Quality score filter was set to separate RNA dots from background. The cell-membrane signal (GFP) got weaker in the deepest z-layers, and thus we could not successfully separate cells and collect data on the ventral-most part (Figure S1). Therefore, we have only included data from cells ...
First, image stacks were broken down into maximum intensity z-projections (50μm depth for each projection). Background signal was subtracted from image projections, with the resultant image thresholded with an Otsu filter. The binarized image was skeletonized and the “Analyze Skeleton” function ...