# Beyond Isotropic Assumptions: Continuity-Constrained Segmentation and GPU Morphometry for Nanoscale GBM Analysis

arXiv: https://arxiv.org/abs/2608.07575 · HTML: https://mlsanity.com/paper/2608.07575/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 10 of its 27 references that are in the map.
- First posted on arXiv 4 Aug 2026.

## Builds on (most cited first, 10 of 10)

- [Adam: A Method for Stochastic Optimization](https://mlsanity.com/paper/1412.6980/) (2014)
- [DeepLab: Semantic Image Segmentation with Deep Convolutional Nets, Atrous Convolution, and Fully Connected CRFs](https://mlsanity.com/paper/1606.00915/) (2016)
- [3D U-Net: Learning Dense Volumetric Segmentation from Sparse Annotation](https://mlsanity.com/paper/1606.06650/) (2016)
- [Swin UNETR: Swin Transformers for Semantic Segmentation of Brain Tumors in MRI Images](https://mlsanity.com/paper/2201.01266/) (2022)
- [clDice -- A Novel Topology-Preserving Loss Function for Tubular Structure Segmentation](https://mlsanity.com/paper/2003.07311/) (2020)
- [A Topological Loss Function for Deep-Learning based Image Segmentation using Persistent Homology](https://mlsanity.com/paper/1910.01877/) (2019)
- [Automatic Brain Tumor Segmentation using Cascaded Anisotropic Convolutional Neural Networks](https://mlsanity.com/paper/1709.00382/) (2017)
- [Isotropic reconstruction of 3D fluorescence microscopy images using convolutional neural networks](https://mlsanity.com/paper/1704.01510/) (2017)
- [Deep learning enables reference-free isotropic super-resolution for volumetric fluorescence microscopy](https://mlsanity.com/paper/2104.09435/) (2021)
- [Feature-prompting GBMSeg: One-Shot Reference Guided Training-Free Prompt Engineering for Glomerular Basement Membrane Segmentation](https://mlsanity.com/paper/2406.16271/) (2024)

## Abstract (arXiv)

Confocal microscopy of optically cleared and swelled tissue resolves complex biological structures in 3D, but such acquisitions are highly anisotropic: along the under-sampled axial direction the structure can appear discontinuous, hampering reconstruction and automated quantitative analysis. The usual remedy upsamples the axial dimension to an isotropic volume before training a segmentation model, which requires dense annotations in the upsampled space, a prohibitive labeling burden. We present an end-to-end, GPU-accelerated framework that overcomes this without additional annotations. The model is trained on the native acquisition volume; random rotation of training patches leverages the well-resolved lateral plane to supply the missing axial information, and a z-axis continuity loss keeps neighboring slices consistent. We adapt both a convolutional (3D U-Net) and a transformer (SwinUNETR) backbone, aggregate overlapping patches by Gaussian consensus, and compute point-spread-function-corrected membrane thickness by ray-surface intersection on the GPU. We apply the method to the glomerular basement membrane (GBM), a thin, highly convoluted part of the kidney's filtration barrier that grows more irregular in disease. Segmentation accuracy matches inter-expert agreement. Continuity-aware training improves reconstruction smoothness and suppresses a periodic terracing artifact at minimal accuracy cost. We quantify GBM thickness across the reconstructed 3D surface and capture disease-related thickening, enabling fully automated anisotropic 3D morphometry of biological structures without dense volumetric labels or image restoration.