Developed for the University of Edinburgh, Scotland
Fluorescent labelling of neurons is a well-established method used to trace the circuitry of the brain, and it is often the first step in identifying the targets of a brain region of interest. Some neurons in the brain branch extensively, sending long-range projections across the brain. In these cases, a brain-wide quantification of axon density in the different brain areas is necessary for identifying which areas these neurons are targeting, as well as the strength of innervation in these areas. For neurons that have been stained with mCherry and/or GFP, APP “10158 – mCherry+GFP, Axon Density” can be used to quantify axon density across brain areas by measuring fluorescence density in brain sections. Fluorescence density is measured as the fraction of pixels in a given area that are above a set threshold value. The APP returns the list of brain areas and their fluorescence density levels. This APP can also be modified to detect pre-synaptic targets that are labelled via retrograde tracing methods.