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Adult dwarf cuttlefish, Sepia bandensis, about 8 cm long. Credit: Tessa Montague/ Axel lab / Columbia’s Zuckerman Institute

Anything with three hearts, blue blood, and skin that can change colors like a screen in Times Square is likely to attract attention. Meet Sepia bandensis, better known as the camouflaged dwarf squid.

Over the past three years, a team led by neuroscientists at Columbia’s Zuckerman, which includes data scientists and web designers, has compiled a brain atlas of this fascinating vulture: a neuroanatomical guide that shows for the first time the complete structure of the brain with 32 lobes along with it. cell organization.

Dvergkolla is a master of camouflage. In a matter of milliseconds, the animal can change both its skin pattern and texture to actively blend into its environment. Camouflage is visually driven, and like the squid and its octopus cousins, the squid controls its skin color with its brain. Neurons inside the brain project their axons all the way to the skin, where they control hundreds of thousands of cell pixels (chromatophores) to achieve color changes.

When a squid hides, it reproduces what it sees on its skin. To achieve this, the squid has to transform its visual input into a neural representation in the brain and then reproduce an analogue of that representation on its skin.

Dr. Richard Axel’s laboratory wants to understand how the squid achieves this incredible feat. Understanding how the visual world is represented in the brain—whether of a spider or a human—and how that representation leads to thought and behavior are among the most compelling topics in neuroscience.

To uncover the neural basis of camouflage, members of the Axel lab need to record the activity of neurons from relevant areas of the squid’s brain. However, to extract the most scientific value from those recordings, they also need a map of the brain, which has not been available. So the team embarked on a project to construct a neuroanatomical atlas of the pygmy marmoset’s brain.






Cutaneous pattern in dwarf squid, Sepia bandensis. Credit: Thomas Barlow/ Axel Lab/Zuckerman Institute

Their research paper describing the project appears online today in Current Biologywith an associated website, Cuttlebase.org.

“One of my favorite ways to learn about the brain is to study creatures that are highly specialized in certain behaviors or tasks, such as bats that use echolocation to navigate, or birds that use impressive spatial memory to recall the locations of hidden food items,” said Tessa G. Montague, Ph.D., the paper’s first author and a postdoctoral fellow in the laboratory of Richard Axel, MD, also an author on the paper.

“We hope and believe that our brain atlas will help the community learn more about how squid use to communicate through their skin, and that this may give us insight into how each brain is able to represent information,” said Dr. Montague.

It took a close and dedicated collaboration of experts in neuroscience, web imaging, computer programming, anatomy and web design to build Cuttlebase. For the underlying foundation of the brain atlas, the team scanned the bodies and brains of four male and four female squid with magnetic resonance imaging (MRI), a mainstay of diagnosis for doctors. A deep learning algorithm, a type of artificial intelligence, helped tease out the animals’ brains from their surrounding tissue in the scan data.

Co-author Sabrina Gjerswold-Selleck, who recently completed her master’s degree at Columbia University and now works at Neuralink, said the team started the study because of related work she had done in co-author Jia Guo’s group at Columbia using MRIs of mice.

“We had developed a deep learning method that was able to separate brain-related data in each MRI scan from data related to other tissue types in these scans,” said Gjerswold-Selleck. “We were surprised at how well we were able to adapt the technology.”






One of the many views in the web tool Cuttlebase of the multifocal brain of the dwarf cuttlefish Sepia bandensis. Credit: Cuttlefish team/ Axel Lab/Zuckerman Institute

Next, by comparing the MRI scans to just a handful of labeled brain images from the 1960s, the researchers had to determine the boundaries of each of the dwarf squid’s cerebral lobes. It was a monumental data analysis effort by six of the co-authors who spent hundreds of hours during the pandemic to delineate the eight squid datasets.

This resulted in hundreds of grayscale images with outlines of brain regions analogous to, say, the outlines of states and counties in a multi-page atlas of the United States. To update their squid brain atlas to cellular resolution—the equivalent of a detailed atlas showing all the states’ roads, hills, lakes, and rivers—the researchers turned to histological techniques, which reveal the microscopic structure of tissue.

This required the biologists on the team to dissect the squid brains and then stain each one with colorful chemical markers that mark the location of brain cells and components, including neurons, glial cells and axons.

Finally, after completing the histological atlas and annotating the eight squid MRI scans, the researchers combined the eight brains into one atlas. A total of 32 cysts were identified in the dwarf brown, most of which could be linked to specific biological functions and behaviors, as a result of classic studies half a century ago.

The two largest lobes, the optic lobes, for example, process visual input from the animal’s mesmerizing eyes. The motor neurons in the chromatin sheets orchestrate color changes in the skin. A vertical leaf has been implicated in learning and memory.

Although this analysis of squid data is itself a result, “the main purpose of the paper is to report on the visualization and research tool, Cuttlebase, and make it all freely available and accessible to everyone,” said Dr. Montague.






View of a histological brain section of the cuttlefish Sepia bandensis, available in the web tool Cuttlebase. Credit: Cuttlefish team/Axel Lab/Zuckerman Institute

With intuitive ease of use, users can call up histological sections that specify different brain regions and nerves; 3D model of the brain that can be rotated and zoomed; and a 3D model of the squid’s 26 organs, including its three hearts, ink sac, beak and nerves that carry signals between its brain and its eight arms. All the data in Cuttlebase is available for other researchers to build on in their labs. Explanations of brain balloons and other user-friendly features provide learning material for non-experts.

Co-authors Sukanya Aneja and Dana Elkis (team web engineer and web designer, respectively) of the Interactive Communications Program at New York University, who are also members of the Cuttlebase team, played leading roles in the website’s development.

“We went back and forth a lot about how to translate everything we had into a web experience that would appeal to both scientists and non-scientists,” Aneja said.

“We had to combine videos, images, the 3D template brain, illustrations, charts and diagrams,” Elkis said.

Co-author Isabelle Rieth, a graduate student in Northwestern University’s neuroscience program and former member of the Cuttlebase team, brought additional design skills to transform what would otherwise have been a black-and-white web experience into one complete with colors that help clarify what users are seeing.

As challenging and labor-intensive as the project has been for the partners, they can’t help but be impressed by the squid they are working with and learning about.

“The trotter is mesmerizing to watch,” said Dr. Montague. “When they’re hiding or communicating with each other, they’re actually showing you on their skin what they’re seeing and how they’re feeling.”

More information:
Tessa G Montague, A Brain Atlas of the Camouflaged Dwarf Brown, Sepia bandensis, Current Biology (2023). DOI: 10.1016/j.cub.2023.06.007. www.cell.com/current-biology/f … 0960-9822(23)00757-1

Diary information:
Current Biology

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