Cellpose

Cellpose is a state-of-the-art, anatomically-aware deep learning framework designed specifically for biological image segmentation. Unlike traditional thresholding methods, Cellpose utilizes a unique vectorized flow representation to distinguish individual cells, even in high-density or low-contrast environments. By 2026, it has solidified its position as the 'gold standard' for zero-shot cellular segmentation, bridging the gap between raw microscopy data and high-throughput quantitative analysis. The architecture is built on a modified U-Net that predicts horizontal and vertical gradients (flows) and cell probabilities, ensuring that segmented objects maintain topological integrity. With the maturation of Cellpose 3.0, the framework now includes advanced image restoration (denoising and deblurring) integrated directly into the segmentation pipeline, significantly reducing the hardware requirements for high-resolution imaging. Its market position is unique: while commercial competitors like Imaris or Arivis offer high-end visualization, Cellpose remains the preferred choice for researchers and developers due to its Python-native integration, Napari-based GUI, and a massive community-driven model zoo that allows for specialized fine-tuning with minimal training data.