AMITO: an open-access application for assisted analysis of mitochondria in transmission electron microscopy images

Analysis of mitochondrial morphology and ultrastructure from transmission electron microscopy images is essential for understanding cellular adaptations in both physiological and pathological conditions. However, these investigations remain time-consuming, poorly standardized, and therefore highly variable. We developed an open-access, standalone MATLAB-based application [Analysis of MITOchondria (AMITO)] that can be run without a license and integrates analyses within a single user-friendly interface. AMITO demonstrated excellent agreement with conventional manual image analysis software, high intra- and interexperimenter reproducibility, and substantial reduction in analysis time. Therefore, AMITO provides a reliable, efficient, and accessible tool to ensure robustness and reproducibility in mitochondrial assessment.NEW & NOTEWORTHY AMITO is an open-access, standalone application for mitochondrial analysis from TEM images that combines automated and manual workflows within a single user-friendly interface. Validated against conventional FIJI analysis, AMITO demonstrated excellent reproducibility while substantially reducing analysis time and experimenter-dependent variability. By integrating morphology and ultrastructure quantification without requiring programming expertise, AMITO provides a reliable and accessible solution to improve robustness, efficiency, and reproducibility in mitochondrial research.