Brain-wide Quantification of Inflammation and Neural Activity at Single-cell Resolution

Sunil Gandhi, Ph.D.

Translucence Biosystems

Dr. Gandhi has focused his scientific career on developing cell technology to tap the brain’s latent capacity to rewire itself. He received his graduate training with Charles Stevens at the Salk Institute, where he studied the fundamental mechanisms of neurotransmitter release. As a postdoctoral fellow in Michael Stryker’s lab at UCSF, he discovered that young interneurons implanted in older brains induce a rejuvenating period of brain plasticity. With the support of a New Innovator Award from the NIH Director, a Searle Scholars Award, and fellowships from the Klingenstein and Whitehall Foundations, he has pioneered the use of embryonic inhibitory neuron transplantation to rewire the adult visual system. His lab discovered that transplanted inhibitory neurons successfully integrate into the circuitry of the adult host brain and correct developmental miswiring of the visual system in mice. More recently, the group has developed new methods for whole-brain visualization using new brain-clearing methods and light sheet microscopy. To disseminate these technologies to the neuroscience community, he co-founded a BRAIN Initiative-supported startup company, Translucence Biosystems. The company successfully partnered with ZEISS Microscopy to develop a new microscopy system for higher-resolution, faster light sheet microscopy of large, cleared samples. Dr. Gandhi’s group has combined expert skill in cell transplantation and advanced brain imaging to forge a collaboration with Drs. Mathew Blurton-Jones and Robert Spitale at UCI. Together, the team has developed a platform for the study of human microglia funded by the NIH BRAIN Initiative that combines stem cell technology, RNA sequencing, CRISPR gene editing, and advanced imaging.


To better establish the link between neural activity, inflammation and behavior, new tools are needed that capture brain-wide histological patterns at cellular resolution. In this talk, I will describe a complete approach for whole-brain quantification using three example applications: 1) detection of a regional focus for brain monocyte infiltration after infection with Toxoplasma gondii, 2) brain-wide neural activity mapping in response to recent experience, and 3) morphological quantification of microglial activity induced by coronavirus infection. By combining advances in tissue clearing, light sheet imaging, computational alignment of anatomy, machine learning-based image processing, and novel statistical methods, our imaging platform quantifies molecular markers of neuronal, monocyte, and microglial activity with unprecedented resolution and fidelity in the mouse brain. For tissue clearing, we optimized the iDISCO+ clearing method for whole-brain immunostaining. For imaging, we have customized a commercial light sheet microscope (ZEISS Lightsheet Z.1) for large-format imaging of iDISCO+ cleared tissue faster and at higher spatial resolution than other systems. Machine learning algorithms efficiently segment out desired cellular features into three dimensional masks. Our automated quantification pipeline aligns samples to a common reference atlas and generates brain-wide cell counts of neuronal, monocyte, and microglial activity across hundreds of identified brain areas. Finally, we have adapted a statistical framework from RNA sequencing for analysis of these large datasets. Altogether, this new imaging platform overcomes the time- and labor-intensive limitations of standard histology. Moreover, the platform can be readily adapted to the precise quantification of diverse cellular features across the entire mouse brain.