New computer program can help map individual nerve cells in worms

A new computer program has been developed by scientists who are focused on interpreting the mechanism of the brain in high-definition, and at the single-cell level of detail.

The researchers aim to detect every nerve cell in fluorescent microscopic images of living worms.

New computer program can help map individual nerve cells in worms

The central DNA-containing cell bodies of C. elegans neurons are shown with the three fluorescent colors used in the genetically modified strain of C. elegans developed by the research team. Note how neighboring cells are in different colors. Successfully annotated neurons are labeled with letters and cells whose identity could not be annotated are labeled with numbers. Not all 302 C. elegans neurons are present in this image. Image Credit: © Toyoshima et al., 2020.

Earlier efforts to automate the detection of individual nerve cells were impeded by the fact that the same type of cell can also be present in largely different sites in different worms.

These creatures include C. elegans, which are minute roundworms often found in soil and commonly used in research laboratories worldwide.

Each of the 959 cells present in the transparent, 1mm-long bodies of the animals has been detected, labeled, and mapped, including the 302 nerve cells present in these creatures.

The nervous system of C. elegans was first mapped completely by researchers in 1986 and since then, the team has been enhancing it. OpenWorm, one of the more recent projects, is an ongoing universal effort to develop a behaviorally precise and cell-by-cell virtual C. elegans—a research-worthy model of a Tamagotchi pet.

Generalized brain atlases, the so-called connectome maps, hold some value but they do not enable the identification of neurons in live, individual worms.

Imagine if you knew the names of all the cities on a map, but the cities moved each time you looked. That is what it’s like, trying to compare current brain atlases to living organisms.”

Yuichi Iino, Study Co-Last Author and Professor, University of Tokyo

The new study was published in the BMC Biology journal.

Iino’s research team prefers to detect and map every nerve cell present in live C. elegans as this would allow it to plot the electrical impulses pathways that make a memory, learning, and behavioral traits feasible.

The brain neurons of C. elegans are not confined in a skull but simply form a loosely packed set of 150 neurons in the animals’ head region.

The neurons are tiny, and in the head of C. elegans they are surrounding this large bulb that’s part of the digestive system, so they get pushed and pulled around a lot as the animal moves or eats,” Iino explained.

The scientists first identified special combinations of genes in their study. When these genes are artificially fixed to fluorescent protein tags, they will cause 35 different and tiny groups of neurons to fluoresce under a microscope.

The new genetically altered strains of C. elegans made the scientists’ computer programming work and all their subsequent image analyses a possibility.

In total, the team detected individual neurons in 311 worms, approximately 10 worms for each of the 35 groups of neurons, and then quantified the distances as well as relative positions between neuronal pairs in the microscopic images.

While neurons were known to move inside each worm, the neurons were not anticipated to have different “home base” sites in different individuals. In certain neurons, the positions of the central cell body can differ by over 0.02 mm among various animals, a major distance for an animal measuring just 1 mm long.

Individual C. elegans are thought to be uniform because they all have almost the same cell lineages and a stereotyped neural circuit. It was really surprising, though, how large the positional differences are between individual animals.”

Yu Toyoshima, Study Co-First Author and Assistant Professor, University of Tokyo

Toyoshima is also a member of Iino’s laboratory.

The researchers eventually developed a computer program to automatically detect neurons by using their latest position variation data and the connectome brain atlas of C. elegans.

The computer program utilizes a mathematical algorithm to study the microscopic image of C. elegans brain and assigns the statistically most probable identity to every neuron depending on the position of that neuron relative to other neurons.

The algorithm is only 60 percent accurate, which is too low for fully automatic cell identification, but it speeds up our work enough to make other projects possible to understand neural networks based on whole-brain imaging data.”

Yu Toyoshima, Study Co-First Author and Assistant Professor, University of Tokyo

Each neuron was already known and labeled which partly made it possible to perform the study on C. elegans.

To apply an analogous method to other animals, fine-tuned genetic manipulation would be required to make neuronal groups fluoresce under a microscope and would also require a complete understanding of the number of neurons that need to be detected.

The human brain has billions of neurons, so understanding our brains at the single-cell level would be extremely difficult. C. elegans have small brains, but they can still learn and change behaviors, so they could allow us to understand how networks of neurons create behavior,” concluded Iino.

Source:
Journal reference:

Toyoshima, Y., et al. (2020) Neuron ID dataset facilitates neuronal annotation for whole-brain activity imaging of C. elegans. BMC Biology. doi.org/10.1186/s12915-020-0745-2.

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