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bioRxiv · 10.64898/2026.06.03.729866

A semi-automated pipeline for quantitation of Pax7+, myonuclei, and cross-sectional area by fiber type

Megowan, H. G.·Luu, M.·Shuaib, A.·Augienello, K. B.·Fries, A. C.·Searcy, J.·Dreyer, H. C.
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Abstract

Manual analysis of skeletal muscle cross-sections is time-consuming and subject to error and user bias. To overcome these limitations, we developed and validated a semi-automated, quantitative, and reproducible image-analysis pipeline specifically tailored to quantify Pax7+ satellite cells, myonuclei, and cross-sectional area by fiber type. The workflow combines FIJI/ImageJ-based image preprocessing with CellProfiler, Cellpose, and a custom Python script to process and analyze immunohistological images of muscle tissue cross-sections. Outcomes include Pax7+ satellite cells and myonuclei quantified per fiber by fiber type, along with cross-sectional area, perimeter, and fiber type classification. This semi-automated approach provides a robust and efficient platform for high-throughput analysis of muscle tissue cross-sections from large datasets. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=141 SRC="FIGDIR/small/729866v1_ufig1.gif" ALT="Figure 1"> View larger version (44K): org.highwire.dtl.DTLVardef@e85bfdorg.highwire.dtl.DTLVardef@ef75e0org.highwire.dtl.DTLVardef@123e461org.highwire.dtl.DTLVardef@166a304_HPS_FORMAT_FIGEXP M_FIG C_FIG

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Megowan, H. G., Luu, M., Shuaib, A., Augienello, K. B., Fries, A. C., Searcy, J., Dreyer, H. C.. 2026-06-08. A semi-automated pipeline for quantitation of Pax7+, myonuclei, and cross-sectional area by fiber type. https://doi.org/10.64898/2026.06.03.729866

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