CellBinDB is a large-scale, multimodal annotated dataset for cell segmentation. It contains 1,044 annotated microscope images and 109,083 cell annotations, covering four staining types: DAPI, ssDNA, H&E, and mIF. CellBinDB contains samples from two species, human and mouse, covering more than 30 histologically different tissue types, including disease-related tissues. The images in CellBinDB come from two sources: 844 mouse images from internal experiments and 200 human images from the open access platform 10x Genomics. We annotated all images in CellBinDB and provide two types of image annotations: semantic and instance masks. A xlsx file is attached to record the detailed information of each image. In addition, we provide the images and annotations of nine other widely used publicly available cell segmentation datasets downloaded from their original sources, retaining their original formats for ease of use. The file 'mixed_licenses.txt' contains the original accessions of the public datasets used in our project and their associated licenses. Please refer to these links for more information about each dataset and its licensing terms, and use it according to the specifications.