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bioRxiv · 10.1101/2025.10.16.682919

MitoXRNet: Deep Learning-enabled 3D Segmentation of Mitochondria and Nucleus in Soft X-ray Tomograms

Yadav, A.·Deshmukh, A.·Bharadwaj, P.·Baliyan, A.·White, K. L.·Singla, J.
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Abstract

Mitochondrial morphology is crucial for cellular function, but large-scale analysis is limited by challenges in high-resolution imaging and segmentation. MitoXRNet, a compact 3D deep-learning model, efficiently segments mitochondria and nuclei from Soft X-ray Tomography data using multi-axis slicing, Sobel-based boundary enhancement, and combined BCE-Robust Dice loss. With 1.4M parameters, it achieves a Dice score of 73.8% on INS-1E cells, outperforming existing models. Automated analysis indicated that glucose induced larger mitochondria and higher matrix density, and that GIP and GKA induced smaller and denser mitochondria, highlighting previously unreported {beta}-cell mitochondrial remodeling. MitoXRNet allows for scalable profiling of organelle-level morpho-biophysical data. HighlightsO_LIA data-efficient method for 3D segmentation of mitochondria and nucleus from Soft X-ray tomograms. C_LIO_LIIncorporates domain-specific Sobel filter-based preprocessing to improve segmentation accuracy and quality under imperfect or noisy labels. C_LIO_LIEnables rapid and automated analysis of mitochondrial morphology, facilitating quantitative assessment of pharmacological effects on cellular ultrastructure. C_LI Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=168 SRC="FIGDIR/small/682919v2_ufig1.gif" ALT="Figure 1"> View larger version (43K): org.highwire.dtl.DTLVardef@8600f6org.highwire.dtl.DTLVardef@1a9230eorg.highwire.dtl.DTLVardef@13c6f09org.highwire.dtl.DTLVardef@9dc9f1_HPS_FORMAT_FIGEXP M_FIG C_FIG

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Yadav, A., Deshmukh, A., Bharadwaj, P., Baliyan, A., White, K. L., Singla, J.. 2025-10-17. MitoXRNet: Deep Learning-enabled 3D Segmentation of Mitochondria and Nucleus in Soft X-ray Tomograms. https://doi.org/10.1101/2025.10.16.682919

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