Figure 2.

Workflow of a semi-automated ImageJ macro used to quantify invasion into ex vivo brain slice cultures. This ImageJ macro is comprised of 9 semi-automated steps for analyzing the number of particles, area of each particle, and distance of each particle from the nearest edge of the spheroid. (i) A raw image is split into individual channels and (ii) the GFP only channel is converted to an 8-bit image (iii). The ImageJ macro then starts by creating a mask of the binary image (iv) and the software places an ellipse over the core of the spheroid, which can be adjusted if necessary to capture the edge of the spheroid (v). The ellipse is subtracted from the image (vi) and particles outside of the spheroid core are watershed (vii). Finally, a colour map (viii) is used by the software to calculate the distance of each particle from the nearest edge of the ellipse (ix) as well as the area of each particle.