Extended Data Fig. 2: Visualizing elongated immune and tumour cells in dense region from vertical growth phase.
From: Highly multiplexed 3D profiling of cell states and immune niches in human tumors
a, 2D CyCIF whole slide image of adjacent section of the primary melanoma sample HTA7_1. White squares indicate the regions of melanoma in-situ (MIS) and the invasive vertical growth phase (VGP) melanoma where high-resolution 3D CyCIF was performed. Marker colours as indicated. Scale bar 1 mm. b, Maximum projection of the region of the invasive margin imaged with 3D CyCIF of Dataset 1 (LSP13626), showing a subset (6) of the total 54 markers. Image corresponds to right ROI indicated in (a). Scale bar 100 μm. c-d, Dendritic cell from Fig. 1j with additional markers highlighting T cell subtypes (c) and the dense neighbourhood of tumour cells (d). See Supplementary Fig. 13 for detailed T cell subtype calling. e, Colour-coded segmentation masks of tumour cells from vertical growth phase of melanoma region. Colour encodes for orientation of tumour cells (spherical cells in yellow; elongated cells in magenta and cyan). Scale bar, 100 µm. f, g, Surface renderings of selected cells from (e). These cells differ in orientation in the tissue rather than aspect ratio.
