Brightfield, maximum projection, and mid focal plane images are shown.
To clearly image host cells and bacteria, collected images from the red and green emission channels were processed by maximum projection of z planes and adjustment of the look up table using Metamorph (Molecular Devices).
Spine number and dendritic length were measured by projecting all the stacks of an image into a single plane (maximum projection) with the observer blind to the experimental conditions.
To assess RGC survival, retinal whole mounts were stained with an anti-mouse Brn-3a mAb (1 : 500, Merk Millipore, Darmstadt, Germany) and examined under confocal microscopy (LSM 710, Carl Zeiss MicroImaging GmbH, Jena, Germany), to generate a single plane maximum projection of the RGC layer in each retina.
Z-stack images (0.27-μm intervals spanning entire embryo) were acquired and projected to a single plane under maximum projection.
Movies were analysed using ImageJ by compiling images from the maximum projection of consecutive focal planes consistently within each experiment.
Thus, a higher number of cells were observed in the maximum projection of the XY-plane in the hybrid gels, even though the initial numbers of encapsulated cells were kept the same.
The Z-optical section series, obtained beginning from the nuclear apex and progressing down in 0.48 μM (at least 12 planes), were converted to maximum projection images to avoid subjectivity in the choice of the plane to be analyzed.
Cells from each stage of PCD were captured with z-stack imaging and compiled into a maximum projection image, to simultaneously show all planes.
A series of optical sections were collected from xy plane and merged into maximum projection images.
