AimSeg is a bioimage analysis tool that blends machine learning, automated post-processing, and user guidance to achieve the segmentation of axons, inner tongue, and compact myelin in electron microscopy data. The workflow relies on pixel and object classifiers trained in ilastik, while a supervised mode empowers users to refine the automated selections made by AimSeg.

If you use AimSeg for your research, please cite:

• Carrillo-Barberà P, Rondelli AM, Morante-Redolat JM, Vernay B, Williams A, Bankhead P (2023) AimSeg: A machine-learning-aided tool for axon, inner tongue and myelin segmentation. PLoS Comput Biol 19(11): e1010845. DOI: doi.org/10.1371/journal.pcbi.1010845

For a more detailed explanation of AimSeg usage, please consult the In-Depth AimSeg Usage Handbook. Setup instructions, a comprehensive list of shortcuts, and a guide on training your own ilastik models for data processing are available in separate documents.

The AimSeg ground truth and classifiers are available in Zenodo.