Publication

Automated neuron tracking inside moving and deforming C. elegans using deep learning and targeted augmentation

Sahand Jamal Rahi, Kseniia Korchagina
2023
Journal Articles

Abstract

Reading out neuronal activity from three-dimensional (3D) functional imaging requires segmenting and tracking individual neurons. This is challenging in behaving animals if the brain moves and deforms. The traditional approach is to train a convolutional neural network with ground-truth (GT) annotations of images representing different brain postures. For 3D images, this is very labor intensive. We introduce 'targeted augmentation', a method to automatically synthesize artificial annotations from a few manual annotations. Our method ('Targettrack') learns the internal deformations of the brain to synthesize annotations for new postures by deforming GT annotations. This reduces the need for manual annotation and proofreading. A graphical user interface allows the application of the method end-to-end. We demonstrate Targettrack on recordings where neurons are labeled as key points or 3D volumes. Analyzing freely moving animals exposed to odor pulses, we uncover rich patterns in interneuron dynamics, including switching neuronal entrainment on and off.

Official source

https://infoscience.epfl.ch/entities/publication/7269b050-b579-4b05-929b-10c6e7611a58

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Sahand Jamal Rahi, Kseniia Korchagina
2023
Journal Articles

Abstract

Official source

https://infoscience.epfl.ch/entities/publication/7269b050-b579-4b05-929b-10c6e7611a58

About this result

Related concepts (32)

Brain

A brain is an organ that serves as the center of the nervous system in all vertebrate and most invertebrate animals. It is located in the head, usually close to the sensory organs for senses such as vision. It is the most complex organ in a vertebrate's body. In a human, the cerebral cortex contains approximately 14–16 billion neurons, and the estimated number of neurons in the cerebellum is 55–70 billion. Each neuron is connected by synapses to several thousand other neurons.

Human brain

The human brain is the central organ of the human nervous system, and with the spinal cord makes up the central nervous system. The brain consists of the cerebrum, the brainstem and the cerebellum. It controls most of the activities of the body, processing, integrating, and coordinating the information it receives from the sense organs, and making decisions as to the instructions sent to the rest of the body. The brain is contained in, and protected by, the skull bones of the head.

Graphical user interface

The graphical user interface, or GUI (ˌdʒi:juːˈaɪ or ˈɡu:i ), is a form of user interface that allows users to interact with electronic devices through graphical icons and audio indicators such as primary notation, instead of text-based UIs, typed command labels or text navigation. GUIs were introduced in reaction to the perceived steep learning curve of command-line interfaces (CLIs), which require commands to be typed on a computer keyboard. The actions in a GUI are usually performed through direct manipulation of the graphical elements.

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