Enabling 3D Multiplexing Spatial Omics Workflows in Neuroscience

The series "From Image to Results" explores various case studies which present how to achieve quantifiable results from your imaging data. Each case study explores different samples, imaging systems, and research questions.

This case study provides a blueprint for the analysis of 3D spatial omics multiplexing datasets from a CODEX multiplex antibody panel imaged with a custom set-up using the Akoya Phenocycler and ZEISS LSM 980 confocal microscope to explore the expression of an extensive list of pre-synaptic markers in the mouse brain. A detailed description of 3D registration of spectral multiplexing data, AI object segmentation, and statistical analyses, including cell neighborhood and dimensionality reduction analyses, are provided. These can provide unique insights not only into neuroscience but also cancer research, immunology, and single-cell analysis experiments.

Key Learnings:

- 3D registration of Spectral Multiplexing Data
- AI object segmentation
- Leverage cell neighborhood and dimensionality reduction analysis to extract unique insights from your experiments

Read the case study here.