Microscopy Protocols
Histology Protocols
Analysis Protocols
This algorithm automatically detects Synaptophysin-mCherry labeled synaptic boutons throughout the brain. A typical use case would be injecting a Cre-conditional Synaptophysin-mCherry vector into a Cre-driver mouse. After four weeks, the mouse is transcardially perfused, and the brain is dissected, fixed, sliced, and immunostained with Nickel-Diaminobenzidine (NiDAB) for mCherry. Afterwards, the sections are mounted on a slide and coverslipped. Finally, these slides are imaged on a slide-scanning microscope. These images are converted into the tif Image format, and processed with the BoutonCount algorithm. For an example of the output of this algorithm, see our paper: Huang, Dake, et al. "Efferent Projections of Vglut2, Foxp2 and Pdyn Parabrachial Neurons in Mice." Journal of Comparative Neurology.
This algorithm, along with a more detailed description, can be found at https://github.com/GeerlingLab/Parabrachial_efferents-v2