Digitizing Spermatogenesis Lineage at Nanoscale Resolution In Tissue-Level Electron Microscopy

School of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China # These authors contributed equally to this work. Email: andrewxiao@bupt.edu.cn;liuliqing@ibp.ac.cn;huj@ibp.ac.cn; feisun@ibp.ac.cn; yangge@ucas.edu.cn;xutao@ibp.ac.cn ABSTRACT Recent advances in 2D large - scale and 3D volume electron microscopy have stimulated the rapid development of nanoscale functional analysis at the tissue and organ levels. To meet the requirements of characterizing intracellular organelle s and their interactions within defined cellular cohorts at tissue level, we have developed DeepOrganelle. It adopts a lightweighted Mask2Former frameworks as a universal segmentor and is capable of segmenting and extracting organelles within different cell types, performing statistical quantitative analysis, as well as visualizing and quantifying the spatial distribution of organelle morphologies and interactions across different cell types at tissue scales. Using DeepOrganelle, we systemically perform cross - scale quantification of membrane contact sites( MCSs) dynamics across the progression of the seminiferous epithelial cycle, covering 12 distinct developmental stages and 24 statuses of germ cells . Noticeably, it discovers a waved pattern of mitochondria(Mito) - endoplasmic reticulum(ER) contact with a significant increase specifically at Stage X pachytene preceding the transition to diplotene, which aligns well with a newly reported experiment that mitochondrial metabolic proteins like PDHA2 are essential for this transition by maintaining ATP supply for double - strand break (DSB) repair.