Confocal microscopy enables the acquisition of high-resolution, optically sectioned images of fluorescently labeled biological specimens. This technique allows for precise three-dimensional visualization of fine structural details within thick samples, such as cultured cells and brain tissue sections. For studies prioritizing faster and more cost-effective imaging, widefield fluorescence microscopy can be used as an alternative.

• To assess the co-expression of target proteins within specific cell types or discrete brain regions.

• To identify neuronal populations activated or inhibited by external stimuli (e.g. Fos staining)

• To investigate protein–protein interactions using techniques such as the proximity ligation assay (PLA).

• To determine the expression patterns or translocation of proteins between subcellular compartments (e.g., dendritic vs. somatic compartments; nuclear vs. cytoplasmic distribution).

• To analyze the structure, distribution, and cellular associations of complex extracellular matrix assemblies, such as perineuronal nets (PNNs), within brain tissue.

• To examine the morphological complexity of neurons, including dendritic arborization, spine density, and synaptic organization.