https://www.andrew.cmu.edu/user/icaoberg/tags/cell-geometry/ Recent content in Cell-Geometry on icaoberg Hugo en-us Sun, 26 Apr 2026 14:14:53 -0400 https://www.andrew.cmu.edu/user/icaoberg/publication/2019-01-01-cellorganizer-spatial-simulations/ Tue, 01 Jan 2019 00:00:00 +0000 https://www.andrew.cmu.edu/user/icaoberg/publication/2019-01-01-cellorganizer-spatial-simulations/ <p>Spatial simulations of cell processes require realistic cell geometries — accurate representations of where organelles are, how they&rsquo;re shaped, and how they vary from cell to cell. Building those geometries by hand doesn&rsquo;t scale. CellOrganizer was designed to learn them directly from microscope images.</p> <p>This chapter describes the full workflow: from image preparation through model training, quality assessment, geometry sampling, and integration with biochemical simulation frameworks.</p> <hr> <h2 id="what-cellorganizer-does">What CellOrganizer Does</h2> <p>CellOrganizer learns generative statistical models of cell spatial organization from fluorescence microscopy images. A trained model captures not just a single representative cell shape, but the full distribution of variation — in overall cell architecture, organelle count, organelle size and shape, and spatial positioning — across a population of imaged cells.</p>