla (ß < 1/3 and > 1/6), and hair (ß < 1/7).
Cell outlines were traced by hand and area was measured in OpenLab (Improvision, Lexington, MA).
The soma of stained cells was outlined manually to ensure all cell outlines were accurate and all non-neuronal material such as blood vessels were excluded.
Rather than having well defined cell outlines, and channels, aggregates displayed a smoothened surface, where borders between cells were filled significantly with ECM (Fig. 4C).
Cell outlines were determined from images of GFP fluorescence in the U2OS cells by image thresholding at a grayscale level 5 units greater than the noise in the background surrounding the cell.
Somal sizes were measured by a computer algorithm within Image Pro Plus 4.0, converting pixels covered by cell outlines to square microns by using a calibration factor for the x20 objective used.
