Article

Penumbria: Advanced 3D cell segmentation for biomedical imaging

2026-07-01

Abstract excerpt

Quantitative analysis of three-dimensional cellular architecture is fundamental to understanding tissue organization, disease progression, and drug response. There are effective approaches for 2D segmentation, yet 3D cell segmentation remains a critical bottleneck due to diverse cell morphologies, low signal-to-noise ratios, and data scarcity. We introduce Penumbria, a general-purpose 3D cell segmentation framewor...

Topics

Open a Topic to create a Post that cites this publication.

Identifiers and source

Literature Corpus work: 63cba876-3fd5-5c25-8e81-7adbd115c906
DOI: 10.64898/2026.06.30.735527

Open publication

Related research

Semantic proximity does not establish scientific evidence.

Click a neighbor to travelStep 1 · 12 closest

Penumbria: Advanced 3D cell segmentation for biomedical imagingDOI 10.64898/2026.06.30.735527Read

CellSAM: A Foundation Model for Cell SegmentationSemantic proximity Read

CellSeg3D: self-supervised 3D cell segmentation for fluorescence microscopySemantic proximity Read

Whole-cell segmentation of tissue images with human-level performance using large-scale data annotation and deep learningSemantic proximity Read

NuSeT: A Deep Learning Tool for Reliably Separating and Analyzing Crowded CellsSemantic proximity Read

The Allen Cell and Structure Segmenter: a new open source toolkit for segmenting 3D intracellular structures in fluorescence microscopy imagesSemantic proximity Read

CellBinDB: A Large-Scale Multimodal Annotated Dataset for Cell Segmentation with Benchmarking of Universal ModelsSemantic proximity Read

SynSeg: Generating Synthetic Datasets for Accurate Subcellular Segmentation with U-netSemantic proximity Read

NanTex enables computational multiplexing and phenotyping of organelles across super-resolution modalitiesSemantic proximity Read

CebraEM: A practical workflow to segment cellular organelles in volume SEM datasets using a transferable CNN-based membrane predictionSemantic proximity Read

Precise cell recovery by cell nucleus united transcript (CellCUT) for enhanced spatial transcriptomicsSemantic proximity Read

Morphology-robust quantification of subcellular organization in complex cellsSemantic proximity Read

A general method for bootstrapping dense 3D segmentations from sparse 2D annotationsSemantic proximity Read