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. 2024 May 2;25(3):bbae189. doi: 10.1093/bib/bbae189

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© The Author(s) 2024. Published by Oxford University Press.

This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (https://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com

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Tumor isolation index (A–D) and tumor MPI (E, F). (A) Expression level of CD3D+ cells in the MEL1 sample. (B) Division of the overall ROI into two subregions based on CD3D+ cells: (1) immune-isolated region, which has almost no immune cells; (2) immune-rich region. (C) Expression level of tumor (SOX10+) cells in the MEL1 sample. (D) Visualization of tumor cells in the immune-isolated region and immune-rich region, respectively. The tumor isolation index for this sample is 46.9%, which quantifies the percentage of tumor cells in the immune-isolated region. (E) Display of Ki67+ and Ki67− tumor cells. Ki67 is a proliferative marker. The overall percentage of proliferative tumor cells (MPI = 1) in the MEL1 sample is 7.4%. (F) Percentage of tumor cells with MPI = 1 in subregions and the zoomed-in CyCIF images. A sliding window of 300 300 microns is applied over the ROI to compute the percentage of tumor cells with MPI = 1. In this example, the MPI is computed using Ki67 due to the availability of markers. Additionally, zoomed-in CyCIF images are provided to visualize areas with varying levels of Ki67+ tumor cells.

Inline graphic — Tumor isolation index (A–D) and tumor MPI (E, F). (A) Expression level of CD3D+ cells in the MEL1 sample. (B) Division of the overall ROI into two subregions based on CD3D+ cells: (1) immune-isolated region, which has almost no immune cells; (2) immune-rich region. (C) Expression level of tumor (SOX10+) cells in the MEL1 sample. (D) Visualization of tumor cells in the immune-isolated region and immune-rich region, respectively. The tumor isolation index for this sample is 46.9%, which quantifies the percentage of tumor cells in the immune-isolated region. (E) Display of Ki67+ and Ki67− tumor cells. Ki67 is a proliferative marker. The overall percentage of proliferative tumor cells (MPI = 1) in the MEL1 sample is 7.4%. (F) Percentage of tumor cells with MPI = 1 in subregions and the zoomed-in CyCIF images. A sliding window of 300 300 microns is applied over the ROI to compute the percentage of tumor cells with MPI = 1. In this example, the MPI is computed using Ki67 due to the availability of markers. Additionally, zoomed-in CyCIF images are provided to visualize areas with varying levels of Ki67+ tumor cells.