Fig. 3

Cell-ACDC analysis pipeline validation. A Representative images of the strain carrying ACT1pr-mKate2. B Representative image of hematopoietic stem cells from wild-type mice stained for DNA (DAPI). C Correlation between budding yeast cell volume calculated from cells segmented with two different methods. The cell volume is calculated from 2D segmentation masks (see [45] and the “Materials and methods” section), which were obtained with two different methods: segmentation with YeaZ on phase-contrast signal and segmentation with Cellpose on the fluorescent signal of mKate2 expressed from an additional ACT1 promoter. We observe a strong agreement between the two methods (n = 113, Pearson’s coefficient=0.98, p value<10⁻¹⁰). D Correlation between the nucleus and cell volume of hematopoietic stems cells (HSCs). For the nuclear volume, we segmented the DAPI signal using StarDist, while for the cell volume, we segmented the bright-field channel using YeaZ. We observe high correlation (n = 519, Pearson’s coefficient=0.86, p value <10⁻¹⁰), indicating that the nuclear volume is a valid proxy for cell size. All segmentation masks were carefully inspected and corrected using Cell-ACDC