HTA MEL Atlas 1 primary data

V1.0 ReadMe

May 17, 2021

The data in this folder represents minimally processed (Level 2) image data from either 2D whole slide or 3D optically-sectioned imaging relevant to HMS HTAN Center Melanoma Atlas 1. Whole slide images are segmented, quantified, and subjected to additional quality control to generate final data. Whole slide scans are saved as OME-TIFF tiled pyramid images whereas 3D datasets are three-dimensional TIFF files. Spatial feature tables are zipped CSV files.

Data were collected using cyclic immunofluorescence (CyCIF), as described in, or brightfield imaging of hematoxylin and eosin (H&E) stained slides. Each file corresponds to a multiplexed image mosaic for FFPE tissue sections 5 microns thick with sample diameter extending up to ~2.9 cm. Each whole slide image is assembled from a series of successive image tiles stitched together (832 x 732 µm tiles; up to 990 tiles/image) and flat-field corrected for illumination using MCMICRO software to generate ~0.2 to ~1.5 gigapixel images. Tiles were collected for each CyCIF round (up to 15 in total depending of the antibody panel used) and these are combined in the mosaic image to generate a composite with 32 to 60 channels. Each 3D image (110 x 110 x 16 µm) requires 3D image registration to assemble all 7 CyCIF rounds.

Whole slide CyCIF images were collected on a RareCyte Inc. CyteFinder slide scanning fluorescence microscope using a 20x/0.75 NA objective and sampled at 650 nm/pixel. 3D high resolution CyCIF images were acquired on a GE Deltavision Elite equipped with a 60x/1.42 NA oil immersion objective lens and sampled at 108 nm/pixel in X & Y, and 200 nm steps in Z axis. H&E images were collected on an Olympus VS120 microscope using a 20x/0.75 NA objective and sampled at 350 nm/pixel.

The files MEL01-1-* to MEL01-3-* derive from a 62-year old male (MEL1), who had a stage IIC primary melanoma with NF1 (c.1008G>A and c.4006C>T) mutation. The tumor had invaded into reticular dermis and was surgically removed.

The files MEL02-1-* to MEL13-2-* derive from 12 additional patients from the Brigham and Women’s Hospital. Additional information on antibodies and specimen are available at

Image files ending in -0-ROI* are H&E images. All others are CyCIF images.

All files below may be downloaded directly. For bulk downloads, please use an Amazon Web Services S3 compatible download tool, at the following address: s3://hta-melatlas-1/data/

OME-TIFF primary image data

Whole-slide images

3D high-resolution images

Spatial feature tables (CSV)