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Journal: bioRxiv

Article Title: 3D Reconstruction of Nanoparticle Distribution in Tumor Spheroids with Volume Electron Microscopy

doi: 10.64898/2026.04.17.719153

Figure Lengend Snippet:

Article Snippet: The fine-tuned Cellpose-SAM models were additionally bench-marked against the AI-assisted segmentation tool in Amira (Thermo Fisher Scientific).

Techniques:

Segmentation of cellular structures and nanoparticles. (a) Orthogonal cross-sections overlaid with cell (yellow) and nucleus (cyan) outlines. (b) Orthogonal cross-sections of the nanoparticle posterior probability maps. (c–d) Aggregated Jaccard Index (AJI) (c) and average precision (AP) at varying intersection over union (IoU) thresholds (d) comparing the fine-tuned and pre-trained Cellpose-SAM models for cell and nucleus segmentation, evaluated on the full labeled dataset ( n = 20 images); ****: p ≤ 10 −4 , Mann–Whitney U test. (e) Voxel intensity probability mass functions for the nanoparticle and background components estimated by expectation–maximization (EM) decomposition.

Journal: bioRxiv

Article Title: 3D Reconstruction of Nanoparticle Distribution in Tumor Spheroids with Volume Electron Microscopy

doi: 10.64898/2026.04.17.719153

Figure Lengend Snippet: Segmentation of cellular structures and nanoparticles. (a) Orthogonal cross-sections overlaid with cell (yellow) and nucleus (cyan) outlines. (b) Orthogonal cross-sections of the nanoparticle posterior probability maps. (c–d) Aggregated Jaccard Index (AJI) (c) and average precision (AP) at varying intersection over union (IoU) thresholds (d) comparing the fine-tuned and pre-trained Cellpose-SAM models for cell and nucleus segmentation, evaluated on the full labeled dataset ( n = 20 images); ****: p ≤ 10 −4 , Mann–Whitney U test. (e) Voxel intensity probability mass functions for the nanoparticle and background components estimated by expectation–maximization (EM) decomposition.

Article Snippet: The fine-tuned Cellpose-SAM models were additionally bench-marked against the AI-assisted segmentation tool in Amira (Thermo Fisher Scientific).

Techniques: Labeling, MANN-WHITNEY

Comparison of segmentation accuracy between fine-tuned Cellpose-SAM and Amira benchmark experiments. Metrics were evaluated on the full labeled dataset ( n = 20 images). Statistical independence for aggregated Jaccard index populations was evaluated with a Mann-Whitney U test. Significance levels: ***: p ≤ 0.001; ns: p > 0.05

Journal: bioRxiv

Article Title: 3D Reconstruction of Nanoparticle Distribution in Tumor Spheroids with Volume Electron Microscopy

doi: 10.64898/2026.04.17.719153

Figure Lengend Snippet: Comparison of segmentation accuracy between fine-tuned Cellpose-SAM and Amira benchmark experiments. Metrics were evaluated on the full labeled dataset ( n = 20 images). Statistical independence for aggregated Jaccard index populations was evaluated with a Mann-Whitney U test. Significance levels: ***: p ≤ 0.001; ns: p > 0.05

Article Snippet: The fine-tuned Cellpose-SAM models were additionally bench-marked against the AI-assisted segmentation tool in Amira (Thermo Fisher Scientific).

Techniques: Comparison, Labeling, MANN-WHITNEY

Images of 2D datasets with overlaid cell outlines predicted by fine-tuned (top row) and pre-trained (bottom row) Cellpose-SAM models. Scale bars: 20 µm.

Journal: bioRxiv

Article Title: 3D Reconstruction of Nanoparticle Distribution in Tumor Spheroids with Volume Electron Microscopy

doi: 10.64898/2026.04.17.719153

Figure Lengend Snippet: Images of 2D datasets with overlaid cell outlines predicted by fine-tuned (top row) and pre-trained (bottom row) Cellpose-SAM models. Scale bars: 20 µm.

Article Snippet: The fine-tuned Cellpose-SAM models were additionally bench-marked against the AI-assisted segmentation tool in Amira (Thermo Fisher Scientific).

Techniques: