Brain organoid data synthesis and evaluation

• Published in: Frontiers in neuroscience Vol. 17; p. 1220172
• Main Authors: Brémond-Martin, Clara, Simon-Chane, Camille, Clouchoux, Cédric, Histace, Aymeric
• Format: Journal Article
• Language: English
• Published: Lausanne Frontiers Research Foundation 15-08-2023; Frontiers; Frontiers Media S.A
• Subjects: AAE; Artificial Intelligence; Automation; brain organoid; Computer Science; Computer Vision and Pattern Recognition; Datasets; Image processing; Life Sciences; metric; Neurobiology; Neurons and Cognition; Neuroscience; Organoids; Physiology; psychovisual; Segmentation; validation; brain organoids; image generation; GAN; small data set
• ISSN: 1662-453X; 1662-4548; 1662-453X
• DOI: 10.3389/fnins.2023.1220172

Introduction
Datasets containing only few images are common in the biomedical field. This poses a global challenge for the development of robust deep-learning analysis tools, which require a large number of images. Generative Adversarial Networks (GANs) are an increasingly used solution to expand small datasets, specifically in the biomedical domain. However, the validation of synthetic images by metrics is still controversial and psychovisual evaluations are time consuming.
Methods
We augment a small brain organoid bright-field database of 40 images using several GAN optimizations. We compare these synthetic images to the original dataset using similitude metrcis and we perform an psychovisual evaluation of the 240 images generated. Eight biological experts labeled the full dataset (280 images) as syntetic or natural using a custom-built software. We calculate the error rate per loss optimization as well as the hesitation time. We then compare these results to those provided by the similarity metrics. We test the psychovalidated images in a training step of a segmentation task.
Results and discussion
Generated images are considered as natural as the original dataset, with no increase of the hesitation time by experts. Experts are particularly misled by perceptual and Wasserstein loss optimization. These optimizations render the most qualitative and similar images according to metrics to the original dataset. We do not observe a strong correlation but links between some metrics and psychovisual decision according to the kind of generation. Particular Blur metric combinations could maybe replace the psychovisual evaluation. Segmentation task which use the most psychovalidated images are the most accurate.