@@ -22,7 +22,7 @@ Most of the time, the morphological measurements are made directly on the 2D seg
When this is not the case, any **morphological measurements made on the segmentation results will be corrupted by geometrical distortions induced by the projection**. Indeed, almost all morphology metrics, such as area, circularity, polarity and orientation will be erroneous when they are measured on the 2D projection. This is illustrated on the figure below:
On this illustration, a cell (in red, top-left quadrant) is located on a region of the tissue that makes a large angle with the XY plane. Its projection on the XY plane (in green, bottom-left quadrant) therefore underestimates its size, and alters its orientation. This is recapitulated on the top-right and bottom-right quadrants, with a side view.
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@@ -154,17 +154,17 @@ It is the results of the segmentation step, and must be a black and white image
For instance, this is good (the ridges can be connected by the pixel diagonals):
The height-map is an image <u>of the exact same size that the segmentation image</u>, and for which the pixel value reports the Z position of the tissue surface. For instance:
On this example the pixel value is an integer that gives the Z-plane from which the projection pixel was taken. Several academic softwares generate this height-map (under varying names) on top of the projection. We list some of them at the end of this documentation.
