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.本数据集包含经过保存级质量处理的Minerva输出文件，无需下载TB级体量的图像文件。如需在浏览器中查看数据，请访问以下链接：https://www.cycif.org/data/gaglia-PCQ-2020/osd-0813。本数据集采用Minerva套件（Minerva Suite）——由系统药理学实验室（Laboratory of Systems Pharmacology）开发的一系列软件工具，用于在网页浏览器中可视化多重组织成像数据。研究人员或病理学家可对图像进行标注与描述以供用户查看，而用户则可通过缩放和平移功能浏览全分辨率图像，无需下载多GB乃至TB级的图像文件。上述带标注及未标注的图像，均通过将经过质量控制的ome.tiffs文件、分割掩码，以及通道元数据与文本描述上传至Minerva Author工具生成。这些输入文件将生成.json格式文件、.html格式文件以及数百个.jpg格式的金字塔文件，从而实现图像的在线浏览功能。本数据集展示了采用基于组织的循环免疫荧光技术（t-CyCIF），搭配20X/0.75NA物镜所采集的多重成像图像。本数据集所对应的研究案例阐释了未接受治疗的人类HER2阳性原发性乳腺癌切除样本中，多元增殖指数（Multivariate Proliferation Index，MPI）与细胞周期一致性这两项新指标的相关背景。在此案例中，研究团队通过谱系标志物CD45、波形蛋白（Vimentin）、上皮钙黏蛋白（e-Cadherin）以及α平滑肌肌动蛋白（aSMA）区分上皮细胞与免疫细胞及基质细胞。随后利用增殖与细胞周期阻滞标志物定义了多元增殖指数（MPI）。最终，研究团队聚焦于增殖群体（MPI+1），并从组织图像中提取细胞周期蛋白的动态变化特征。