Temporal and spatial topography of cell proliferation in cancer

The collection comprises preservation-quality files of Minerva output files without needing download terabyte scale images. To view data in a browser follow this link: https://www.cycif.org/data/gaglia-PCQ-2020/osd-0813. This dataset uses the Minerva Suite, a series of software tools developed by the Laboratory of Systems Pharmacology to visualize multiplexed tissue image data in a web browser. Researchers or pathologists can annotate and describe images for users and users can use zooming and panning features to explore the full resolution images without needing to download multi-GB/TB image files. These annotated and unannotated images are created by uploading quality controlled ome.tiffs and segmentation masks, along with channel metadata and text descriptions, into the Minerva Author tool. These input files produce .json files, an .html file, and hundreds of .jpg pyramid files that make the images browsable online. This dataset displays multiplexed images generated using tissue-based cyclic immunofluorescence (t-CyCIF) with a 20X/0.75NA objective. This story contextualizes new metrics of Multivariate Proliferation Index (MPI) and cell cycle coherence in an untreated human HER2 positive primary breast cancer resection. In this story, we established lineage markers (CD45, Vimentin, e-Cadherin and aSMA) to distinguish epithelial cells from immune and stromal cells. Then we use proliferation and cell cycle arrest markers to define a Multivariate Proliferation Index, or MPI. Finally we focus on the proliferative population (MPI+1) and extract cell cycle protein dynamics from tissue images.