Cluster area was quantified and measured from maximum intensity Z-projections of confocal image stacks, using automated edge finding and area measurement in ImageJ software (NIH, Bethesda MD).
For both sets of images, maximum intensity z-projections were calculated from slices of image stacks to ensure complete detection of fluorophores within a cell.
Stacks are presented as the maximum intensity Z projections.
z-stack images were acquired (Olympus FV1000 or FV300 confocal microscope) and ImageJ software (Wayne Rasband, NIH) was used to create maximum intensity z-projections; these span only one side of the embryo unless otherwise stated.
Images represent maximum intensity Z-series projections.
The maximum intensity projection of Z-stack images for a sample thickness of 50 μm evidences clearly the nanowires of several tens of micrometers (see Figure 10a).
(a) Maximum intensity projection of Z-stack for section thickness of 50 μm; 500- to 550-nm single-band band-pass filter.
Each panel represents a maximum intensity projection of z-stack images obtained with two-photon microscopy.
All measurements describing the morphology (area, perimeter, shape factor and aspect ratio) of nuclei were analyzed from maximum intensity projections of Z-stack images of teased muscle fibers or cells using ImageJ or Zeiss ZEN software.
RNA foci were counted in maximum intensity projections of z-stack images using the touch count tool in Volocity image analysis software (Perkin Elmer), and then scored for co-occurrence with staining of the nucleus and cell type markers.
