Author: Adam Zhang
Institution: Georgia Institute of Technology
We have all heard Descartes’ famous quote “cogito ergo sum”—I think, therefore I am. But what does it mean to think? Or perhaps, what is it to think? To answer this question, the Allen Institute for Brain Science has released the Allen Brain Observatory (1), a collective, standardized “survey of cellular activity in the mouse visual system.” This first-of-its-kind open source database is unprecedented both in size and comprehensiveness, and it allows researchers all over the world to begin discerning the neural circuitry underlying how we experience the world around us.
The Allen Institute for Brain Science was founded in 2003 by Microsoft co-founder Paul Allen as an independent, nonprofit research organization to study how the brain works in cognition and disease. This includes everything from the neurobiological structure of the brain to the coordination of its neural circuits. In 2012, the Allen Institute launched a ten-year program to build a publicly accessible repository of resources on neural activity that constitute perception, creating research tools that would be unwieldy for a single lab to produce (2). This program led to the creation of the Allen Cell Types Database in 2015. Their newest project uses mice to explore how the brain processes the visual world by recording the cellular activity of different areas in the cortex.
“It’s known that human [brains] have much more elaborate visual acuity [than mice brains], but they have enough similarity with the overall structure that there’s a lot we can create a parallel to by looking at a mouse in terms of the basic circuitry,” said Amy Bernard, Product Architect (3).
The mice were shown a variety of visual stimuli, including still images as well as dynamic visuals, to measure the mechanics of visual processing. Scientists curated a "collection of 120 images from natural scenes that [included] some pictures of animals, [and] some pictures of street scenes,” said Saskia De Vries, senior scientist. It was important that this was stimuli the mice brain would be sensitive to, and elicit a full range of responses.
The mice were genetically altered to have markers tracking activity in all their neurons, and, as they are shown the visual stimuli, an attached two-photon microscope spots any fluorescently marked neurons that light up in real time. These results are used to determine how each individual neuron reacts to differences in motion and shape as well as how they decipher complex images to reveal the integrated network of neuronal interactions. Altogether, the data samples over 18,000 neurons, surveying different depths of four areas in the visual cortex (4).
With all of the processed and registered data, researchers created a website with all the information presented in a compact visual, compounded with a downloadable raw data set for direct analysis to be accessed for free. Various analysis packages were also provided to parse the wealth of data. By making all of this data publicly available, researchers in all backgrounds, from mathematicians to physiologists, modelers to theoreticians, may conduct their own work on the standardized data and draw new conclusions on the process of cognition (5).
The Allen Brain Observatory eliminates the most expensive and time-consuming work while also leveraging computational tools of the entire scientific community to accelerate neuroscience research. However, the success of this project will depend largely on the findings other labs produce.
“How it all comes together, that’s going to take an entire community of people, also looking at the data with us,” said Dr. Bernard.