Supporting material for submission of the manuscript:

Highly multiplexed molecular and cellular mapping of breast cancer tissue in three dimensions using mass tomography.

Catena et al.

Supplementary Videos:

Supplementary Video 1: Mass tomography rendered voxel data.
Supplementary Video 2: SMA (Blue) and Cytokeratin 5 (Green) markeres in voxel 3D reconstruction of a breast cancer sample shows patchy Cytokeratin 5 coverage within the eipithelial basal membrane.
Supplementary Video 3: Detail of nuclear signal (iridium 191) in 3D.
Supplementary Video 4: Detail resulting cell mask after performing 3D segmentation over the nuclear signal shown in supplementary Video 2.
Supplementary Video 5: Cell model showing expression of different measured markers.
Supplementary Video 6: 3D tSNE map showing examples of different measured markers, cluster labels, and labels from a supervised random forests classifier.
Supplementary Video 7: Flock, k-Means, and supervised classification labels displayed over the 3D tumor cell model.
Supplementary Video 8: Blood vessel structural mask and resulting computation of distance to vessel mask for all cells or different cell subsets.
Supplementary Video 9: Section of a hypoxic area of a tumor showing distance to stromal areas, a stromal marker (SMA), and a hypoxia marker (Carbonic Anhidrase IX).
Supplementary Video 10: 3D axial tour through a 3D tumor model displaying epithelial and B-lymphocyte surfaces. In the middle of the video, from the center and towards the lower right quadrant, a protrussion from which disseminated cells spring.
Supplementary Video 11: 3D axial tour through a 3D tumor model displaying epithelial and B-lymphocyte surfaces and pS6 signal.
Supplementary Video 12: 3D tumor cell atlas Isosurface rendering.
Supplementary Video 13: 3D tumor cell atlas showing spheric representation of cells with blended or striped marker colorings.
Supplementary Video 14: histoCAT-mobile demo

histoCAT-mobile:

Download from the (Apple's App Store)
The code is available here github repo

histoCAT-3D:

Download histoCAT-3D from the Bodenmiller laboratory website
Download from here the stable precursor version (histoCAT++, Catena et. al 2018, Journal of Pathology)
The code is available here github repo
Find intructions to use histoCAT-3D in this manual

Data:

Download the original 2D files here
Download the histoCAT-3D workspace here
Download the 3D cell data (as tsv file) here