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bioRxiv · 10.64898/2026.05.21.723734

CardioSeg: An interactive platform for integrated spatial transcriptomics data and nuclear morphological analysis of mouse heart tissue

Kancherla, S. K.·Melleby, A. O.·Aronsen, J. M.
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Abstract

MotivationSpatial transcriptomics enables gene expression profiling within its spatial context in intact tissue sections. Existing workflows for segmentation, spatial annotation, and morphological analysis are often code-heavy and poorly integrated. This limits the joint analysis of spatial gene expression at a single-nucleus resolution, and corresponding nuclear morphology. ResultsWe present CardioSeg, an integrated computational platform for nuclei-resolved spatial transcriptomic analysis combining multi-threshold segmentation, transcriptomic aggregation, cell-type annotation, and interactive morphometric querying within a unified graphical interface. CardioSeg achieved robust segmentation performance across heterogeneous imaging conditions, with union-based inference outperforming the individual parameter configurations. CardioSeg achieved 0.88 in accuracy and 0.85 in balanced accuracy against reference labels, while also resolving spatial heterogeneity not captured by spot-based approaches. Analyses of pressure-overloaded cardiac tissue indicated altered cell composition, nuclear morphology and gene expression in specific segments, indicating the potential of CardioSeg to couple disease-specific nuclear morphology with the associated transcriptomics. Availability and ImplementationSource code is available at GitHub under the CC BY 4.0 license (https://github.com/SrijanKancherla/CardioSeg). A versioned release was archived in Zenodo (DOI: 10.5281/zenodo.20177171).

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Kancherla, S. K., Melleby, A. O., Aronsen, J. M.. 2026-05-25. CardioSeg: An interactive platform for integrated spatial transcriptomics data and nuclear morphological analysis of mouse heart tissue. https://doi.org/10.64898/2026.05.21.723734

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