Programming-free Single Cell Analysis of CODEX TMA with MIKAIA®

CODEX, now called PhenoCycler, by Akoya Biosciences, along with other sequential immunofluorescence technologies (e.g., Lunaphore (Comet), Miltenyi Biotech (MACSima), Leica Microsystems (Cell DIVE), or other vendors) enables researchers to measure co-expression of a multitude of proteins spatially at sub-cellular granularity. The image analysis of such datasets remains a challenge. At the inaugural conference of the European Society of Spatial Biology (ESSB) in December 2024 in Berlin, we presented the various types of spatial analyses that are possible with MIKAIA^®.

We thank our co-authors from TU Munich and University of Freiburg.

The poster discusses a sequence of potential analysis steps:

1. Tissue detection and TMA de-arraying
2. Division of TMA cores into two (or more) subsets representing different tumor subtypes
3. Creation of ROIs by thresholding fluorescent channels with the Mask by Color App
4. Cell segmentation and cell phenotyping with the FL Cell Analysis App
   • Especially for higher plexities, we recommend configuring a cell lineage. For example, a rule could look like this: Call it “Treg”, when markers CD3, CD4 and FoxP3 are positive.
5. Analyze cell interactions with the Cell-Cell Connections App.
6. Identify cellular neighborhoods.
7. Measure distance from immune cells to tumor front with the Proximity Analysis App.
8. Analyze spatial heterogeneity of certain cell types with the Grid Analysis App

(click image to enlarge)