Multiplexed 3D atlas of state transitions and immune interactions in colorectal cancer (Introduction)

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://labsyspharm.github.io/HTA-CRCATLAS-1/minerva/crc01-introduction.html. 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 Minerva introduction accompanies the analysis in Lin et al 2021 of specimen CRC1, a poorly differentiated stage IIIB adenocarcinoma (pT3N1bM0) with microsatellite instability (MSI-H) and a BRAFV600E (c.1799T>A) mutation. The tumor along with adjacent normal tissue was imaged using 24-plex cyclic immunofluorescence at a nominal resolution of 0.5 micron.