Automated segmentation of cell organelles in volume electron microscopy using deep learning.
Nebojša NešićXavier HeiligensteinLydia ZopfValentin BlümlKatharina S KeuenhofMichael WagnerJohanna L HöögHeng QiZhiyang LiGeorgios TsaramirsisChristopher J PeddieMiloš StojmenovićAndreas WalterPublished in: Microscopy research and technique (2024)
Recent advances in computing power triggered the use of artificial intelligence in image analysis in life sciences. To train these algorithms, a large enough set of certified labeled data is required. The trained neural network is then capable of producing accurate instance segmentation results that will then need to be re-assembled into the original dataset: the entire process requires substantial expertise and time to achieve quantifiable results. To speed-up the process, from cell organelle detection to quantification across electron microscopy modalities, we propose a deep-learning based approach for fast automatic outline segmentation (FAMOUS), that involves organelle detection combined with image morphology, and 3D meshing to automatically segment, visualize and quantify cell organelles within volume electron microscopy datasets. From start to finish, FAMOUS provides full segmentation results within a week on previously unseen datasets. FAMOUS was showcased on a HeLa cell dataset acquired using a focused ion beam scanning electron microscope, and on yeast cells acquired by transmission electron tomography. RESEARCH HIGHLIGHTS: Introducing a rapid, multimodal machine-learning workflow for the automatic segmentation of 3D cell organelles. Successfully applied to a variety of volume electron microscopy datasets and cell lines. Outperforming manual segmentation methods in time and accuracy. Enabling high-throughput quantitative cell biology.
Keyphrases
- deep learning
- electron microscopy
- artificial intelligence
- machine learning
- convolutional neural network
- single cell
- big data
- cell therapy
- high throughput
- neural network
- chronic pain
- randomized controlled trial
- signaling pathway
- bone marrow
- loop mediated isothermal amplification
- cell proliferation
- induced apoptosis
- high intensity
- pain management
- positron emission tomography
- cell death
- high speed
- pet imaging